NPASS Compound

Natural Product: NPC271921

Natural Product ID	NPC271921
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	2,3-Dihydroxypropyl (9Z,12Z,15Z)-Octadeca-9,12,15-Trienoate
IUPAC Name	2,3-dihydroxypropyl (9Z,12Z,15Z)-octadeca-9,12,15-trienoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL255922
PubChem CID	5367328
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000504] Lineolic acids 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 61 60 0 0 0 0 0 0 0 0999 V2000 -8.3253 0.1073 1.9508 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5339 1.2885 1.1194 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7509 1.7045 0.0049 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7113 1.1394 -0.5203 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0368 -0.1132 -0.1074 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0517 -1.0781 -1.2561 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9433 -1.5311 -1.7458 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6136 -1.1343 -1.2087 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8533 -0.4496 -2.2756 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7026 -0.8586 -2.7042 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0069 -2.0402 -2.1917 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3498 -1.4930 -1.6541 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0430 -0.4980 -0.5886 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1526 0.1561 0.0692 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0489 -0.8374 0.7396 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2066 -0.0928 1.3661 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0201 0.6640 0.3724 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1177 1.3456 1.1175 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8912 2.4097 1.7059 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3614 0.7733 1.1334 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4662 1.3462 1.8133 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6458 0.4022 1.5850 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8033 0.2021 0.0856 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1901 1.3915 -0.5106 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2569 -0.8278 2.1280 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.4068 0.1438 2.5604 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1328 0.0943 2.8061 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5432 -0.8824 1.4885 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.6751 1.3404 0.8348 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5383 2.1840 1.8636 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0719 2.6810 -0.5174 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2279 1.6284 -1.4050 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9702 0.1400 0.1058 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4889 -0.6538 0.7140 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0182 -1.4045 -1.6886 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9528 -2.2480 -2.6025 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0456 -2.1029 -0.9804 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5668 -0.5986 -0.2834 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2657 0.4583 -2.7470 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1512 -0.3164 -3.5190 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4056 -2.5935 -1.3649 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7369 -2.7612 -3.0131 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8326 -1.0249 -2.5209 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9425 -2.3119 -1.2495 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6937 -1.0105 0.1520 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6382 0.3203 -1.0491 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6695 0.7374 -0.7250 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7392 0.8245 0.8603 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4672 -1.3884 1.4801 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4020 -1.5448 -0.0541 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7756 0.6116 2.1117 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8692 -0.8025 1.8862 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4157 -0.0579 -0.3777 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4867 1.4521 -0.1735 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2796 1.4917 2.8921 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7444 2.2958 1.3006 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5611 0.7674 2.0536 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5555 -0.5889 -0.1157 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8543 -0.1166 -0.3530 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1834 1.4101 -0.6406 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8134 -1.5752 1.8424 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 1 0 6 7 2 0 7 8 1 0 8 9 1 0 9 10 2 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 16 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 22 25 1 0 1 26 1 0 1 27 1 0 1 28 1 0 2 29 1 0 2 30 1 0 3 31 1 0 4 32 1 0 5 33 1 0 5 34 1 0 6 35 1 0 7 36 1 0 8 37 1 0 8 38 1 0 9 39 1 0 10 40 1 0 11 41 1 0 11 42 1 0 12 43 1 0 12 44 1 0 13 45 1 0 13 46 1 0 14 47 1 0 14 48 1 0 15 49 1 0 15 50 1 0 16 51 1 0 16 52 1 0 17 53 1 0 17 54 1 0 21 55 1 0 21 56 1 0 22 57 1 0 23 58 1 0 23 59 1 0 24 60 1 0 25 61 1 0 M END

Standard InCHIKey	GGJRAQULURVTAJ-PDBXOOCHSA-N
Standard InCHI	InChI=1S/C21H36O4/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-21(24)25-19-20(23)18-22/h3-4,6-7,9-10,20,22-23H,2,5,8,11-19H2,1H3/b4-3-,7-6-,10-9-
SMILES	CC/C=CC/C=CC/C=CCCCCCCCC(=O)OCC(CO)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	352.26	Volume:	396.387 ? Van der Waals volume.
Dense:	0.889	LogP:	4.518 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.387 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.796 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	17.0	Rigid Bonds:	4.0
TPSA:	66.76 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	2.0	Rings:	0.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.244	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.211	Fsp³:	0.667
MCE-18:	2.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.076	Fluc inhibitor:	0.004 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.004 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.813	Promiscuous compounds:	0.03

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.053	MDCK Permeability:	-4.86
Pgp-inhibitor:	0.011	Pgp-substrate:	0.003
PAMPA:	0.012 ? 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):	0.019
20% Bioavailability (F20%):	0.723	30% Bioavailability (F30%):	0.704
50% Bioavailability (F50%):	0.922

