NPASS Compound

Natural Product: NPC530485

Natural Product ID	NPC530485
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(2~{S},3~{R},4~{S},5~{R},6~{R})-2-[[(2~{S},3~{S},4~{S},5~{R},6~{R})-6-[(2~{S},3~{R},4~{R},5~{R})-3,4-dihydroxy-2,5-bis(hydroxymethyl)tetrahydrofuran-2-yl]oxy-3,4,5-trihydroxy-tetrahydropyran-2-yl]methoxy]-6-(hydroxymethyl)tetrahydropyran-3,4,5-triol
IUPAC Name	(2~{S},3~{R},4~{S},5~{R},6~{R})-2-[[(2~{S},3~{S},4~{S},5~{R},6~{R})-6-[(2~{S},3~{R},4~{R},5~{R})-3,4-dihydroxy-2,5-bis(hydroxymethyl)tetrahydrofuran-2-yl]oxy-3,4,5-trihydroxy-tetrahydropyran-2-yl]methoxy]-6-(hydroxymethyl)tetrahydropyran-3,4,5-triol
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 66 68 0 0 0 0 0 0 0 0999 V2000 -4.6456 1.1556 2.3599 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2385 -0.0107 1.9005 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6534 0.2247 0.4611 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5869 0.5334 -0.3470 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7396 -0.5224 -0.6083 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5994 -0.0162 -1.2121 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4835 -0.2770 -0.4229 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2126 0.2622 -1.0494 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8256 -0.0234 -0.2372 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9957 0.6282 -0.3795 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4937 0.9122 0.8885 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6862 0.2728 1.1668 C 0 0 2 0 0 0 0 0 0 0 0 0 4.0238 0.6414 2.6188 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9337 0.1528 3.3757 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7075 0.5900 0.3118 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6932 -0.3426 0.5263 C 0 0 2 0 0 0 0 0 0 0 0 0 6.7367 -0.3573 -0.5700 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3562 0.8695 -0.6712 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9104 -1.6446 0.4611 C 0 0 2 0 0 0 0 0 0 0 0 0 4.7442 -1.9609 -0.8817 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6019 -1.2237 1.1155 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5915 -1.7973 2.3954 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9442 1.8376 -1.2609 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0126 2.6929 -1.0910 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6909 2.5934 -0.8621 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6762 3.8301 -1.4565 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4466 1.7023 -1.3725 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6228 2.2100 -0.8618 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4002 -1.5962 -1.4409 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.9104 -1.6426 -2.7424 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8832 -1.3270 -1.4987 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.6018 -2.4656 -1.8865 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3705 -0.9823 -0.0939 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0885 -2.0776 0.7334 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7291 1.9080 1.7307 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6245 -0.9062 2.0282 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1650 -0.1639 2.4937 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3325 1.1064 0.4704 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4575 -1.0083 0.3581 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6687 0.1351 0.5780 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4351 -1.3899 -0.2953 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0839 -0.3171 -2.0099 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7389 -0.0785 -0.8514 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0234 1.7279 2.7417 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9057 0.1210 2.9860 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1060 0.1244 2.8367 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2379 -0.2245 1.4807 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4959 -1.1174 -0.3143 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2291 -0.6226 -1.5091 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1576 1.4870 0.0594 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4169 -2.4512 1.0260 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1924 -2.8082 -1.1297 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7811 -1.6110 0.4926 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4255 -2.2912 2.5960 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8936 1.4886 -2.3220 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7130 3.6089 -1.2642 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6566 2.6305 0.2517 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4000 4.4949 -0.7679 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4660 1.8570 -2.4722 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9807 2.9170 -1.4667 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2781 -2.6135 -0.9958 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1284 -2.2628 -2.8116 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0455 -0.4963 -2.1956 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9618 -3.1803 -2.0316 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4596 -0.8396 -0.0825 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6983 -2.0661 1.5062 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 1 0 10 11 1 0 12 11 1 6 12 13 1 0 13 14 1 0 12 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 16 19 1 0 19 20 1 0 19 21 1 0 21 22 1 0 10 23 1 0 23 24 1 0 23 25 1 0 25 26 1 0 25 27 1 0 27 28 1 0 5 29 1 0 29 30 1 0 29 31 1 0 31 32 1 0 31 33 1 0 33 34 1 0 33 3 1 0 27 8 1 0 21 12 1 0 1 35 1 0 2 36 1 0 2 37 1 0 3 38 1 1 5 39 1 1 7 40 1 0 7 41 1 0 8 42 1 6 10 43 1 6 13 44 1 0 13 45 1 0 14 46 1 0 16 47 1 1 17 48 1 0 17 49 1 0 18 50 1 0 19 51 1 1 20 52 1 0 21 53 1 6 22 54 1 0 23 55 1 6 24 56 1 0 25 57 1 1 26 58 1 0 27 59 1 6 28 60 1 0 29 61 1 1 30 62 1 0 31 63 1 6 32 64 1 0 33 65 1 6 34 66 1 0 M END

Standard InCHIKey	MUPFEKGTMRGPLJ-RMMQSMQOSA-N
Standard InCHI	InChI=1S/C18H32O16/c19-1-5-8(22)11(25)13(27)16(31-5)30-3-7-9(23)12(26)14(28)17(32-7)34-18(4-21)15(29)10(24)6(2-20)33-18/h5-17,19-29H,1-4H2/t5-,6-,7+,8+,9-,10+,11+,12+,13-,14-,15-,16+,17-,18+/m1/s1
SMILES	OC[C@H]1O[C@H](OC[C@@H]2O[C@H](O[C@]3(CO)O[C@H](CO)[C@H](O)[C@H]3O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@H]1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	504.17	Volume:	434.858 ? Van der Waals volume.
Dense:	1.159	LogP:	-3.123 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-2.09 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-0.302 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	17.0
TPSA:	268.68 ? Topological Polar Surface Area.	H-Bond Acceptor:	16.0
H-Bond Donor:	11.0	Rings:	3.0
Heavy Atoms:	16.0

