NPASS Compound

Natural Product: NPC318590

Natural Product ID	NPC318590
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Deoxyguanosine Diphosphate
IUPAC Name	[(2R,3S,5R)-5-(2-amino-6-oxo-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1232205
PubChem CID	439220
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues [CHEMONTID:0001506] Purine nucleotides [CHEMONTID:0002134] Purine deoxyribonucleotides [CHEMONTID:0002136] Purine deoxyribonucleoside diphosphates [CHEMONTID:0002139] Purine 2'-deoxyribonucleoside diphosphates

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 42 44 0 0 0 0 0 0 0 0999 V2000 -0.3890 -2.7745 1.1659 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1208 -1.4333 1.0194 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3569 -1.1168 0.8379 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4255 -0.5614 -0.4998 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1890 0.1233 -0.6296 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6930 -0.9054 -0.3031 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1058 -0.4036 -0.0872 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8905 -1.4945 0.2281 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4944 -1.1147 0.5006 P 0 0 0 0 0 0 0 0 0 0 0 0 -5.2887 -2.3999 0.5414 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1261 -0.1795 -0.7585 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3597 0.8312 -0.1999 P 0 0 0 0 0 0 0 0 0 0 0 0 -6.4998 0.7563 1.3023 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8365 0.3797 -0.8781 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0192 2.4130 -0.6864 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7242 -0.3276 1.9809 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5100 0.2828 -0.8786 N 0 0 0 0 0 0 0 0 0 0 0 0 2.3459 1.1603 -1.9085 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4903 1.8366 -2.0735 N 0 0 0 0 0 0 0 0 0 0 0 0 4.3843 1.4156 -1.1760 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7444 0.4265 -0.4232 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3874 -0.1985 0.5710 N 0 0 0 0 0 0 0 0 0 0 0 0 5.6588 0.1463 0.8274 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2882 -0.4518 1.7857 N 0 0 0 0 0 0 0 0 0 0 0 0 6.2908 1.0957 0.1135 N 0 0 0 0 0 0 0 0 0 0 0 0 5.6980 1.7507 -0.8882 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3133 2.7348 -1.6478 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2792 -2.8778 1.5378 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5910 -0.8492 1.8206 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6062 -0.3907 1.6383 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8510 -2.1089 0.9823 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3604 -1.3867 -1.2610 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6344 -1.6580 -1.1041 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4451 0.1754 -0.9505 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0584 0.2680 0.8188 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1654 -0.4852 -0.5563 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4757 2.9049 -0.0355 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2602 0.5533 1.9930 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4547 1.3131 -2.5147 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8769 -0.9258 1.1052 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2841 -0.1990 2.0053 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9410 3.6751 -1.6883 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 1 0 12 13 2 0 12 14 1 0 12 15 1 0 9 16 1 0 4 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 1 0 23 24 2 3 23 25 1 0 25 26 2 0 26 27 1 0 6 2 1 0 21 17 1 0 26 20 1 0 1 28 1 0 2 29 1 1 3 30 1 0 3 31 1 0 4 32 1 6 6 33 1 6 7 34 1 0 7 35 1 0 14 36 1 0 15 37 1 0 16 38 1 0 18 39 1 0 22 40 1 0 24 41 1 0 27 42 1 0 M END

Standard InCHIKey	CIKGWCTVFSRMJU-KVQBGUIXSA-N
Standard InCHI	InChI=1S/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
SMILES	O[C@H]1C[C@@H](O[C@@H]1COP(=O)(OP(=O)(O)O)O)n1cnc2c1[nH]c(=N)nc2O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	427.03	Volume:	327.842 ? Van der Waals volume.
Dense:	1.303	LogP:	-3.148 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-1.166 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.277 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	18.0
TPSA:	233.33 ? Topological Polar Surface Area.	H-Bond Acceptor:	15.0
H-Bond Donor:	7.0	Rings:	3.0
Heavy Atoms:	17.0

MedChem Properties

QED Drug-Likeness Score:	0.27	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.58	Fsp³:	0.5
MCE-18:	81.267 ? 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:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.077	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.028 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.026 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.272	Promiscuous compounds:	0.133

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.005	MDCK Permeability:	-5.103
Pgp-inhibitor:	0.0	Pgp-substrate:	0.0
PAMPA:	0.999 ? 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):	0.075
20% Bioavailability (F20%):	0.003	30% Bioavailability (F30%):	0.741
50% Bioavailability (F50%):	0.896

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.619
Plasma Protein Binding (PPB):	16.983%	Volume Distribution (VD):	-0.134
Fu:	74.317% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.996
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.014
BSEP inhibitor:	0.022

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.716	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
HLM stability:	0.001 ? 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):

1.848

Half-life (T1/2):