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.021	MRP1:	0.997
Plasma Protein Binding (PPB):	97.911%	Volume Distribution (VD):	-0.315
Fu:	2.243% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.001
OATP1B3 inhibitor:	0.308	BCRP inhibitor:	0.248
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.085
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.999	CYP2D6-substrate:	1.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.001	CYP2C8-inhibitor:	1.0
HLM stability:	0.009 ? 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):

6.08

Half-life (T1/2):

0.35

ADMET: Toxicity

hERG Blockers:	0.205	hERG Blockers (10um):	0.551
Human Hepatotoxicity (H-HT):	0.01	Drug-induced Liver Injury (DILI):	0.0
AMES Toxicity:	0.883	Rat Oral Acute Toxicity:	0.006
Maximum Recommended Daily Dose:	0.0	Skin Sensitization:	1.0
Carcinogencity:	0.002	Eye Corrosion:	1.0
Eye Irritation:	1.0	Respiratory Toxicity:	0.51
Drug-induced Neurotoxicity:	0.011	Ototoxicity:	0.24
Hematotoxicity:	0.0	Drug-induced Nephrotoxicity:	0.531
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.014
A549 Cytotoxicity:	0.082	Hek293 Cytotoxicity:	0.002
BCF:	1.64 ? 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:	4.834 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.169 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.076 ? 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
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0031-9422(99)00119-3]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	n.a.	Oued Nougued, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	Seeds	Tidda, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	Seeds	Ouled Ziad, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	n.a.	Boghar, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	n.a.	Bougtob, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	n.a.	Djemaa Ouled Chikh, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	n.a.	Maarif, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	n.a.	Metlili, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	n.a.	Mougheul, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	Seeds	Oued Nougued, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	n.a.	Ouled Ziad, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	n.a.	Tidda, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	Seeds	Boghar, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	Seeds	Bougtob, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	Seeds	Djemaa Ouled Chikh, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	Seeds	Maarif, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	Seeds	Metlili, Algeria		DOI[10.2139/ssrn.4105036]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	Seeds	Mougheul, Algeria		DOI[10.2139/ssrn.4105036]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	fruit	n.a.	PMID[10606547]
NPO31458	Cinnamomum cassia	Species	Lauraceae	Eukaryota	twigs	n.a.	n.a.	PMID[19555125]
NPO31458	Cinnamomum cassia	Species	Lauraceae	Eukaryota	twigs	n.a.	n.a.	PMID[22677314]
NPO31457	Amomum kravanh	Species	Zingiberaceae	Eukaryota	fruits	n.a.	n.a.	PMID[23394284]
NPO31458	Cinnamomum cassia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[34332066]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[34771092]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	Roots	Beni Mellal, Morocco	Between 2016-Sep and 2016-Oct	PMID[35056798]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	Seeds	Beni Mellal, Morocco	Between 2016-Sep and 2016-Oct	PMID[35056798]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	Leaves	Beni Mellal, Morocco	Between 2016-Sep and 2016-Oct	PMID[35056798]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	n.a.	Beni Mellal, Morocco	Between 2016-Sep and 2016-Oct	PMID[35056798]
NPO55200	Sitophilus granarius	Species	Curculionidae	Eukaryota	n.a.	n.a.	n.a.	PMID[35638325]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37049761]
NPO31458	Cinnamomum cassia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37446712]
NPO31457	Amomum kravanh	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38067483]
NPO31458	Cinnamomum cassia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38688144]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38786901]
NPO30971	Cheiranthus cheiri	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[39575377]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10082	Citrus unshiu	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO31458	Cinnamomum cassia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO31457	Amomum kravanh	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO30971	Cheiranthus cheiri	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO42044	Anredera scandens	Genus	Basellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO30971	Cheiranthus cheiri	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO10082	Citrus unshiu	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31458	Cinnamomum cassia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31457	Amomum kravanh	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO10082	Citrus unshiu	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10082	Citrus unshiu	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31458	Cinnamomum cassia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31457	Amomum kravanh	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30971	Cheiranthus cheiri	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25443	Citrus reticulata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10082	Citrus unshiu	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27288	Citrus maxima	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10082	Citrus unshiu	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25443	Citrus reticulata	Species	Rutaceae	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
NPO30971	Cheiranthus cheiri	n-hexane extract	n.a.	1.35	n.a.	n.a.	%	PMID[39575377]
NPO31457	Amomum kravanh	CO2 extract	n.a.	1.43	n.a.	n.a.	%	PMID[38067483]
NPO31458	Cinnamomum cassia	Oil	Bark	0.12	n.a.	n.a.	%	PMID[38688144]
NPO42044	Anredera scandens	n.a.	Leaves	84	n.a.	n.a.	mg/g of DW	PMID[35056798]
NPO55200	Sitophilus granarius	Oil	n.a.	27.93	n.a.	n.a.	%	PMID[35638325]

