NPASS Compound

Natural Product: NPC155763

Natural Product ID	NPC155763
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	6-[2-(3,4-Dihydroxyphenyl)-5,7-Dihydroxy-4-Oxochromen-3-Yl]Oxy-3,4,5-Trihydroxyoxane-2-Carboxylic Acid
IUPAC Name	6-[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxochromen-3-yl]oxy-3,4,5-trihydroxyoxane-2-carboxylic acid
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1506682
PubChem CID	12004528
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0002934] Flavonoid O-glucuronides [CHEMONTID:0003532] Flavonoid-3-O-glucuronides

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 52 55 0 0 0 0 0 0 0 0999 V2000 -4.6248 3.1900 -4.3933 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5128 2.5391 -3.8436 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2334 2.8271 -4.2841 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1493 2.1823 -3.7377 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1211 2.4883 -4.1952 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2934 1.2213 -2.7273 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5636 0.9252 -2.2796 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6331 1.5955 -2.8542 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6854 0.0433 -1.3548 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6801 -0.6275 -0.7717 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4111 -0.3622 -1.1798 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1972 0.5896 -2.1913 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9481 0.8717 -2.6090 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7556 -0.9614 -0.6588 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4807 -0.2700 0.3611 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6195 0.2878 -0.2840 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5549 0.7656 0.5832 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2290 1.9963 0.0925 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9236 2.4863 -1.0067 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1972 2.5866 0.8733 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9335 1.0958 1.9423 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5551 -0.2236 2.5493 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9238 -1.1193 1.4892 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8797 -2.0395 1.0128 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6954 -0.7889 3.1071 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9330 1.7233 2.7051 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0179 -1.5947 0.2574 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3022 -1.5881 0.8088 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7020 -2.5146 1.7460 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8420 -3.4971 2.1830 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5875 -3.5197 1.6568 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1951 -2.5752 0.7075 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6883 -4.4893 2.0660 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2035 -4.4476 3.1239 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9591 4.0103 -3.8724 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1504 3.5713 -5.0629 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5988 3.2644 -3.7249 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6214 1.3573 -2.4981 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8477 0.5642 0.7164 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3754 0.0353 0.7960 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6778 3.4217 0.5566 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0759 1.7816 1.7904 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8047 -0.0124 3.3461 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1127 -1.6484 1.9836 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9237 -2.0048 0.0261 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7505 -0.4031 4.0372 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5515 2.2907 3.4215 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9974 -0.8257 0.4817 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6908 -2.5180 2.1788 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1937 -2.6750 0.3216 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2758 -4.5320 2.9751 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0579 -4.4733 3.6329 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 4 6 2 0 6 7 1 0 7 8 2 0 7 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 11 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 17 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 22 25 1 0 21 26 1 0 10 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 8 2 1 0 23 15 1 0 32 27 1 0 12 6 1 0 1 35 1 0 3 36 1 0 5 37 1 0 8 38 1 0 15 39 1 0 17 40 1 0 20 41 1 0 21 42 1 0 22 43 1 0 23 44 1 0 24 45 1 0 25 46 1 0 26 47 1 0 28 48 1 0 29 49 1 0 32 50 1 0 33 51 1 0 34 52 1 0 M END

Standard InCHIKey	DUBCCGAQYVUYEU-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C21H18O13/c22-7-4-10(25)12-11(5-7)32-17(6-1-2-8(23)9(24)3-6)18(13(12)26)33-21-16(29)14(27)15(28)19(34-21)20(30)31/h1-5,14-16,19,21-25,27-29H,(H,30,31)
SMILES	Oc1cc(O)c2c(c1)oc(c(c2=O)OC1OC(C(=O)O)C(C(C1O)O)O)c1ccc(c(c1)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	478.07	Volume:	428.091 ? Van der Waals volume.
Dense:	1.117	LogP:	0.199 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.887 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.729 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	25.0
TPSA:	227.58 ? Topological Polar Surface Area.	H-Bond Acceptor:	13.0
H-Bond Donor:	8.0	Rings:	4.0
Heavy Atoms:	13.0

