NPASS Compound

Natural Product: NPC187011

Natural Product ID	NPC187011
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	UJGRGFLENARMJS-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	20405942
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000134] Phenols [CHEMONTID:0000190] Methoxyphenols

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 27 26 0 0 0 0 0 0 0 0999 V2000 -2.7628 -0.6932 -0.6704 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9498 0.4564 -0.6387 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6425 0.4448 -0.2363 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0044 -0.7147 0.1808 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3203 -0.7001 0.5808 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0277 0.4965 0.5713 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4097 1.6620 0.1619 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0768 1.6240 -0.2389 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5696 2.7851 -0.6561 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9947 -1.9156 1.0169 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3499 -2.9806 1.0207 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9704 -0.0880 0.0593 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4402 0.2802 -0.0538 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7793 1.4810 -0.2088 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4314 -0.6676 0.0053 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2085 -1.5937 -0.9458 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2579 -0.8461 0.3312 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5882 -0.5588 -1.4001 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5208 -1.6600 0.1985 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0558 0.4925 0.8867 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9323 2.6190 0.1411 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6874 3.0164 -1.6367 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0161 -1.9338 1.3329 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6187 0.7634 -0.2809 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2600 -0.9373 -0.6214 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2095 -0.4150 1.0787 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4077 -0.4168 0.0216 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 5 10 1 0 10 11 2 0 12 13 1 0 13 14 2 0 13 15 1 0 8 3 1 0 1 16 1 0 1 17 1 0 1 18 1 0 4 19 1 0 6 20 1 0 7 21 1 0 9 22 1 0 10 23 1 0 12 24 1 0 12 25 1 0 12 26 1 0 15 27 1 0 M END

Standard InCHIKey	UJGRGFLENARMJS-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C8H8O3.C2H4O2/c1-11-8-4-6(5-9)2-3-7(8)10;1-2(3)4/h2-5,10H,1H3;1H3,(H,3,4)
SMILES	COc1cc(ccc1O)C=O.CC(=O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	152.05	Volume:	154.193 ? Van der Waals volume.
Dense:	0.986	LogP:	1.124 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.265 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.773 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	2.0	Rigid Bonds:	7.0
TPSA:	46.53 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	1.0	Rings:	1.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.648	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.822	Fsp³:	0.125
MCE-18:	6.0 ? 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:	Accepted	BMS Rule:	1
Chelating Alert:	1	PAINS Alert:	0
Colloidal aggregators:	0.293	Fluc inhibitor:	0.002 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.016 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.098 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.999	Promiscuous compounds:	0.45

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.81	MDCK Permeability:	-4.724
Pgp-inhibitor:	0.344	Pgp-substrate:	0.086
PAMPA:	0.132 ? 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):	0.116
20% Bioavailability (F20%):	0.41	30% Bioavailability (F30%):	0.448
50% Bioavailability (F50%):	0.85

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.13	MRP1:	0.517
Plasma Protein Binding (PPB):	59.865%	Volume Distribution (VD):	-0.386
Fu:	37.151% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.965
OATP1B3 inhibitor:	0.985	BCRP inhibitor:	0.746
BSEP inhibitor:	0.566

ADMET: Metabolism

CYP1A2-inhibitor:	0.427	CYP1A2-substrate:	0.185
CYP2C19-inhibitor:	0.871	CYP2C19-substrate:	0.202
CYP2C9-inhibitor:	0.184	CYP2C9-substrate:	0.079
CYP2D6-inhibitor:	0.592	CYP2D6-substrate:	0.502
CYP3A4-inhibitor:	0.004	CYP3A4-substrate:	0.027
CYP2B6-substrate:	0.004	CYP2C8-inhibitor:	0.588
HLM stability:	0.607 ? 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):

10.28

Half-life (T1/2):

