NPASS Compound

Natural Product: NPC116850

Natural Product ID	NPC116850
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Bergenin
IUPAC Name	(2R,3S,4S,4aR,10bS)-3,4,8,10-tetrahydroxy-2-(hydroxymethyl)-9-methoxy-3,4,4a,10b-tetrahydro-2H-pyrano[3,2-c]isochromen-6-one
Synonyms	Bergenin
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL273019
PubChem CID	66065
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002279] Benzene and substituted derivatives [CHEMONTID:0000176] Benzoic acids and derivatives [CHEMONTID:0001248] Hydroxybenzoic acid derivatives [CHEMONTID:0001251] Gallic acid and derivatives

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 39 41 0 0 0 0 0 0 0 0999 V2000 4.5411 1.4138 -0.6479 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9637 0.3823 -1.4231 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9710 -0.4061 -0.8324 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3433 -1.5335 -0.1679 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3848 -2.3250 0.4217 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0418 -1.9310 0.3117 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6804 -0.7972 -0.3588 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6743 -0.0206 -0.9422 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2522 1.1255 -1.6134 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7434 -0.4162 -0.4787 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4999 -0.8601 0.7197 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9589 -0.5891 0.5743 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.1593 0.5228 -0.4091 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0383 1.4973 -0.4902 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9939 2.4559 0.6792 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2347 3.0345 0.9271 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7918 0.9559 -0.6897 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3236 -0.0440 -1.6872 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5380 -0.3376 1.8161 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3097 -2.2769 0.8175 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0094 -2.7525 0.9544 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3115 -3.7866 1.5669 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6691 -1.9166 -0.0630 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6400 1.3318 -0.7293 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2112 1.3586 0.4169 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2244 2.4005 -1.0690 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6363 -3.2355 0.9633 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3465 2.0243 -1.1479 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1855 -0.9351 -1.3761 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1220 -0.4198 1.6554 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4844 -1.4990 0.1720 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0859 1.0683 -0.1961 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2447 2.1455 -1.3951 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2907 3.2947 0.4994 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6256 1.9249 1.5807 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6845 3.1386 0.0514 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6933 -0.9552 -1.6133 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8328 -0.1458 2.5042 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9400 -2.8919 -0.0562 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 7 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 14 17 1 0 13 18 1 0 12 19 1 0 11 20 1 0 20 21 1 0 21 22 2 0 4 23 1 0 8 3 1 0 17 10 1 0 21 6 1 0 1 24 1 0 1 25 1 0 1 26 1 0 5 27 1 0 9 28 1 0 10 29 1 6 11 30 1 1 12 31 1 6 13 32 1 1 14 33 1 6 15 34 1 0 15 35 1 0 16 36 1 0 18 37 1 0 19 38 1 0 23 39 1 0 M END

Standard InCHIKey	YWJXCIXBAKGUKZ-HJJNZUOJSA-N
Standard InCHI	InChI=1S/C14H16O9/c1-21-11-5(16)2-4-7(9(11)18)12-13(23-14(4)20)10(19)8(17)6(3-15)22-12/h2,6,8,10,12-13,15-19H,3H2,1H3/t6-,8-,10+,12+,13-/m1/s1
SMILES	COc1c(cc2c(c1O)[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)OC2=O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	328.08	Volume:	293.597 ? Van der Waals volume.
Dense:	1.117	LogP:	-1.518 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-0.735 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-0.792 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	2.0	Rigid Bonds:	17.0
TPSA:	145.91 ? Topological Polar Surface Area.	H-Bond Acceptor:	9.0
H-Bond Donor:	5.0	Rings:	3.0
Heavy Atoms:	9.0

MedChem Properties

QED Drug-Likeness Score:	0.422	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.089	Fsp³:	0.5
MCE-18:	69.524 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	1	PAINS Alert:	0
Colloidal aggregators:	0.601	Fluc inhibitor:	0.067 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.32 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.036 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.214	Promiscuous compounds:	0.437

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.112	MDCK Permeability:	-5.338
Pgp-inhibitor:	0.0	Pgp-substrate:	0.579
PAMPA:	0.997 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.936
20% Bioavailability (F20%):	0.293	30% Bioavailability (F30%):	0.924
50% Bioavailability (F50%):	0.953

