NPASS Compound

Natural Product: NPC65333

Natural Product ID	NPC65333
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3,4,5-Trihydroxy-Benzoic Acid (2R,3R,4R,2'r,3'r)-3,5,7,5',7'-Pentahydroxy-2,2'-Bis-(3,4,5-Trihydroxy-Phenyl)-3,4,3',4'-Tetrahydro-2H,2'h-[4,8']Bichromenyl-3'-Yl Ester
IUPAC Name	[(2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-8-[(2R,3R,4R)-3,5,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-4-yl]-3,4-dihydro-2H-chromen-3-yl] 3,4,5-trihydroxybenzoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL161077
PubChem CID	467305
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001586] Biflavonoids and polyflavonoids

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 85 91 0 0 0 0 0 0 0 0999 V2000 0.5015 3.1262 -1.0684 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6072 2.9520 -0.2477 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7967 3.4961 -0.6294 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8826 4.2138 -1.8313 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7831 4.3801 -2.6360 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5780 3.8308 -2.2516 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5102 4.0197 -3.0895 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8663 5.1008 -3.8443 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0895 4.7663 -2.2204 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4508 2.2083 0.9949 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7097 1.6717 1.6194 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3519 1.0724 2.9937 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1903 0.1801 2.8746 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9840 -0.7297 3.9079 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0941 -1.5840 3.8396 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9556 -1.5328 2.7559 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7741 -0.6466 1.7269 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6892 -0.5756 0.5589 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6028 -1.7589 -0.3022 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4019 -2.4003 -0.4925 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2794 -3.5109 -1.3130 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3928 -3.9944 -1.9626 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5936 -3.3792 -1.7919 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6963 -2.2525 -0.9537 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8994 -1.6007 -0.7538 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1649 -1.0855 0.5329 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.4633 -0.3419 0.5552 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8582 0.5462 -0.4167 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0629 1.2091 -0.3539 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9218 1.0019 0.6967 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5517 0.1187 1.6827 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3293 -0.5430 1.6028 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4079 -0.1033 2.7527 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.1567 1.6722 0.7747 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.4209 2.0961 -1.3557 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0618 -0.1294 0.8965 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4195 1.0773 0.2306 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3395 -5.1070 -2.8026 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7178 -1.9366 0.1435 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3434 0.2227 1.8202 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5343 1.1197 0.7849 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0123 -2.4001 2.7302 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8772 -0.7402 4.9719 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3817 0.7070 0.8575 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7141 0.6878 0.5210 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4221 1.6519 0.9578 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3142 -0.3669 -0.2918 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6059 -1.4281 -0.7911 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2034 -2.4142 -1.5606 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5420 -2.3241 -1.8291 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2896 -1.2725 -1.3453 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6561 -0.3027 -0.5774 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6452 -1.2049 -1.6322 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1851 -3.2961 -2.6008 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4898 -3.4882 -2.0668 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4417 2.6907 -0.7576 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6952 3.4110 -0.0403 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5922 4.8275 -3.6929 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3648 5.9937 -3.7752 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4439 5.6181 -1.8054 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9206 2.8746 1.7172 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3983 2.4861 1.8570 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1876 0.4855 3.4044 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1291 1.8794 3.7128 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2421 -2.2849 4.6486 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2597 0.2624 -0.0943 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6766 -3.9990 -1.4472 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4849 -3.7393 -2.2924 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2386 -1.9508 1.2243 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1694 0.7110 -1.2603 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0939 -1.2321 2.4182 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3843 -0.9075 3.3417 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.9666 1.2332 1.2060 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0527 1.8093 -2.0916 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1516 0.1864 1.9858 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6317 1.4704 -0.2202 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1557 -5.6192 -3.0446 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1982 -2.4491 0.8910 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4949 -2.7442 3.5565 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6231 -1.4304 4.9993 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5506 -1.5131 -0.5883 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2646 0.5045 -0.2145 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0240 -1.6811 -2.4337 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2904 -3.1758 -3.6008 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9396 -4.3959 -2.0266 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 5 8 1 0 4 9 1 0 2 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 2 0 28 29 1 0 29 30 2 0 30 31 1 0 31 32 2 0 31 33 1 0 30 34 1 0 29 35 1 0 26 36 1 0 36 37 1 0 22 38 1 0 20 39 1 0 17 40 2 0 40 41 1 0 16 42 1 0 14 43 1 0 11 44 1 0 44 45 1 0 45 46 2 0 45 47 1 0 47 48 2 0 48 49 1 0 49 50 2 0 50 51 1 0 51 52 2 0 51 53 1 0 50 54 1 0 49 55 1 0 6 1 1 0 41 10 1 0 52 47 1 0 40 13 1 0 36 18 1 0 24 19 1 0 32 27 1 0 1 56 1 0 3 57 1 0 7 58 1 0 8 59 1 0 9 60 1 0 10 61 1 1 11 62 1 1 12 63 1 0 12 64 1 0 15 65 1 0 18 66 1 6 21 67 1 0 23 68 1 0 26 69 1 1 28 70 1 0 32 71 1 0 33 72 1 0 34 73 1 0 35 74 1 0 36 75 1 1 37 76 1 0 38 77 1 0 39 78 1 0 42 79 1 0 43 80 1 0 48 81 1 0 52 82 1 0 53 83 1 0 54 84 1 0 55 85 1 0 M END

