NPASS Compound

Natural Product: NPC554056

Natural Product ID	NPC554056
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ADP-D-glycero-beta-D-manno-heptose
IUPAC Name	[[(2~{S},3~{S},4~{R},5~{S})-5-(6-aminopurin-9-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphoryl] [(2~{S},3~{R},4~{S},5~{S},6~{S})-6-[(1~{R})-1,2-dihydroxyethyl]-3,4,5-trihydroxy-tetrahydropyran-2-yl] hydrogen phosphate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 67 70 0 0 0 0 0 0 0 0999 V2000 10.9797 1.1895 1.2223 N 0 0 0 0 0 0 0 0 0 0 0 0 9.6187 1.3282 0.8820 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0494 2.5200 0.6153 N 0 0 0 0 0 0 0 0 0 0 0 0 7.7454 2.5849 0.2974 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9597 1.4985 0.2296 N 0 0 0 0 0 0 0 0 0 0 0 0 7.4952 0.3070 0.4882 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8217 0.2086 0.8151 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1494 -1.0831 1.0356 N 0 0 0 0 0 0 0 0 0 0 0 0 8.0117 -1.7781 0.8411 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0002 -0.9187 0.5054 N 0 0 0 0 0 0 0 0 0 0 0 0 5.6809 -1.3420 0.2391 C 0 0 1 0 0 0 0 0 0 0 0 0 4.7115 -0.7244 1.0612 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5735 -1.4104 0.6050 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3057 -0.7951 1.1417 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2237 -1.4953 0.6721 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2467 -0.9234 1.2098 P 0 0 2 0 0 5 0 0 0 0 0 0 -0.1663 -0.2751 2.5701 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3364 -2.2109 1.3401 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9174 0.2139 0.1475 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3633 0.8289 0.7213 P 0 0 2 0 0 5 0 0 0 0 0 0 -2.4943 2.3221 0.5153 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4843 0.5344 2.3954 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6404 0.0559 -0.0494 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5865 0.9161 -0.5568 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.7867 0.6590 0.1407 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2957 -0.5259 -0.3329 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.0769 -1.2872 0.7080 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.5756 -2.4802 0.1905 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.1957 -0.5113 1.3152 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7223 0.7025 1.8475 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.0443 -0.2926 -1.6007 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.3205 0.1993 -1.4411 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2664 0.7665 -2.3935 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.4090 0.5865 -3.7603 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7956 0.7199 -2.0523 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1910 1.7803 -2.7239 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6484 -1.3352 -0.9032 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8441 -0.3246 -1.4137 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1387 -1.0253 -1.1211 C 0 0 1 0 0 0 0 0 0 0 0 0 5.2011 0.3330 -1.4141 O 0 0 0 0 0 0 0 0 0 0 0 0 11.2674 0.7628 2.1178 H 0 0 0 0 0 0 0 0 0 0 0 0 11.7070 1.5209 0.5644 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3528 3.5919 0.0930 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9418 -2.8507 0.9429 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5285 -2.4369 0.4021 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7053 -2.4582 0.9437 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2068 0.2520 0.8053 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3285 -0.8077 2.2500 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2211 -2.8644 0.5986 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3131 1.3841 2.9041 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3481 1.9812 -0.3726 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4115 -1.1751 -0.5899 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3736 -1.5655 1.5291 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4622 -2.3702 -0.2325 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5370 -1.0963 2.2196 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.0786 -0.3881 0.6884 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3928 0.9978 2.5405 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0227 -1.2370 -2.1955 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2869 1.1695 -1.3939 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6207 1.7851 -2.1415 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5880 0.2750 -4.1892 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4054 -0.2574 -2.3897 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2339 1.8458 -2.5751 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4391 -2.3176 -1.3703 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5290 -0.5353 -2.3305 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5513 -1.6537 -1.9268 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4946 0.7814 -0.8818 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 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 16 15 1 6 16 17 2 0 16 18 1 0 16 19 1 0 20 19 1 6 20 21 2 0 20 22 1 0 20 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 27 29 1 0 29 30 1 0 26 31 1 0 31 32 1 0 31 33 1 0 33 34 1 0 33 35 1 0 35 36 1 0 13 37 1 0 37 38 1 0 37 39 1 0 39 40 1 0 7 2 1 0 39 11 1 0 10 6 1 0 35 24 1 0 1 41 1 0 1 42 1 0 4 43 1 0 9 44 1 0 11 45 1 1 13 46 1 6 14 47 1 0 14 48 1 0 18 49 1 0 22 50 1 0 24 51 1 6 26 52 1 6 27 53 1 1 28 54 1 0 29 55 1 0 29 56 1 0 30 57 1 0 31 58 1 6 32 59 1 0 33 60 1 1 34 61 1 0 35 62 1 6 36 63 1 0 37 64 1 6 38 65 1 0 39 66 1 6 40 67 1 0 M END