MedChem Properties

QED Drug-Likeness Score:	0.223	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.073	Fsp³:	0.238
MCE-18:	94.769 ? 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:	Rejected	BMS Rule:	0
Chelating Alert:	1	PAINS Alert:	1
Colloidal aggregators:	0.291	Fluc inhibitor:	0.15 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.951 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.857 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.335	Promiscuous compounds:	0.699

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.3	MDCK Permeability:	-4.907
Pgp-inhibitor:	0.0	Pgp-substrate:	0.482
PAMPA:	1.0 ? 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):	0.679
20% Bioavailability (F20%):	0.934	30% Bioavailability (F30%):	0.995
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.983
Plasma Protein Binding (PPB):	80.342%	Volume Distribution (VD):	-0.267
Fu:	17.38% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.01
OATP1B3 inhibitor:	0.881	BCRP inhibitor:	0.153
BSEP inhibitor:	0.001

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.347	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.001	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.99
HLM stability:	0.008 ? 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):

1.405

Half-life (T1/2):

3.188

ADMET: Toxicity

hERG Blockers:	0.012	hERG Blockers (10um):	0.143
Human Hepatotoxicity (H-HT):	0.383	Drug-induced Liver Injury (DILI):	0.879
AMES Toxicity:	0.346	Rat Oral Acute Toxicity:	0.355
Maximum Recommended Daily Dose:	0.692	Skin Sensitization:	0.629
Carcinogencity:	0.138	Eye Corrosion:	0.0
Eye Irritation:	0.888	Respiratory Toxicity:	0.264
Drug-induced Neurotoxicity:	0.006	Ototoxicity:	0.836
Hematotoxicity:	0.014	Drug-induced Nephrotoxicity:	0.037
Genotoxicity:	0.98	RPMI-8226 Immunitoxicity:	0.016
A549 Cytotoxicity:	0.189	Hek293 Cytotoxicity:	0.387
BCF:	0.278 ? 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:	2.87 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.311 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.558 ? 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
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[ 17560738]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11240-015-0798-z]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11816-015-0350-y]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.fitote.2006.01.011]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jarmap.2018.11.004]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.plaphy.2005.07.013]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/S0031-9422(00)94055-X]
NPO3057	Polygonum aviculare	Species	Polygonaceae	Eukaryota	n.a.	whole plant	n.a.	DOI[10.1016/S1572-557X(05)02007-6]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1078/0176-1617-00195]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1155/2014/609649]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	flower	n.a.	DOI[10.3390/70200245]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10757735]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	seed	n.a.	PMID[11540412]
NPO21963	Hypericum japonicum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11914965]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14735439]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	callus	n.a.	PMID[15715262]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[17520525]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18220354]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19919095]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22966846]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	flower buds and leaves	Khon Kaen province, Thailand	2010	PMID[23270663]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[23642481]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24617303]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[26462418]
NPO21963	Hypericum japonicum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27116034]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28445039]
NPO21963	Hypericum japonicum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29667821]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	Roots	n.a.	n.a.	PMID[30024167]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32560389]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36336219]
NPO3057	Polygonum aviculare	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36558187]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38217369]
NPO3057	Polygonum aviculare	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21963	Hypericum japonicum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3057	Polygonum aviculare	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Rhizome	n.a.	n.a.	Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3057	Polygonum aviculare	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21963	Hypericum japonicum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21963	Hypericum japonicum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3057	Polygonum aviculare	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21963	Hypericum japonicum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3057	Polygonum aviculare	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3057	Polygonum aviculare	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21963	Hypericum japonicum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	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
Potency	29
IC50	9
EC50	1