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	2
GI50	60

Activity Type	# Activity
Individual protein	2
Cell line	60

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT3172	Individual protein	Phospholipase A2 group IIA	Homo sapiens	Inhibition	=	32.0	%	PMID[18487046]
NPT31	Individual protein	Cyclooxygenase-2	Homo sapiens	Inhibition	=	-12.8	%	PMID[18487046]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT368	Cell line	SN12C	Homo sapiens	GI50	n.a.	95060.48	nM	PubChem BioAssay data set
NPT369	Cell line	ACHN	Homo sapiens	GI50	n.a.	58479.01	nM	PubChem BioAssay data set
NPT370	Cell line	NCI-H23	Homo sapiens	GI50	n.a.	74473.2	nM	PubChem BioAssay data set
NPT371	Cell line	UO-31	Homo sapiens	GI50	n.a.	16368.17	nM	PubChem BioAssay data set
NPT372	Cell line	HOP-92	Homo sapiens	GI50	n.a.	68076.94	nM	PubChem BioAssay data set
NPT116	Cell line	HL-60	Homo sapiens	GI50	n.a.	20749.14	nM	PubChem BioAssay data set
NPT373	Cell line	SK-MEL-5	Homo sapiens	GI50	n.a.	59156.16	nM	PubChem BioAssay data set
NPT374	Cell line	SF-539	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT375	Cell line	Malme-3M	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT111	Cell line	K562	Homo sapiens	GI50	n.a.	2460.37	nM	PubChem BioAssay data set
NPT376	Cell line	A498	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT377	Cell line	OVCAR-3	Homo sapiens	GI50	n.a.	40926.07	nM	PubChem BioAssay data set
NPT112	Cell line	MOLT-4	Homo sapiens	GI50	n.a.	46238.1	nM	PubChem BioAssay data set
NPT379	Cell line	HOP-62	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT380	Cell line	U-251	Homo sapiens	GI50	n.a.	57809.6	nM	PubChem BioAssay data set
NPT381	Cell line	OVCAR-8	Homo sapiens	GI50	n.a.	67764.15	nM	PubChem BioAssay data set
NPT382	Cell line	OVCAR-5	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT572	Cell line	DMS-273	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT383	Cell line	SNB-19	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT385	Cell line	SR	Homo sapiens	GI50	n.a.	1000.0	nM	PubChem BioAssay data set
NPT384	Cell line	TK-10	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT573	Cell line	M19-MEL	Homo sapiens	GI50	n.a.	63679.55	nM	PubChem BioAssay data set
NPT323	Cell line	SW-620	Homo sapiens	GI50	n.a.	58210.32	nM	PubChem BioAssay data set
NPT386	Cell line	KM12	Homo sapiens	GI50	n.a.	56885.29	nM	PubChem BioAssay data set
NPT455	Cell line	NCI-H522	Homo sapiens	GI50	n.a.	22029.26	nM	PubChem BioAssay data set
NPT388	Cell line	NCI-H322M	Homo sapiens	GI50	n.a.	67764.15	nM	PubChem BioAssay data set
NPT574	Cell line	XF498	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT387	Cell line	M14	Homo sapiens	GI50	n.a.	61659.5	nM	PubChem BioAssay data set
NPT389	Cell line	RPMI-8226	Homo sapiens	GI50	n.a.	43351.09	nM	PubChem BioAssay data set
NPT456	Cell line	OVCAR-4	Homo sapiens	GI50	n.a.	84333.48	nM	PubChem BioAssay data set
NPT390	Cell line	LOX IMVI	Homo sapiens	GI50	n.a.	39902.49	nM	PubChem BioAssay data set
NPT575	Cell line	KM-20L2	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT147	Cell line	SK-MEL-2	Homo sapiens	GI50	n.a.	97949.0	nM	PubChem BioAssay data set
NPT391	Cell line	HCC 2998	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT81	Cell line	A549	Homo sapiens	GI50	n.a.	84918.05	nM	PubChem BioAssay data set
NPT392	Cell line	SNB-75	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT148	Cell line	HCT-15	Homo sapiens	GI50	n.a.	63386.97	nM	PubChem BioAssay data set
NPT393	Cell line	HCT-116	Homo sapiens	GI50	n.a.	55590.43	nM	PubChem BioAssay data set
NPT395	Cell line	SF-268	Homo sapiens	GI50	n.a.	90782.05	nM	PubChem BioAssay data set
NPT394	Cell line	EKVX	Homo sapiens	GI50	n.a.	88715.6	nM	PubChem BioAssay data set
NPT146	Cell line	SK-OV-3	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT731	Cell line	LXFL 529	Homo sapiens	GI50	n.a.	56885.29	nM	PubChem BioAssay data set
