NPASS Compound

Natural Product: NPC102253

Natural Product ID	NPC102253
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	20(R)-Protopanaxatriol
IUPAC Name	(3S,5R,6S,8R,9R,10R,12R,13R,14R,17S)-17-[(2R)-2-hydroxy-6-methylhept-5-en-2-yl]-4,4,8,10,14-pentamethyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthrene-3,6,12-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3634637
PubChem CID	9847853
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

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 86 89 0 0 0 0 0 0 0 0999 V2000 7.4492 3.2096 -0.7004 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7454 1.9038 -0.8703 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4897 1.7588 -0.4824 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7666 0.4534 -0.6454 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3617 0.0179 0.7469 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6248 -1.2675 0.8103 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3435 -1.4152 0.0997 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8839 -2.8570 0.3934 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4221 -2.7371 0.8138 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0333 -1.4723 0.1616 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2154 -0.5266 0.4363 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9885 0.6833 -0.3745 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6959 1.7985 0.1474 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3799 1.1759 -0.5876 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5040 0.2535 -0.2904 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1793 -0.7887 0.7427 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9158 -0.2592 2.1040 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3140 -1.7701 0.8204 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6489 -1.0784 1.0781 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.8795 -0.1376 -0.0857 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8301 0.9488 -0.0765 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9065 1.8644 1.0703 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0187 1.7778 -1.3554 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4005 2.3065 -1.4997 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4294 1.2413 -1.3739 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2839 0.3251 -0.2083 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8787 0.8644 1.0607 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1200 -0.9214 -0.5582 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7038 1.8133 -1.4090 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6089 -2.0896 1.0724 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0643 -1.7145 -1.3163 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5307 -1.6097 2.1644 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5809 -2.3113 0.1992 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4281 0.7229 -1.4796 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5981 3.4478 0.3766 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8116 4.0218 -1.1199 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3938 3.2201 -1.2676 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9929 2.6146 -0.0401 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8782 0.6468 -1.2413 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4522 -0.2956 -1.0663 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3628 -0.1913 1.2462 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9478 0.8364 1.3635 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4919 -1.3956 -1.0062 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0509 -3.5321 -0.4398 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3934 -3.2864 1.2758 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2755 -2.8163 1.8869 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0991 -3.5791 0.2700 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2736 -0.3348 1.5429 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4983 0.5130 -1.3709 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9110 2.4426 -0.5668 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4906 1.5102 -1.6665 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6216 2.1427 -0.0447 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6886 -0.3424 -1.2395 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3682 0.6779 2.1725 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8282 -0.1513 2.7301 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2903 -1.0198 2.6588 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4391 -2.3634 -0.0940 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1086 -2.4736 1.6463 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6989 -0.5876 2.0482 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6594 -0.7556 -1.0085 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4542 1.4351 1.9604 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9845 2.2844 1.4588 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5402 2.7597 0.7915 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2747 2.5920 -1.4086 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8269 1.0766 -2.1933 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6263 3.1948 -0.8739 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4717 2.6961 -2.5604 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3690 0.6041 -2.3045 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7631 1.9586 1.1817 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9967 0.7100 0.9870 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5506 0.2687 1.9104 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6732 -1.2960 0.3281 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9156 -0.6570 -1.3016 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4999 -1.6908 -1.0504 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9597 2.1716 -0.5187 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5189 -2.6408 1.8838 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1348 -0.8660 -1.9613 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7260 -2.4820 -1.5730 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0219 -2.2409 -1.5514 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9247 -2.4679 2.3821 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3401 -3.2656 0.7071 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6233 -2.0703 0.4180 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3652 -2.4546 -0.8765 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8723 0.3750 -2.3684 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4672 0.9797 -1.7839 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4605 -0.0867 -0.7413 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 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 11 12 1 0 12 13 1 0 12 14 1 0 14 15 1 0 15 16 1 0 16 17 1 1 16 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 1 21 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 26 28 1 0 25 29 1 0 19 30 1 0 10 31 1 6 6 32 1 1 6 33 1 0 2 34 1 0 11 7 1 0 21 15 1 0 16 10 1 0 26 20 1 0 1 35 1 0 1 36 1 0 1 37 1 0 3 38 1 0 4 39 1 0 4 40 1 0 5 41 1 0 5 42 1 0 7 43 1 6 8 44 1 0 8 45 1 0 9 46 1 0 9 47 1 0 11 48 1 1 12 49 1 6 13 50 1 0 14 51 1 0 14 52 1 0 15 53 1 6 17 54 1 0 17 55 1 0 17 56 1 0 18 57 1 0 18 58 1 0 19 59 1 1 20 60 1 6 22 61 1 0 22 62 1 0 22 63 1 0 23 64 1 0 23 65 1 0 24 66 1 0 24 67 1 0 25 68 1 6 27 69 1 0 27 70 1 0 27 71 1 0 28 72 1 0 28 73 1 0 28 74 1 0 29 75 1 0 30 76 1 0 31 77 1 0 31 78 1 0 31 79 1 0 32 80 1 0 33 81 1 0 33 82 1 0 33 83 1 0 34 84 1 0 34 85 1 0 34 86 1 0 M END