1.527

ADMET: Toxicity

hERG Blockers:	0.087	hERG Blockers (10um):	0.556
Human Hepatotoxicity (H-HT):	0.316	Drug-induced Liver Injury (DILI):	0.276
AMES Toxicity:	0.464	Rat Oral Acute Toxicity:	0.205
Maximum Recommended Daily Dose:	0.236	Skin Sensitization:	0.8
Carcinogencity:	0.576	Eye Corrosion:	0.991
Eye Irritation:	0.999	Respiratory Toxicity:	0.831
Drug-induced Neurotoxicity:	0.497	Ototoxicity:	0.14
Hematotoxicity:	0.133	Drug-induced Nephrotoxicity:	0.14
Genotoxicity:	0.102	RPMI-8226 Immunitoxicity:	0.055
A549 Cytotoxicity:	0.123	Hek293 Cytotoxicity:	0.169
BCF:	0.507 ? 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:	2.992 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.755 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.109 ? 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
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.indcrop.2008.08.002]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1402962]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	tuber	n.a.	PMID[15180301]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[15577254]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15621610]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	roots	purchased from Kiu Shun Trading Ltd., Vancouver, Canada	2000	PMID[16643021]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17381154]
NPO11100	Artemisia capillaris	Species	Asteraceae	Eukaryota	n.a.	whole plant	n.a.	PMID[21428416]
NPO11100	Artemisia capillaris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22870812]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[23327905]
NPO11100	Artemisia capillaris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23435948]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25538068]
NPO11100	Artemisia capillaris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25737008]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25843525]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	roots	n.a.	n.a.	PMID[26259802]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Flower Buds	n.a.	n.a.	PMID[26977531]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27400088]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[28453270]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[34770801]
NPO23017	Urtica dioica	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36447306]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36838931]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36985392]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37480748]
NPO31073	Ligusticum chuanxiong	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37656744]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37836118]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39684253]
NPO23017	Urtica dioica	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39696148]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39699537]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8904847]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23017	Urtica dioica	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11100	Artemisia capillaris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6956	Citrus limonia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9662	Conioselinum vaginatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11291	Styrax benzoin	Species	Styracaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5665	Ulva pertusa	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO31073	Ligusticum chuanxiong	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Essential Oil	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11100	Artemisia capillaris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31073	Ligusticum chuanxiong	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5665	Ulva pertusa	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6956	Citrus limonia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7916	Vanilla planifolia	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23017	Urtica dioica	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11291	Styrax benzoin	Species	Styracaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9662	Conioselinum vaginatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11100	Artemisia capillaris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11291	Styrax benzoin	Species	Styracaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6956	Citrus limonia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23017	Urtica dioica	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5665	Ulva pertusa	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7916	Vanilla planifolia	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9662	Conioselinum vaginatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO31073	Ligusticum chuanxiong	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23017	Urtica dioica	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5665	Ulva pertusa	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6956	Citrus limonia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11100	Artemisia capillaris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11291	Styrax benzoin	Species	Styracaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9662	Conioselinum vaginatum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11100	Artemisia capillaris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11291	Styrax benzoin	Species	Styracaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22309	Gastrodia elata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21373	Vitex trifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6956	Citrus limonia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5665	Ulva pertusa	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29401	Bupleurum chinense	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11100	Artemisia capillaris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7916	Vanilla planifolia	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11291	Styrax benzoin	Species	Styracaceae	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

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

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

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 NPC187011 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	21493
0.1-0.2	22342
0.2-0.3	5198
0.3-0.4	677
0.4-0.5	129
0.5-0.6	10
0.6-0.7	2
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8182	Intermediate Similarity	NPC203719
0.6316	Remote Similarity	NPC298268
0.6098	Remote Similarity	NPC281020
0.5952	Remote Similarity	NPC129889
0.5952	Remote Similarity	NPC307006
0.5682	Remote Similarity	NPC194416
0.5682	Remote Similarity	NPC70744
0.5556	Remote Similarity	NPC66518
0.5405	Remote Similarity	NPC7097
0.525	Remote Similarity	NPC32163
0.525	Remote Similarity	NPC309203
0.525	Remote Similarity	NPC604189
0.5135	Remote Similarity	NPC274613

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC187011 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	2599
0.1-0.2	5864
0.2-0.3	657
0.3-0.4	25
0.4-0.5	5
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