NPT576	Cell line	DMS-114	Homo sapiens	GI50	n.a.	44360.86	nM	PubChem BioAssay data set
NPT397	Cell line	NCI-H460	Homo sapiens	GI50	n.a.	69342.58	nM	PubChem BioAssay data set
NPT308	Cell line	CAKI-1	Homo sapiens	GI50	n.a.	38018.94	nM	PubChem BioAssay data set
NPT398	Cell line	UACC-62	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT399	Cell line	SF-295	Homo sapiens	GI50	n.a.	83176.38	nM	PubChem BioAssay data set
NPT458	Cell line	IGROV-1	Homo sapiens	GI50	n.a.	92257.14	nM	PubChem BioAssay data set
NPT401	Cell line	786-0	Homo sapiens	GI50	n.a.	63095.73	nM	PubChem BioAssay data set
NPT577	Cell line	RXF 631	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT403	Cell line	UACC-257	Homo sapiens	GI50	n.a.	86099.38	nM	PubChem BioAssay data set
NPT578	Cell line	SNB-78	Homo sapiens	GI50	n.a.	58748.94	nM	PubChem BioAssay data set
NPT579	Cell line	DLD-1	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT404	Cell line	CCRF-CEM	Homo sapiens	GI50	n.a.	47752.93	nM	PubChem BioAssay data set
NPT139	Cell line	HT-29	Homo sapiens	GI50	n.a.	68548.82	nM	PubChem BioAssay data set
NPT405	Cell line	NCI-H226	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT170	Cell line	SK-MEL-28	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT406	Cell line	RXF 393	Homo sapiens	GI50	n.a.	100000.0	nM	PubChem BioAssay data set
NPT407	Cell line	COLO 205	Homo sapiens	GI50	n.a.	70469.31	nM	PubChem BioAssay data set
NPT732	Cell line	HOP-18	Homo sapiens	GI50	n.a.	52239.62	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 NPC271921 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	15642
0.1-0.2	31024
0.2-0.3	2786
0.3-0.4	313
0.4-0.5	47
0.5-0.6	19
0.6-0.7	15
0.7-0.8	0
0.8-0.85	2
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8919	High Similarity	NPC330426
0.8919	High Similarity	NPC127091
0.8919	High Similarity	NPC22101
0.8158	Intermediate Similarity	NPC321919
0.8108	Intermediate Similarity	NPC104537
0.7381	Intermediate Similarity	NPC473772
0.7297	Intermediate Similarity	NPC10316
0.7297	Intermediate Similarity	NPC200845
0.725	Intermediate Similarity	NPC475443
0.725	Intermediate Similarity	NPC473829
0.7073	Intermediate Similarity	NPC209327
0.6905	Remote Similarity	NPC273508
0.6829	Remote Similarity	NPC476654
0.6829	Remote Similarity	NPC476655
0.6829	Remote Similarity	NPC476656
0.65	Remote Similarity	NPC277597
0.6486	Remote Similarity	NPC488257
0.6486	Remote Similarity	NPC469937
0.6486	Remote Similarity	NPC94699
0.6486	Remote Similarity	NPC320588
0.6486	Remote Similarity	NPC53463
0.641	Remote Similarity	NPC28779
0.6316	Remote Similarity	NPC139545
0.6304	Remote Similarity	NPC473559
0.6304	Remote Similarity	NPC324981
0.6	Remote Similarity	NPC609455
0.5918	Remote Similarity	NPC474321
0.5789	Remote Similarity	NPC236649
0.5778	Remote Similarity	NPC54925
0.5652	Remote Similarity	NPC48218
0.5652	Remote Similarity	NPC141481
0.5652	Remote Similarity	NPC464342
0.5641	Remote Similarity	NPC128061
0.5636	Remote Similarity	NPC489083
0.55	Remote Similarity	NPC39633
0.5333	Remote Similarity	NPC110813
0.5323	Remote Similarity	NPC38295
0.5254	Remote Similarity	NPC21693
0.5238	Remote Similarity	NPC223677
0.5156	Remote Similarity	NPC470313
0.5156	Remote Similarity	NPC473500
0.5156	Remote Similarity	NPC611497
0.5122	Remote Similarity	NPC71761
0.5111	Remote Similarity	NPC81896
0.5082	Remote Similarity	NPC133377

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC271921 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6079
0.1-0.2	2911
0.2-0.3	139
0.3-0.4	16
0.4-0.5	1
0.5-0.6	2
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	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6316	Remote Similarity	NPD5343	Phase 4
0.6	Remote Similarity	NPD6096	Phase 4
0.5385	Remote Similarity	NPD6097	Approved
0.5106	Remote Similarity	NPD3728	Approved

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