Standard InCHIKey	SHCBCKBYTHZQGZ-DLHMIPLTSA-N
Standard InCHI	InChI=1S/C30H52O4/c1-18(2)10-9-13-30(8,34)19-11-15-28(6)24(19)20(31)16-22-27(5)14-12-23(33)26(3,4)25(27)21(32)17-29(22,28)7/h10,19-25,31-34H,9,11-17H2,1-8H3/t19-,20+,21-,22+,23-,24-,25-,27+,28+,29+,30+/m0/s1
SMILES	CC(=CCC[C@]([C@H]1CC[C@@]2([C@@H]1[C@H](O)C[C@H]1[C@@]2(C)C[C@@H]([C@@H]2[C@]1(C)CC[C@@H](C2(C)C)O)O)C)(O)C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	476.39	Volume:	525.735 ? Van der Waals volume.
Dense:	0.906	LogP:	4.058 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.752 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.143 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	21.0
TPSA:	80.92 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	4.0	Rings:	4.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.406	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.052	Fsp³:	0.933
MCE-18:	90.517 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.699	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.003 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.381	Promiscuous compounds:	0.316

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.465	MDCK Permeability:	-5.077
Pgp-inhibitor:	0.06	Pgp-substrate:	0.618
PAMPA:	0.993 ? 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):	0.012
20% Bioavailability (F20%):	0.943	30% Bioavailability (F30%):	0.456
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.515	MRP1:	0.959
Plasma Protein Binding (PPB):	86.625%	Volume Distribution (VD):	-0.366
Fu:	10.784% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.994	BCRP inhibitor:	0.199
BSEP inhibitor:	0.678

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.714	CYP2C19-substrate:	0.005
CYP2C9-inhibitor:	0.006	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.314
CYP3A4-inhibitor:	0.609	CYP3A4-substrate:	0.067
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.207
HLM stability:	0.061 ? 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):

12.946

Half-life (T1/2):