Activity Type	# Activity
Individual protein	34
Others	5

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.	39810.7	nM	PubChem BioAssay data set
NPT199	Individual protein	DNA polymerase kappa	Homo sapiens	Potency	n.a.	14125.4	nM	PubChem BioAssay data set
NPT2966	Individual protein	T-complex protein 1 subunit beta	Macaaca fascicularis	Potency	n.a.	11220.2	nM	PubChem BioAssay data set
NPT100	Individual protein	Glutaminase kidney isoform, mitochondrial	Homo sapiens	Potency	n.a.	35481.3	nM	PubChem BioAssay data set
NPT11	Individual protein	Guanine nucleotide-binding protein G(s), subunit alpha	Homo sapiens	Potency	n.a.	11220.2	nM	PubChem BioAssay data set
NPT1854	Individual protein	Phosphoglycerate kinase	Trypanosoma brucei brucei (strain 927/4 GUTat10.1)	Potency	n.a.	10311.9	nM	PubChem BioAssay data set
NPT105	Individual protein	Muscleblind-like protein 1	Homo sapiens	Potency	n.a.	19952.6	nM	PubChem BioAssay data set
NPT1040	Individual protein	Human immunodeficiency virus type 1 Tat protein	Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)(HIV-1)	IC50	n.a.	2124.0	nM	PubChem BioAssay data set
NPT483	Individual protein	Prelamin-A/C	Homo sapiens	Potency	=	12589.3	nM	PubChem BioAssay data set
NPT55	Individual protein	Putative fructose-1,6-bisphosphate aldolase	Giardia intestinalis	Potency	=	15811.4	nM	PubChem BioAssay data set
NPT801	Individual protein	Intestinal alkaline phosphatase	Homo sapiens	IC50	=	3150.0	nM	PubChem BioAssay data set
NPT801	Individual protein	Intestinal alkaline phosphatase	Homo sapiens	IC50	=	891.0	nM	PubChem BioAssay data set
NPT803	Individual protein	Flap endonuclease 1	Homo sapiens	Potency	n.a.	11220.2	nM	PubChem BioAssay data set
NPT9	Individual protein	DNA polymerase eta	Homo sapiens	Potency	n.a.	6309.6	nM	PubChem BioAssay data set
NPT48	Individual protein	Lysine-specific demethylase 4D-like	Homo sapiens	Potency	=	4466.8	nM	PubChem BioAssay data set
NPT94	Individual protein	Aldehyde dehydrogenase 1A1	Homo sapiens	Potency	=	39810.7	nM	PubChem BioAssay data set
NPT798	Individual protein	Alkaline phosphatase placental-like	Homo sapiens	EC50	>	100000.0	nM	PubChem BioAssay data set
NPT802	Individual protein	Alkaline phosphatase, tissue-nonspecific isozyme	Homo sapiens	IC50	>	100000.0	nM	PubChem BioAssay data set
NPT51	Individual protein	Microtubule-associated protein tau	Homo sapiens	Potency	=	11220.2	nM	PubChem BioAssay data set
NPT60	Individual protein	Lysosomal alpha-glucosidase	Homo sapiens	Potency	=	3981.1	nM	PubChem BioAssay data set
NPT59	Individual protein	DNA polymerase beta	Homo sapiens	Potency	=	8912.5	nM	PubChem BioAssay data set
NPT799	Individual protein	Intestinal alkaline phosphatase	Mus musculus	IC50	=	3290.0	nM	PubChem BioAssay data set
NPT63	Individual protein	Bromodomain adjacent to zinc finger domain protein 2B	Homo sapiens	Potency	n.a.	35481.3	nM	PubChem BioAssay data set
NPT8	Individual protein	DNA polymerase iota	Homo sapiens	Potency	n.a.	22387.2	nM	PubChem BioAssay data set
NPT534	Individual protein	Phosphoglycerate kinase, glycosomal	Trypanosoma brucei brucei	Potency	n.a.	25118.9	nM	PubChem BioAssay data set
NPT821	Individual protein	Werner syndrome ATP-dependent helicase	Homo sapiens	Potency	n.a.	44668.4	nM	PubChem BioAssay data set
NPT755	Individual protein	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	Homo sapiens	Potency	n.a.	56234.1	nM	PubChem BioAssay data set
NPT535	Individual protein	Parathyroid hormone receptor	Homo sapiens	Potency	n.a.	158489.3	nM	PubChem BioAssay data set
NPT4744	Individual protein	M17 leucyl aminopeptidase	Plasmodium falciparum 3D7	IC50	=	48150.0	nM	PubChem BioAssay data set
NPT532	Individual protein	Lysine-specific demethylase 4A	Homo sapiens	Potency	n.a.	31622.8	nM	PubChem BioAssay data set
NPT62	Individual protein	6-phospho-1-fructokinase	Trypanosoma brucei	Potency	n.a.	37933.0	nM	PubChem BioAssay data set
NPT4	Individual protein	Large T antigen	Simian virus 40	IC50	n.a.	9800.0	nM	PubChem BioAssay data set
NPT5	Individual protein	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3	Homo sapiens	Potency	n.a.	31622.8	nM	PubChem BioAssay data set
NPT49	Individual protein	DNA-(apurinic or apyrimidinic site) lyase	Homo sapiens	Potency	n.a.	7079.5	nM	PubChem BioAssay data set