Standard InCHIKey	JSBXKZFDEDBAQA-WUFIRYPCSA-N
Standard InCHI	InChI=1S/C37H30O18/c38-14-7-17(40)27-25(8-14)53-35(12-3-21(44)31(49)22(45)4-12)33(51)29(27)28-18(41)10-16(39)15-9-26(54-37(52)13-5-23(46)32(50)24(47)6-13)34(55-36(15)28)11-1-19(42)30(48)20(43)2-11/h1-8,10,26,29,33-35,38-51H,9H2/t26-,29-,33-,34-,35-/m1/s1
SMILES	c1c(cc(c(c1O)O)O)[C@@H]1[C@@H](Cc2c(cc(c([C@H]3c4c(cc(cc4O[C@H](c4cc(c(c(c4)O)O)O)[C@@H]3O)O)O)c2O1)O)O)OC(=O)c1cc(c(c(c1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	762.14	Volume:	704.653 ? Van der Waals volume.
Dense:	1.082	LogP:	0.968 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.112 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.265 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	41.0
TPSA:	327.98 ? Topological Polar Surface Area.	H-Bond Acceptor:	18.0
H-Bond Donor:	14.0	Rings:	7.0
Heavy Atoms:	18.0

MedChem Properties

QED Drug-Likeness Score:	0.09	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.019	Fsp³:	0.162
MCE-18:	157.395 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	1	PAINS Alert:	1
Colloidal aggregators:	0.995	Fluc inhibitor:	0.143 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.242 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.635 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.641	Promiscuous compounds:	0.64

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-7.86	MDCK Permeability:	-4.741
Pgp-inhibitor:	0.0	Pgp-substrate:	0.003
PAMPA:	0.64 ? 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):	0.0
20% Bioavailability (F20%):	1.0	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	1.0
Plasma Protein Binding (PPB):	87.829%	Volume Distribution (VD):	0.041
Fu:	14.392% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.997	BCRP inhibitor:	0.289
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.93
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.002	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.0 ? 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):

5.4

Half-life (T1/2):

4.738

ADMET: Toxicity

hERG Blockers:	0.016	hERG Blockers (10um):	0.983
Human Hepatotoxicity (H-HT):	0.458	Drug-induced Liver Injury (DILI):	0.996
AMES Toxicity:	0.937	Rat Oral Acute Toxicity:	0.746
Maximum Recommended Daily Dose:	0.992	Skin Sensitization:	1.0
Carcinogencity:	0.033	Eye Corrosion:	0.0
Eye Irritation:	0.924	Respiratory Toxicity:	0.869
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.998
Hematotoxicity:	0.001	Drug-induced Nephrotoxicity:	0.001
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.001
A549 Cytotoxicity:	1.0	Hek293 Cytotoxicity:	0.971
BCF:	0.843 ? 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:	3.422 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.572 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.073 ? 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
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[12088434]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	stem	n.a.	n.a.	PMID[16643054]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	leaves	n.a.	n.a.	PMID[17125218]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	n.a.	root	n.a.	PMID[17315960]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	roots	n.a.	n.a.	PMID[17315960]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18590313]
NPO22791	Astraeus pteridis	Species	Astraeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19067555]
NPO3152	Morella rubra	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19407970]
NPO23452	Parapiptadenia rigida	Species	Fabaceae	Eukaryota	bark	Santa Maria, Rio Grande do Sul, Brazil	2007-OCT	PMID[21080642]
NPO23452	Parapiptadenia rigida	Species	Fabaceae	Eukaryota	n.a.	bark	n.a.	PMID[21080642]
NPO23452	Parapiptadenia rigida	Species	Fabaceae	Eukaryota	n.a.	bark	n.a.	PMID[21553897]
NPO3152	Morella rubra	Species	Myricaceae	Eukaryota	n.a.	bark	n.a.	PMID[21553897]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21707257]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29726697]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[34443694]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[34770961]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[35631245]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36840093]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37020229]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37226152]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38257205]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38370080]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38381096]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38695450]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39407547]
NPO5054	Limonium gmelinii	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23494	Centaurea linifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3152	Morella rubra	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4594	Vitellaria paradoxa	Species	Sapotaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO4594	Vitellaria paradoxa	Species	Sapotaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	Essential Oil	n.a.	n.a.	Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5054	Limonium gmelinii	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO3152	Morella rubra	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5054	Limonium gmelinii	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5054	Limonium gmelinii	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO23879	Serratula inermis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4594	Vitellaria paradoxa	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21956	Alyxia reinwardtii	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21327	Ramalina stenospora	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19472	Thymus vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20604	Cneoridium dumosum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23452	Parapiptadenia rigida	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25848	Oscillochloris trichoides	Species	Oscillochloridaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO23614	Ovophis okinavensis	Species	Viperidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5054	Limonium gmelinii	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22791	Astraeus pteridis	Species	Astraeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24327	Machilus macrantha	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23954	Tridachia crispata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO3152	Morella rubra	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23494	Centaurea linifolia	Species	Asteraceae	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