Standard InCHIKey	KMSFWBYFWSKGGR-XSLHVOBASA-N
Standard InCHI	InChI=1S/C17H27N5O16P2/c18-14-7-15(20-3-19-14)22(4-21-7)16-11(28)8(25)6(35-16)2-34-39(30,31)38-40(32,33)37-17-12(29)9(26)10(27)13(36-17)5(24)1-23/h3-6,8-13,16-17,23-29H,1-2H2,(H,30,31)(H,32,33)(H2,18,19,20)/t5-,6+,8-,9+,10+,11-,12-,13+,16+,17+/m1/s1
SMILES	NC1=NC=NC2=C1N=CN2[C@H]1O[C@@H](CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]2O[C@@H]([C@H](O)CO)[C@@H](O)[C@H](O)[C@H]2O)[C@@H](O)[C@H]1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	619.09	Volume:	493.098 ? Van der Waals volume.
Dense:	1.256	LogP:	-2.231 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-0.834 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-0.831 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	10.0	Rigid Bonds:	23.0
TPSA:	331.98 ? Topological Polar Surface Area.	H-Bond Acceptor:	21.0
H-Bond Donor:	11.0	Rings:	4.0
Heavy Atoms:	23.0

MedChem Properties

QED Drug-Likeness Score:	0.112	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.103	Fsp³:	0.706
MCE-18:	115.862 ? 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:	0
Colloidal aggregators:	0.056	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.005 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.022 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.387	Promiscuous compounds:	0.163

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.337	MDCK Permeability:	-5.286
Pgp-inhibitor:	0.0	Pgp-substrate:	0.0
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):	0.001
20% Bioavailability (F20%):	0.0	30% Bioavailability (F30%):	0.118
50% Bioavailability (F50%):	0.399

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.11
Plasma Protein Binding (PPB):	21.341%	Volume Distribution (VD):	-0.723
Fu:	68.817% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.15

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	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:	0.646
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):

1.069

Half-life (T1/2):

2.716

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.029
Human Hepatotoxicity (H-HT):	0.608	Drug-induced Liver Injury (DILI):	0.998
AMES Toxicity:	0.164	Rat Oral Acute Toxicity:	0.118
Maximum Recommended Daily Dose:	0.995	Skin Sensitization:	0.994
Carcinogencity:	0.349	Eye Corrosion:	0.0
Eye Irritation:	0.058	Respiratory Toxicity:	0.592
Drug-induced Neurotoxicity:	0.049	Ototoxicity:	0.895
Hematotoxicity:	0.899	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.016
A549 Cytotoxicity:	0.004	Hek293 Cytotoxicity:	0.075
BCF:	-0.103 ? 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:	2.237 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.811 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.61 ? 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]
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]
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]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[12369847]
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]
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]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15292242]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15610037]
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]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[170247]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17765195]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[179975]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19026742]
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]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21437340]
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]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[22855027]
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]
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]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24783849]
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]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[2543976]
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]
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]
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]
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]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[398096]
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]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[6102982]
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]
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]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8852895]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9470222]
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]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Molecular-level activity

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

In vitro activity

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

In vivo activity

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

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC554056 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	35651
0.1-0.2	13649
0.2-0.3	450
0.3-0.4	45
0.4-0.5	29
0.5-0.6	21
0.6-0.7	7
0.7-0.8	1
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
0.7662	Intermediate Similarity	NPC324198
0.7662	Intermediate Similarity	NPC326529
0.7662	Intermediate Similarity	NPC319100
0.7375	Intermediate Similarity	NPC174802
0.7284	Intermediate Similarity	NPC606410
0.7195	Intermediate Similarity	NPC323091
0.6914	Remote Similarity	NPC130586
0.6588	Remote Similarity	NPC316618
0.65	Remote Similarity	NPC185991
0.65	Remote Similarity	NPC321814
0.6076	Remote Similarity	NPC136349
0.6076	Remote Similarity	NPC219313
0.6061	Remote Similarity	NPC21461
0.5673	Remote Similarity	NPC90902
0.5647	Remote Similarity	NPC328479
0.5556	Remote Similarity	NPC161224
0.5556	Remote Similarity	NPC481375
0.5517	Remote Similarity	NPC302778
0.5517	Remote Similarity	NPC329404
0.5517	Remote Similarity	NPC212551
0.5506	Remote Similarity	NPC324484
0.5506	Remote Similarity	NPC321458
0.5443	Remote Similarity	NPC156461
0.5443	Remote Similarity	NPC107374
0.5443	Remote Similarity	NPC600382
0.5443	Remote Similarity	NPC612067
0.5319	Remote Similarity	NPC484196
0.5227	Remote Similarity	NPC164952
0.5213	Remote Similarity	NPC484199
0.519	Remote Similarity	NPC317821
0.5172	Remote Similarity	NPC158055
0.5091	Remote Similarity	NPC611055
0.5053	Remote Similarity	NPC155087
0.5053	Remote Similarity	NPC149843

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC554056 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6858
0.1-0.2	2153
0.2-0.3	69
0.3-0.4	46
0.4-0.5	15
0.5-0.6	6
0.6-0.7	2
0.7-0.8	1
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
0.7375	Intermediate Similarity	NPD339	Phase 2
0.65	Remote Similarity	NPD283	Phase 4
0.6076	Remote Similarity	NPD548	Clinical (unspecified phase)
0.5765	Remote Similarity	NPD4171	Clinical (unspecified phase)
0.5673	Remote Similarity	NPD4716	Approved
0.5632	Remote Similarity	NPD338	Approved
0.5443	Remote Similarity	NPD249	Phase 4
0.5443	Remote Similarity	NPD250	Phase 4
0.5172	Remote Similarity	NPD6840	Pre-clinical

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