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	n.a.	IC50	=	8720.0	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	3162.3	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	18356.4	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	501.2	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	IC50	n.a.	2700.0	nM	PubChem BioAssay data set

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 NPC155763 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	23900
0.1-0.2	23480
0.2-0.3	1705
0.3-0.4	407
0.4-0.5	207
0.5-0.6	105
0.6-0.7	43
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC235260
0.875	High Similarity	NPC138927
0.72	Intermediate Similarity	NPC276222
0.72	Intermediate Similarity	NPC274618
0.72	Intermediate Similarity	NPC118284
0.72	Intermediate Similarity	NPC608147
0.6923	Remote Similarity	NPC127546
0.6923	Remote Similarity	NPC57625
0.6923	Remote Similarity	NPC173637
0.6923	Remote Similarity	NPC317489
0.6923	Remote Similarity	NPC223424
0.6923	Remote Similarity	NPC600591
0.6835	Remote Similarity	NPC145038
0.6835	Remote Similarity	NPC56077
0.6835	Remote Similarity	NPC281131
0.6835	Remote Similarity	NPC253662
0.6835	Remote Similarity	NPC179950
0.6835	Remote Similarity	NPC88789
0.6835	Remote Similarity	NPC491374
0.6667	Remote Similarity	NPC67037
0.6667	Remote Similarity	NPC255615
0.6667	Remote Similarity	NPC600989
0.6585	Remote Similarity	NPC49344
0.6585	Remote Similarity	NPC175107
0.6471	Remote Similarity	NPC116864
0.6471	Remote Similarity	NPC244776
0.641	Remote Similarity	NPC54802
0.641	Remote Similarity	NPC197304
0.6386	Remote Similarity	NPC135277
0.619	Remote Similarity	NPC20505
0.6173	Remote Similarity	NPC111929
0.6173	Remote Similarity	NPC320283
0.6173	Remote Similarity	NPC41121
0.6145	Remote Similarity	NPC52550
0.6098	Remote Similarity	NPC77672
0.6098	Remote Similarity	NPC133671
0.6098	Remote Similarity	NPC135391
0.6098	Remote Similarity	NPC78263
0.6098	Remote Similarity	NPC250069
0.6067	Remote Similarity	NPC67326
0.6056	Remote Similarity	NPC286342
0.6	Remote Similarity	NPC203259
0.6	Remote Similarity	NPC33054
0.6	Remote Similarity	NPC176740
0.6	Remote Similarity	NPC471725
0.6	Remote Similarity	NPC210094
0.6	Remote Similarity	NPC134532
0.6	Remote Similarity	NPC156869
0.6	Remote Similarity	NPC602582
0.5976	Remote Similarity	NPC135599
0.5976	Remote Similarity	NPC73855
0.5976	Remote Similarity	NPC113968
0.5976	Remote Similarity	NPC328940
0.5976	Remote Similarity	NPC277174
0.5976	Remote Similarity	NPC606877
0.5955	Remote Similarity	NPC29958
0.5926	Remote Similarity	NPC288084
0.5914	Remote Similarity	NPC37668
0.5909	Remote Similarity	NPC254855
0.5909	Remote Similarity	NPC94610
0.5909	Remote Similarity	NPC95866
0.5904	Remote Similarity	NPC19388
0.5904	Remote Similarity	NPC240431
0.5904	Remote Similarity	NPC55786
0.5889	Remote Similarity	NPC471748
0.5824	Remote Similarity	NPC605592
0.5814	Remote Similarity	NPC282169
0.5732	Remote Similarity	NPC34531
0.5699	Remote Similarity	NPC154741
0.5682	Remote Similarity	NPC223747
0.567	Remote Similarity	NPC223426
0.5652	Remote Similarity	NPC155877
0.5647	Remote Similarity	NPC64305
0.5632	Remote Similarity	NPC60735