2.066

ADMET: Toxicity

hERG Blockers:	0.034	hERG Blockers (10um):	0.056
Human Hepatotoxicity (H-HT):	0.75	Drug-induced Liver Injury (DILI):	0.95
AMES Toxicity:	0.08	Rat Oral Acute Toxicity:	0.143
Maximum Recommended Daily Dose:	0.995	Skin Sensitization:	1.0
Carcinogencity:	0.967	Eye Corrosion:	0.0
Eye Irritation:	0.396	Respiratory Toxicity:	1.0
Drug-induced Neurotoxicity:	0.166	Ototoxicity:	0.057
Hematotoxicity:	0.018	Drug-induced Nephrotoxicity:	0.992
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.113
A549 Cytotoxicity:	0.009	Hek293 Cytotoxicity:	0.569
BCF:	0.04 ? 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:	2.367 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.854 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.455 ? 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
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	DOI[10.1016/0006-291X(79)91731-5]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	DOI[10.1093/emboj/18.8.2021]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1172/JCI16309]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1371/journal.pone.0115359]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[10557354]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[1091286]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[10977898]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[1100617]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[11034610]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[11419736]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[11530998]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[11745165]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[11750815]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[1175644]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[12369847]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12391014]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[12467448]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[12805358]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12812989]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12840027]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[12878451]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	ChEBI[131529]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[13610867]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[13831814]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[14973046]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15031653]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15084647]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[1521032]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15230696]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15292242]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15314235]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15610037]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[16112079]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[1644759]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[16630633]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[16770722]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[1687010]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[170247]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[17116739]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[17190852]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17765195]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[17875433]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[179975]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[18311922]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[18544912]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[18799520]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19026742]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[19425150]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19514719]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19561621]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[19961175]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[20506249]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[20601097]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	faeces	n.a.	PMID[20708442]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	urine	n.a.	PMID[20708442]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	bile	n.a.	PMID[20708442]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[20876113]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21437340]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[21798258]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21988831]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[22289691]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[2268561]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[22711758]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[22855027]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[23315938]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23537328]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23676670]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[23717534]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[23752203]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[23810710]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[23811455]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[23868375]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[23919613]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[24101735]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[241475]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24206068]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[24399466]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[24494566]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[24558969]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24783849]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[24816727]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24831709]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24939187]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24966042]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24967680]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[25114169]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[25181601]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[25293588]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[2543976]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[25644343]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25867074]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[26195826]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[26236990]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[26337258]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[26670289]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[26826371]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[27471436]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[29897754]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[30302998]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[3179836]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[318639]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[3283102]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[347637]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[398096]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[4696527]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[4877125]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[4879561]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[4908789]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[5332408]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[5432584]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[6102982]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[6121420]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[6284709]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[6338507]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[6780563]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[7042909]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[7601837]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[8600370]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8852895]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[8987136]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[9192820]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9470222]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	PMID[9800648]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	DOI[https://doi.org/10.1016/j.jbiosc.2016.12.008]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO20338	Mus musculus	Species	Muridae	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
Ki	1
IC50	1
Inhibition	1
Activity	1

Activity Type	# Activity
Individual protein	3
Others	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT3583	Individual protein	Fucosyltransferase 9	Homo sapiens	Ki	=	50300.0	nM	PMID[25438767]
NPT3583	Individual protein	Fucosyltransferase 9	Homo sapiens	IC50	=	49000.0	nM	PMID[25438767]
NPT3583	Individual protein	Fucosyltransferase 9	Homo sapiens	Inhibition	<=	80.0	%	PMID[25438767]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	n.a.	Activity	=	60.0	%	PMID[25438767]

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 NPC318590 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	28715
0.1-0.2	20984
0.2-0.3	112
0.3-0.4	22
0.4-0.5	14
0.5-0.6	1
0.6-0.7	7
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9275	High Similarity	NPC317746
0.8657	High Similarity	NPC186619
0.7432	Intermediate Similarity	NPC177169
0.6923	Remote Similarity	NPC64705
0.6625	Remote Similarity	NPC232408
0.6571	Remote Similarity	NPC262926
0.641	Remote Similarity	NPC14590
0.6316	Remote Similarity	NPC211820
0.6076	Remote Similarity	NPC89147
0.6076	Remote Similarity	NPC274384
0.5132	Remote Similarity	NPC61198

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC318590 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5640
0.1-0.2	3388
0.2-0.3	91
0.3-0.4	13
0.4-0.5	13
0.5-0.6	4
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
0.6742	Remote Similarity	NPD3086	Phase 3
0.5682	Remote Similarity	NPD4074	Clinical (unspecified phase)
0.5325	Remote Similarity	NPD194	Clinical (unspecified phase)
0.5132	Remote Similarity	NPD252	Clinical (unspecified phase)
0.51	Remote Similarity	NPD3085	Phase 1

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