Activity Type	# Activity
IC50	1
EC50	1

Activity Type	# Activity
Cell line	1
Organism	1

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
NPT759	Cell line	H9	Homo sapiens	IC50	=	28.0	ug.mL-1	DOI[10.1016/0960-894X(96)00095-9]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	15.0	ug.mL-1	DOI[10.1016/0960-894X(96)00095-9]

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 NPC65333 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	21793
0.1-0.2	26154
0.2-0.3	1664
0.3-0.4	150
0.4-0.5	49
0.5-0.6	33
0.6-0.7	13
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	Natural Product ID
0.7571	Intermediate Similarity	NPC100251
0.7059	Intermediate Similarity	NPC96576
0.6923	Remote Similarity	NPC291948
0.6923	Remote Similarity	NPC104983
0.6923	Remote Similarity	NPC250436
0.6923	Remote Similarity	NPC300845
0.6923	Remote Similarity	NPC88803
0.6842	Remote Similarity	NPC98583
0.6197	Remote Similarity	NPC38779
0.6197	Remote Similarity	NPC114179
0.6197	Remote Similarity	NPC68324
0.6197	Remote Similarity	NPC289322
0.6197	Remote Similarity	NPC156818
0.6197	Remote Similarity	NPC160512
0.6	Remote Similarity	NPC603842
0.5946	Remote Similarity	NPC58190
0.5946	Remote Similarity	NPC108811
0.5946	Remote Similarity	NPC170103
0.5946	Remote Similarity	NPC236202
0.5946	Remote Similarity	NPC262911
0.5946	Remote Similarity	NPC202742
0.5867	Remote Similarity	NPC246202
0.5867	Remote Similarity	NPC224161
0.5867	Remote Similarity	NPC46335
0.5867	Remote Similarity	NPC87317
0.5867	Remote Similarity	NPC279406
0.5867	Remote Similarity	NPC486519
0.5854	Remote Similarity	NPC135021
0.5641	Remote Similarity	NPC603291
0.5556	Remote Similarity	NPC278548
0.55	Remote Similarity	NPC601997
0.55	Remote Similarity	NPC609211
0.55	Remote Similarity	NPC610665
0.5455	Remote Similarity	NPC600812
0.5432	Remote Similarity	NPC600630
0.5432	Remote Similarity	NPC607896
0.5432	Remote Similarity	NPC611369
0.5309	Remote Similarity	NPC211561
0.5238	Remote Similarity	NPC602382
0.5176	Remote Similarity	NPC602962
0.5147	Remote Similarity	NPC268266
0.5147	Remote Similarity	NPC42760
0.5147	Remote Similarity	NPC220825
0.5147	Remote Similarity	NPC268342
0.5132	Remote Similarity	NPC474656
0.5128	Remote Similarity	NPC601196
0.5122	Remote Similarity	NPC226809
0.5068	Remote Similarity	NPC178054

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC65333 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5747
0.1-0.2	3385
0.2-0.3	14
0.3-0.4	0
0.4-0.5	2
0.5-0.6	1
0.6-0.7	1
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
0.6923	Remote Similarity	NPD4868	Phase 3
0.5165	Remote Similarity	NPD7993	Clinical (unspecified phase)

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