0.5632	Remote Similarity	NPC219904
0.5632	Remote Similarity	NPC26230
0.5625	Remote Similarity	NPC471669
0.5619	Remote Similarity	NPC480444
0.5618	Remote Similarity	NPC203050
0.5618	Remote Similarity	NPC225434
0.5612	Remote Similarity	NPC81042
0.5591	Remote Similarity	NPC255157
0.5591	Remote Similarity	NPC144097
0.5591	Remote Similarity	NPC259896
0.5568	Remote Similarity	NPC43211
0.5568	Remote Similarity	NPC120099
0.5517	Remote Similarity	NPC472459
0.5517	Remote Similarity	NPC101191
0.5465	Remote Similarity	NPC265530
0.5464	Remote Similarity	NPC135831
0.5455	Remote Similarity	NPC159579
0.5435	Remote Similarity	NPC471079
0.5426	Remote Similarity	NPC129264
0.5417	Remote Similarity	NPC122467
0.5417	Remote Similarity	NPC270448
0.5412	Remote Similarity	NPC476771
0.5402	Remote Similarity	NPC305811
0.5393	Remote Similarity	NPC85707
0.5376	Remote Similarity	NPC173582
0.5376	Remote Similarity	NPC470405
0.5376	Remote Similarity	NPC265885
0.5376	Remote Similarity	NPC181465
0.5376	Remote Similarity	NPC215710
0.5376	Remote Similarity	NPC473438
0.5376	Remote Similarity	NPC253788
0.5368	Remote Similarity	NPC153755
0.5349	Remote Similarity	NPC476772
0.5341	Remote Similarity	NPC42773
0.5341	Remote Similarity	NPC45522
0.5341	Remote Similarity	NPC325555
0.5341	Remote Similarity	NPC226304
0.5312	Remote Similarity	NPC245452
0.5306	Remote Similarity	NPC89127
0.5294	Remote Similarity	NPC292019
0.5294	Remote Similarity	NPC202908
0.5287	Remote Similarity	NPC136042
0.5281	Remote Similarity	NPC182121
0.5281	Remote Similarity	NPC129217
0.5275	Remote Similarity	NPC170052
0.5275	Remote Similarity	NPC476215
0.5275	Remote Similarity	NPC135846
0.527	Remote Similarity	NPC103342
0.5269	Remote Similarity	NPC139320
0.5263	Remote Similarity	NPC35167
0.5227	Remote Similarity	NPC271692
0.5222	Remote Similarity	NPC259957
0.5222	Remote Similarity	NPC189913
0.5222	Remote Similarity	NPC608742
0.5222	Remote Similarity	NPC609478
0.5213	Remote Similarity	NPC39834
0.5208	Remote Similarity	NPC253521
0.5208	Remote Similarity	NPC470125
0.5208	Remote Similarity	NPC296018
0.5208	Remote Similarity	NPC113836
0.5204	Remote Similarity	NPC97119
0.5172	Remote Similarity	NPC104677
0.5169	Remote Similarity	NPC216496
0.5169	Remote Similarity	NPC599850
0.5158	Remote Similarity	NPC473862
0.5152	Remote Similarity	NPC85751
0.5152	Remote Similarity	NPC19240
0.5149	Remote Similarity	NPC214621
0.5149	Remote Similarity	NPC34267
0.514	Remote Similarity	NPC480445
0.5111	Remote Similarity	NPC48093
0.5111	Remote Similarity	NPC237435
0.5106	Remote Similarity	NPC609888
0.5056	Remote Similarity	NPC27640
0.5055	Remote Similarity	NPC115760
0.5055	Remote Similarity	NPC484158
0.5055	Remote Similarity	NPC224530
0.5055	Remote Similarity	NPC610187
0.5053	Remote Similarity	NPC163242
0.5053	Remote Similarity	NPC272068

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC155763 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4526
0.1-0.2	4550
0.2-0.3	67
0.3-0.4	2
0.4-0.5	3
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
0.6	Remote Similarity	NPD6797	Phase 2
0.5111	Remote Similarity	NPD4338	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