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.186	MRP1:	0.809
Plasma Protein Binding (PPB):	52.538%	Volume Distribution (VD):	-0.425
Fu:	45.744% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.021
OATP1B3 inhibitor:	0.921	BCRP inhibitor:	0.003
BSEP inhibitor:	0.014

ADMET: Metabolism

CYP1A2-inhibitor:	0.119	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.163	CYP2C19-substrate:	0.012
CYP2C9-inhibitor:	0.994	CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	0.003	CYP2D6-substrate:	0.003
CYP3A4-inhibitor:	0.004	CYP3A4-substrate:	0.576
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.995
HLM stability:	0.816 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

3.101

Half-life (T1/2):

2.761

ADMET: Toxicity

hERG Blockers:	0.01	hERG Blockers (10um):	0.101
Human Hepatotoxicity (H-HT):	0.702	Drug-induced Liver Injury (DILI):	0.953
AMES Toxicity:	0.926	Rat Oral Acute Toxicity:	0.089
Maximum Recommended Daily Dose:	0.037	Skin Sensitization:	1.0
Carcinogencity:	0.437	Eye Corrosion:	0.008
Eye Irritation:	0.803	Respiratory Toxicity:	0.053
Drug-induced Neurotoxicity:	0.088	Ototoxicity:	0.792
Hematotoxicity:	0.614	Drug-induced Nephrotoxicity:	0.9
Genotoxicity:	0.725	RPMI-8226 Immunitoxicity:	0.157
A549 Cytotoxicity:	0.69	Hek293 Cytotoxicity:	0.129
BCF:	0.173 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	2.515 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.793 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.051 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO25715	Senna siamea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10757709]
NPO2130	Ehretia dicksonii	Species	Ehretiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[10830513]
NPO2130	Ehretia dicksonii	Species	Ehretiaceae	Eukaryota	n.a.	twig	n.a.	PMID[10830513]
NPO2130	Ehretia dicksonii	Species	Ehretiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10830513]
NPO6774	Khaya senegalensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12193039]
NPO18851	Psychotria klugii	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12880315]
NPO18851	Psychotria klugii	Species	Rubiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[12880315]
NPO2430	Detarium microcarpum	Species	Fabaceae	Eukaryota	fruits	n.a.	n.a.	PMID[16724838]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	whole plants	Sendai, Miyagi Prefecture, Japan	2000-Sep	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17397219]
NPO25715	Senna siamea	Species	Fabaceae	Eukaryota	n.a.	leaf	n.a.	PMID[17685627]
NPO19728	Saxifraga stolonifera	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17997321]
NPO670	Hyrtios gumminae	Species	Thorectidae	Eukaryota	n.a.	Thai	n.a.	PMID[19788270]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[21353549]
NPO13504	Lotus japonicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21510636]
NPO30462	Cenostigma gardnerianum	Species	Fabaceae	Eukaryota	n.a.	stem	n.a.	PMID[21939182]
NPO33666	Mallotus philippenensis	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	PMID[22437110]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22940450]
NPO25715	Senna siamea	Species	Fabaceae	Eukaryota	Stems	n.a.	n.a.	PMID[23078294]
NPO6774	Khaya senegalensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23210623]
NPO25715	Senna siamea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23513740]
NPO8960	Flueggea virosa	Species	Phyllanthaceae	Eukaryota	roots	Pingtung County, Taiwan	2011-SEP	PMID[24400834]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26767291]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	bark	n.a.	PMID[26767291]
NPO14089	Hypericum ascyron	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30379546]
NPO14089	Hypericum ascyron	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31596079]
NPO11882	Cedrus libani	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32092041]
NPO60707	Uromyrtus metrosideros	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36007634]
NPO15116	Astilbe thunbergii	Species	Saxifragaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[9722485]
NPO1253	Nasturtium officinale	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19728	Saxifraga stolonifera	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25715	Senna siamea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13504	Lotus japonicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14615	Streptomyces paulus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6179	Aframomum amaniense	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14504	Alectoria divergens	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14200	Aristolochia zollingeriana	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3199	Balanophora involucrata	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1661	Bartramia pomiformis	Species	Bartramiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7752	Beilschmiedia anacardioides	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11882	Cedrus libani	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13076	Cephalaria grossheimii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12754	Cerinthe minor	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21498	Coccus ilicis	Species	Coccidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12585	Craspidospermum verticillatum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9669	Dictyopteris acrostichoides	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2130	Ehretia dicksonii	Species	Ehretiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14089	Hypericum ascyron	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12069	Isaria felina	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12910	Ixeris stolonifera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12061	Justicia paniculata	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12234	Khaya ivorensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6774	Khaya senegalensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10389	Larix cajanderi	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3458	Lupinus verbasciformis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13701	Melaleuca rhaphiophylla	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7169	Nama hispidum	Species	Namaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12414	Penicillium paxilli	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14289	Pieris napi	Species	Pieridae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13907	Senecio renardii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10865	Sextonia rubra	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10012	Triaenophora rupestris	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25774	Virola multinervia	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12235	Trachelospermum jasminoides	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8960	Flueggea virosa	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO650	Gazania krebsiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO18851	Psychotria klugii	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO670	Hyrtios gumminae	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15116	Astilbe thunbergii	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2430	Detarium microcarpum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO26639	Ardisia crenata	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1253	Nasturtium officinale	Species	Brassicaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO1253	Nasturtium officinale	Species	Brassicaceae	Eukaryota	Herb	n.a.	n.a.	Database[FooDB]