MedChem Properties

QED Drug-Likeness Score:	0.146	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.983	Fsp³:	1.0
MCE-18:	69.444 ? 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:	0	PAINS Alert:	0
Colloidal aggregators:	0.33	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.311 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.004 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.529	Promiscuous compounds:	0.01

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-7.195	MDCK Permeability:	-4.958
Pgp-inhibitor:	0.0	Pgp-substrate:	0.998
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):	1.0
20% Bioavailability (F20%):	1.0	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.705
Plasma Protein Binding (PPB):	20.329%	Volume Distribution (VD):	-0.454
Fu:	93.507% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.217
OATP1B3 inhibitor:	0.228	BCRP inhibitor:	0.0
BSEP inhibitor:	0.0

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:	0.441
HLM stability:	0.012 ? 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):

1.031

Half-life (T1/2):

2.403

ADMET: Toxicity

hERG Blockers:	0.001	hERG Blockers (10um):	0.012
Human Hepatotoxicity (H-HT):	0.361	Drug-induced Liver Injury (DILI):	0.276
AMES Toxicity:	0.988	Rat Oral Acute Toxicity:	0.006
Maximum Recommended Daily Dose:	0.001	Skin Sensitization:	1.0
Carcinogencity:	0.124	Eye Corrosion:	0.0
Eye Irritation:	0.167	Respiratory Toxicity:	0.005
Drug-induced Neurotoxicity:	0.005	Ototoxicity:	0.991
Hematotoxicity:	0.807	Drug-induced Nephrotoxicity:	0.939
Genotoxicity:	0.037	RPMI-8226 Immunitoxicity:	0.24
A549 Cytotoxicity:	0.793	Hek293 Cytotoxicity:	0.238
BCF:	0.001 ? 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:	1.439 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.058 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	2.136 ? 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
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jarmap.2018.11.004]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0014-5793(03)00033-4]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1021/ac991142i]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1034/j.1399-3054.2003.00030.x]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1046/j.1365-3040.2001.00686.x]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1074/jbc.274.1.397]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1074/jbc.M302362200]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1074/jbc.M314195200]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1074/jbc.M411109200]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1104/pp.103.022368]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	leaf	n.a.	PMID[10952545]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10952545]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11005203]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12637544]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12805618]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14745019]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15280363]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15820655]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15834012]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	aerial parts	n.a.	n.a.	PMID[15844959]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	flowers	n.a.	n.a.	PMID[16180811]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1684022]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17611796]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18057039]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18235971]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18318836]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[18409045]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	leaf	n.a.	PMID[19521717]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[19926279]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	root	n.a.	PMID[2092947]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21193570]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21194489]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	berry	n.a.	n.a.	PMID[21216145]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21395888]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21800258]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	branch	n.a.	PMID[22014228]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22014228]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014228]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	Roots	n.a.	n.a.	PMID[22916954]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23265441]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23370715]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23950498]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	root	n.a.	PMID[24163311]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24285094]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	leaves	n.a.	n.a.	PMID[24290061]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2488968]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24968750]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25152999]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	root	n.a.	PMID[25457500]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	seed	n.a.	PMID[2610694]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	stems-leaves	n.a.	n.a.	PMID[26420067]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	root	n.a.	PMID[27363486]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27432888]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	stem	n.a.	PMID[27914541]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[28134521]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	Flower Buds	n.a.	n.a.	PMID[28345906]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32129622]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32415726]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37667613]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37917799]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38005226]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38067590]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39355945]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39588261]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7561894]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7908950]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8278506]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO55421	FOOD SAKE	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Flower	n.a.	n.a.	Database[FooDB]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Sprout Seedling	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	Stem Bark	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	root	n.a.	Database[MetaboLights]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5067	Taxus baccata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9138	Syzygium cumini	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19866	Arabidopsis thaliana	Species	Brassicaceae	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

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 NPC530485 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	34899
0.1-0.2	11417
0.2-0.3	2957
0.3-0.4	501
0.4-0.5	67
0.5-0.6	12
0.6-0.7	1
0.7-0.8	2
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC34877
0.7619	Intermediate Similarity	NPC130683
0.6522	Remote Similarity	NPC145112
0.5952	Remote Similarity	NPC323574
0.5769	Remote Similarity	NPC147292
0.569	Remote Similarity	NPC479398
0.569	Remote Similarity	NPC479397
0.549	Remote Similarity	NPC89145
0.549	Remote Similarity	NPC157514
0.549	Remote Similarity	NPC322314
0.549	Remote Similarity	NPC269166
0.5441	Remote Similarity	NPC219677
0.5357	Remote Similarity	NPC12040
0.5263	Remote Similarity	NPC285003
0.5111	Remote Similarity	NPC124963

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC530485 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8101
0.1-0.2	966
0.2-0.3	62
0.3-0.4	16
0.4-0.5	2
0.5-0.6	1
0.6-0.7	0
0.7-0.8	2
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
0.7619	Intermediate Similarity	NPD887	Approved
0.7619	Intermediate Similarity	NPD895	Phase 4
0.566	Remote Similarity	NPD3181	Phase 3

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