1.393

ADMET: Toxicity

hERG Blockers:	0.063	hERG Blockers (10um):	0.2
Human Hepatotoxicity (H-HT):	0.46	Drug-induced Liver Injury (DILI):	0.049
AMES Toxicity:	0.305	Rat Oral Acute Toxicity:	0.202
Maximum Recommended Daily Dose:	0.403	Skin Sensitization:	0.991
Carcinogencity:	0.632	Eye Corrosion:	0.033
Eye Irritation:	0.636	Respiratory Toxicity:	0.774
Drug-induced Neurotoxicity:	0.073	Ototoxicity:	0.829
Hematotoxicity:	0.586	Drug-induced Nephrotoxicity:	0.903
Genotoxicity:	0.182	RPMI-8226 Immunitoxicity:	0.089
A549 Cytotoxicity:	0.589	Hek293 Cytotoxicity:	0.339
BCF:	0.907 ? 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:	3.354 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.99 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.201 ? 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
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[ 12877918]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jarmap.2018.11.004]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jarmap.2018.11.004]
NPO210	Uvaria calamistrata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075755]
NPO210	Uvaria calamistrata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11000019]
NPO11248	Tachigalia paniculata	n.a.	n.a.	n.a.	leaves	n.a.	n.a.	PMID[12444671]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	leaf	n.a.	PMID[18409045]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[19926279]
NPO10540	Passiflora incarnata	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2026709]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	root	n.a.	PMID[2092947]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	berry	n.a.	n.a.	PMID[21216145]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	leaves	n.a.	n.a.	PMID[24290061]
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]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	leaves and stems	n.a.	n.a.	PMID[25442304]
NPO41756	Saccharomyces cerevisiae D20RG1 [UGTPg29, UGTPg45]	Strain	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25769286]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	stems-leaves	n.a.	n.a.	PMID[26420067]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	stem	n.a.	PMID[27914541]
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]
NPO13166	Nicotiana undulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7998	Senecio paludaffinis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11488	Alstonia muelleriana	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10540	Passiflora incarnata	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5189	Glycine tomentella	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12684	Trigonella grandiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13568	Hypoxylon rubiginosum	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11642	Dacrydium cupressinum	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO210	Uvaria calamistrata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11248	Tachigalia paniculata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14354	Artemisia cina	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14255	Streptomyces flocculus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10540	Passiflora incarnata	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO10540	Passiflora incarnata	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19635	Coreopsis nodosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11248	Tachigalia paniculata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO14255	Streptomyces flocculus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO210	Uvaria calamistrata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18805	Tripolium pannonicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21854	Pterocladiella tenuis	Species	Gelidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12001	Saccharomyces pastori	Species	Saccharomycetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5189	Glycine tomentella	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7998	Senecio paludaffinis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22666	Haematococcus lacustris	Species	Haematococcaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13166	Nicotiana undulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO731	Panax schinseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11488	Alstonia muelleriana	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14354	Artemisia cina	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10540	Passiflora incarnata	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11642	Dacrydium cupressinum	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12684	Trigonella grandiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13568	Hypoxylon rubiginosum	Species	Xylariaceae	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	2

Activity Type	# Activity
Cell line	2
Individual protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT99	Individual protein	Peroxisome proliferator-activated receptor gamma	Homo sapiens	Ki	=	54200.0	nM	PMID[33992930]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT116	Cell line	HL-60	Homo sapiens	IC50	=	28680.0	nM	PMID[26420067]
NPT65	Cell line	HepG2	Homo sapiens	IC50	=	58290.0	nM	PMID[26420067]

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 NPC102253 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	26438
0.1-0.2	20654
0.2-0.3	2502
0.3-0.4	205
0.4-0.5	32
0.5-0.6	16
0.6-0.7	5
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC322313
1.0	High Similarity	NPC236237
0.7636	Intermediate Similarity	NPC80530
0.7636	Intermediate Similarity	NPC273410
0.6897	Remote Similarity	NPC244385
0.6667	Remote Similarity	NPC138621
0.6333	Remote Similarity	NPC207013
0.6333	Remote Similarity	NPC6978
0.6333	Remote Similarity	NPC167037
0.5738	Remote Similarity	NPC301707
0.5667	Remote Similarity	NPC66407
0.5645	Remote Similarity	NPC3403
0.56	Remote Similarity	NPC47566
0.56	Remote Similarity	NPC129372
0.5484	Remote Similarity	NPC285761
0.5484	Remote Similarity	NPC34930
0.5455	Remote Similarity	NPC474574
0.5309	Remote Similarity	NPC473199
0.5195	Remote Similarity	NPC160734
0.5152	Remote Similarity	NPC470071
0.5152	Remote Similarity	NPC157422
0.5152	Remote Similarity	NPC100586
0.5152	Remote Similarity	NPC109457
0.5122	Remote Similarity	NPC473020
0.5075	Remote Similarity	NPC187471

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC102253 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8119
0.1-0.2	1002
0.2-0.3	28
0.3-0.4	0
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD7525	Registered

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