NPO1253	Nasturtium officinale	Species	Brassicaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO1253	Nasturtium officinale	Species	Brassicaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12235	Trachelospermum jasminoides	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14089	Hypericum ascyron	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13907	Senecio renardii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25774	Virola multinervia	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19728	Saxifraga stolonifera	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1253	Nasturtium officinale	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14834	Trachelospermum asiaticum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26639	Ardisia crenata	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4572	Gossypium indicum	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1253	Nasturtium officinale	Species	Brassicaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3199	Balanophora involucrata	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14089	Hypericum ascyron	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26639	Ardisia crenata	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19728	Saxifraga stolonifera	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4572	Gossypium indicum	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1253	Nasturtium officinale	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12235	Trachelospermum jasminoides	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13907	Senecio renardii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25715	Senna siamea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14834	Trachelospermum asiaticum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25774	Virola multinervia	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12235	Trachelospermum jasminoides	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14089	Hypericum ascyron	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1253	Nasturtium officinale	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12235	Trachelospermum jasminoides	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14834	Trachelospermum asiaticum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19728	Saxifraga stolonifera	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26639	Ardisia crenata	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21498	Coccus ilicis	Species	Coccidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9669	Dictyopteris acrostichoides	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2130	Ehretia dicksonii	Species	Ehretiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3199	Balanophora involucrata	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25774	Virola multinervia	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14089	Hypericum ascyron	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1103	Dioscorea japonica	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25715	Senna siamea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13701	Melaleuca rhaphiophylla	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12235	Trachelospermum jasminoides	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12069	Isaria felina	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1661	Bartramia pomiformis	Species	Bartramiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13907	Senecio renardii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12910	Ixeris stolonifera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13504	Lotus japonicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14200	Aristolochia zollingeriana	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14504	Alectoria divergens	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12754	Cerinthe minor	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1253	Nasturtium officinale	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14289	Pieris napi	Species	Pieridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10012	Triaenophora rupestris	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7169	Nama hispidum	Species	Namaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7752	Beilschmiedia anacardioides	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12414	Penicillium paxilli	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10389	Larix cajanderi	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10865	Sextonia rubra	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11882	Cedrus libani	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3458	Lupinus verbasciformis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14615	Streptomyces paulus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12234	Khaya ivorensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14717	Grevillea striata	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6774	Khaya senegalensis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13076	Cephalaria grossheimii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12061	Justicia paniculata	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1549	Amaroria soulameoides	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8960	Flueggea virosa	Species	Phyllanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12585	Craspidospermum verticillatum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO650	Gazania krebsiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6179	Aframomum amaniense	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15116	Astilbe thunbergii	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26639	Ardisia crenata	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14834	Trachelospermum asiaticum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO670	Hyrtios gumminae	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6749.1	Bergenia crassifolia var. cordifolia	Varieties	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18851	Psychotria klugii	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11431	Jacobaea aquatica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15035	Eria ramosissima	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4572	Gossypium indicum	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16850	Eucommia ulmoides	Species	Eucommiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18718	Capparis decidua	Species	Capparaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19728	Saxifraga stolonifera	Species	Saxifragaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16485	Calycanthus praecox	Species	Calycanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5109	Dacryodes hexandra	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2430	Detarium microcarpum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
NPO60707	Uromyrtus metrosideros	n.a.	n.a.	12.7	n.a.	n.a.	%	PMID[36007634]

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
Inhibition	31
IC50	15
Potency	4
GI	4
Activity	12
EC50	1
IZ	4
Stability	1
Inhibition index	1
TC50	1

Activity Type	# Activity
Individual protein	13
Cell line	18
Single protein	3
Organism	22
Unchecked	3
Others	10
Non-molecular	4
Tissue	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT135	Individual protein	Chromobox protein homolog 1	Homo sapiens	Potency	n.a.	89125.1	nM	PubChem BioAssay data set
NPT11	Individual protein	Guanine nucleotide-binding protein G(s), subunit alpha	Homo sapiens	Potency	n.a.	50118.7	nM	PubChem BioAssay data set
NPT72	Individual protein	Solute carrier organic anion transporter family member 1B3	Homo sapiens	Inhibition	=	94.52	%	PMID[23571415]
NPT27519	Single protein	Interleukin-6	Homo sapiens	IC50	=	208.0	nM	PMID[28843845]
NPT589	Individual protein	Serum albumin	Bos taurus	Inhibition	=	20.63	%	PMID[21752643]
NPT589	Individual protein	Serum albumin	Bos taurus	IC50	=	163600.0	nM	PMID[21752643]
NPT67	Individual protein	Cholinesterase	Equus caballus	Inhibition	=	-0.62	%	PMID[23062825]
NPT73	Individual protein	Solute carrier organic anion transporter family member 1B1	Homo sapiens	Inhibition	=	14.59	%	PMID[23571415]
NPT516	Individual protein	TNF-alpha	Homo sapiens	IC50	=	12500.0	nM	PMID[28843845]
NPT20556	Single protein	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	0.03	%	DOI[10.6019/CHEMBL4495564]
NPT20556	Single protein	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	10.77	%	DOI[10.6019/CHEMBL4495564]
NPT692	Individual protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	-4.97	%	HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators
NPT692	Individual protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	-8.45	%	HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators
NPT66	Individual protein	Acetylcholinesterase	Electrophorus electricus	Inhibition	=	7.33	%	PMID[23062825]
NPT43	Individual protein	Tyrosinase	Agaricus bisporus	Inhibition	=	0.6	%	PMID[24268551]
NPT43	Individual protein	Tyrosinase	Agaricus bisporus	IC50	>	100000.0	nM	PMID[24268551]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT547	Cell line	BGC-823	Homo sapiens	GI	=	-0.8	%	PMID[17997321]
NPT547	Cell line	BGC-823	Homo sapiens	GI	=	2.2	%	PMID[17997321]
NPT547	Cell line	BGC-823	Homo sapiens	GI	=	6.1	%	PMID[17997321]
NPT547	Cell line	BGC-823	Homo sapiens	GI	=	10.8	%	PMID[17997321]
NPT1597	Cell line	J774.2	n.a.	Inhibition	=	4.3	%	PMID[22437110]
NPT1970	Cell line	THP-1	Homo sapiens	Activity	=	7.91	%	PMID[22437110]
NPT1970	Cell line	THP-1	Homo sapiens	IC50	=	208.0	nM	PMID[25111439]
NPT1970	Cell line	THP-1	Homo sapiens	IC50	=	84000.0	nM	PMID[25111439]
NPT1970	Cell line	THP-1	Homo sapiens	IC50	=	12500.0	nM	PMID[25111439]
NPT1970	Cell line	THP-1	Homo sapiens	IC50	=	130000.0	nM	PMID[25111439]
NPT1970	Cell line	THP-1	Homo sapiens	Inhibition	=	24.0	%	PMID[25111439]
NPT1970	Cell line	THP-1	Homo sapiens	Inhibition	=	39.0	%	PMID[25111439]
NPT83	Cell line	MCF7	Homo sapiens	IC50	>	100000.0	nM	PMID[28395218]
NPT65	Cell line	HepG2	Homo sapiens	IC50	=	34560.0	nM	PMID[28395218]
NPT515	Cell line	SGC-7901	Homo sapiens	IC50	=	23560.0	nM	PMID[28395218]
NPT81	Cell line	A549	Homo sapiens	IC50	=	77280.0	nM	PMID[28395218]
NPT306	Cell line	PC-3	Homo sapiens	IC50	>	100000.0	nM	PMID[28395218]
NPT1452	Cell line	C8166	Homo sapiens	TC50	>	1000.0	ug ml-1	PMID[8786362]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	18526.0	nM	PubChem BioAssay data set
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	13115.4	nM	PubChem BioAssay data set
NPT20555	Organism	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition index	=	0.01908	n.a.	DOI[10.1101/2020.04.03.023846]
NPT20555	Organism	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	66.38	%	DOI[10.21203/rs.3.rs-23951/v1]
NPT20555	Organism	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-0.01	%	DOI[10.6019/CHEMBL4495565]
NPT20555	Organism	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	0.14	%	DOI[10.6019/CHEMBL4495565]
NPT28438	Unchecked	Unchecked	n.a.	Inhibition	=	11.7	%	PMID[34825192]
NPT28438	Unchecked	Unchecked	n.a.	Inhibition	=	-6.2	%	PMID[34825192]
NPT28438	Unchecked	Unchecked	n.a.	Inhibition	=	18.3	%	PMID[34825192]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	IZ	=	1.3	mm	PMID[21474216]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	IZ	=	2.5	mm	PMID[21474216]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Inhibition	=	2.0	%	PMID[21752643]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	303120.0	nM	PMID[22437110]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Activity	=	1.69	equiv	PMID[24268551]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Inhibition	=	54.8	%	PMID[25111439]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	40.0	ug.mL-1	PMID[8786362]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IZ	=	2.1	mm	PMID[21474216]
NPT19	Organism	Escherichia coli	Escherichia coli	IZ	=	3.3	mm	PMID[21474216]
NPT2	Others	Unspecified	n.a.	Activity	=	105.9	%	PMID[9722485]
NPT2	Others	Unspecified	n.a.	Activity	=	356.9	%	PMID[9722485]
NPT2	Others	Unspecified	n.a.	Inhibition	=	92.0	%	PMID[8786362]
NPT2	Others	Unspecified	n.a.	Inhibition	=	84.0	%	PMID[8786362]
NPT2	Others	Unspecified	n.a.	Inhibition	=	62.0	%	PMID[8786362]
NPT2	Others	Unspecified	n.a.	Inhibition	=	39.0	%	PMID[25111439]
NPT2	Others	Unspecified	n.a.	Inhibition	=	0.0	%	PMID[8786362]
NPT2	Others	Unspecified	n.a.	Inhibition	=	78.0	%	DOI[10.1007/s00044-011-9762-6]
NPT2	Others	Unspecified	n.a.	IC50	=	21700.0	nM	DOI[10.1007/s00044-011-9762-6]
NPT2	Others	Unspecified	n.a.	Inhibition	=	51.2	%	PMID[25111439]
NPT614	Tissue	Plasma	Rattus norvegicus	Stability	=	82.58	%	PMID[28843845]
NPT20632	Organism	Chikungunya virus	Chikungunya virus	Activity	=	100.0	%	PMID[36940609]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	667.0	pg/ml	PMID[25111439]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	509.0	pg/ml	PMID[25111439]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	282.0	pg/ml	PMID[25111439]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	55.0	pg/ml	PMID[25111439]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	2.62	uM	PMID[25111439]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	3.29	uM	PMID[25111439]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	32.0	%	PMID[25111439]

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC116850 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	19003
0.1-0.2	27440
0.2-0.3	3341
0.3-0.4	63
0.4-0.5	4
0.5-0.6	0
0.6-0.7	2
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC43872
1.0	High Similarity	NPC144801
1.0	High Similarity	NPC238672
1.0	High Similarity	NPC197188
1.0	High Similarity	NPC291510
0.6667	Remote Similarity	NPC24627
0.6429	Remote Similarity	NPC268366

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC116850 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4941
0.1-0.2	4105
0.2-0.3	104
0.3-0.4	0
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data