NPASS Compound

Natural Product: NPC234287

Natural Product ID	NPC234287
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Ginsenoside Rk2
IUPAC Name	(2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[[(3S,5R,8R,9R,10R,12R,13R,14R,17S)-12-hydroxy-4,4,8,10,14-pentamethyl-17-(6-methylhepta-1,5-dien-2-yl)-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]oxy]oxane-3,4,5-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3594354
PubChem CID	90472238
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 103107 0 0 0 0 0 0 0 0999 V2000 -9.3126 -0.6473 3.7164 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.9760 -0.9525 3.4680 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4188 -0.0785 2.3609 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.1087 -0.3409 2.0815 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8849 -0.4754 0.6794 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5410 -0.4682 0.4622 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0334 0.6977 -0.1097 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.2772 1.5153 0.9198 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8260 1.2820 1.0170 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2794 0.1653 0.1122 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8142 0.4008 -1.2465 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3040 0.4978 -1.3632 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8132 -0.7326 -2.0723 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6668 1.6620 -2.3124 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1940 -0.4936 -2.2898 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2956 -0.1233 -2.3347 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9384 -0.4206 -0.9712 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2273 0.4029 0.0180 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8949 0.5060 1.3708 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2390 1.1945 1.0723 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8446 1.7103 2.1717 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0291 0.2007 0.3053 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3751 0.0284 -1.0660 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4891 1.2159 -1.9482 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3191 -1.0327 -1.5469 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6657 -0.3359 -1.2546 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4093 0.5737 -0.0447 C 0 0 2 0 0 0 0 0 0 0 0 0 5.4279 0.3200 1.0419 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0972 -0.2979 2.1695 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8300 0.8353 0.9311 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5615 0.1760 -0.1694 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9749 0.6663 -0.2830 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0011 -0.1611 -0.1576 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7187 -1.5996 0.1007 C 0 0 0 0 0 0 0 0 0 0 0 0 11.4124 0.3245 -0.2699 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9221 -1.8898 -0.7973 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6148 -1.1112 0.7912 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6879 -1.6393 0.2722 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.1427 -1.1411 0.1845 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.3666 -0.0897 1.2152 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.5033 1.1908 0.6272 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.0318 -2.1942 0.2437 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4224 -2.2365 -0.9228 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.5306 0.2960 3.6025 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4398 -0.7693 4.4446 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8422 -2.0191 3.2556 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4474 0.9715 2.7823 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3132 0.4750 0.2621 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9535 1.3288 -0.3058 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8397 1.3467 1.8870 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4307 2.6169 0.7216 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6326 0.9238 2.0620 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2076 2.1927 0.8358 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4264 1.4348 -1.5239 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3793 -0.8846 -3.0838 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8995 -0.4902 -2.3026 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8267 -1.6337 -1.4633 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7801 2.5839 -1.6902 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8061 1.8467 -2.9834 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6119 1.4838 -2.8214 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3850 -1.5471 -2.1788 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5424 -0.2094 -3.3193 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2662 0.9844 -2.4139 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8217 -0.6204 -3.1487 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2777 1.4682 -0.3737 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3725 1.2507 1.9896 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0387 -0.4713 1.8528 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9757 2.0255 0.3800 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1089 2.6485 2.0047 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9861 -0.7961 0.7680 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2203 0.8583 -2.9873 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4887 1.6371 -2.0455 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8164 2.0627 -1.6491 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2212 -1.3099 -2.5877 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3541 -1.9142 -0.8400 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4216 -1.0974 -0.9896 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0154 0.2050 -2.1379 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5349 1.6380 -0.3008 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8493 -0.4611 2.9225 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1089 -0.6399 2.3405 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3304 0.7717 1.9184 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7482 1.9341 0.6592 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0948 0.5204 -1.1394 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5823 -0.9071 -0.1335 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1678 1.7074 -0.4694 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0812 -1.6752 0.9859 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1639 -1.9885 -0.7779 H 0 0 0 0 0 0 0 0 0 0 0 0 10.6680 -2.1723 0.2262 H 0 0 0 0 0 0 0 0 0 0 0 0 12.0766 -0.5550 -0.2372 H 0 0 0 0 0 0 0 0 0 0 0 0 11.6836 1.0404 0.5041 H 0 0 0 0 0 0 0 0 0 0 0 0 11.5757 0.8011 -1.2784 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0408 -2.3988 -0.9203 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5372 -2.3136 -1.6516 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4629 -2.1904 0.1240 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1536 -1.8574 0.2145 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2010 -0.9849 1.7532 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6387 -1.5120 1.2087 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7408 -2.4203 1.0956 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2228 -0.6661 -0.8257 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3995 -0.2772 1.6391 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1091 1.8349 1.2390 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.6775 -2.1619 -0.5091 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0256 -3.1411 -0.7625 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 11 12 1 0 12 13 1 0 12 14 1 0 11 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 20 22 1 0 22 23 1 0 23 24 1 6 23 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 2 0 28 30 1 0 30 31 1 0 31 32 1 0 32 33 2 3 33 34 1 0 33 35 1 0 17 36 1 1 10 37 1 1 5 38 1 0 38 39 1 0 39 40 1 0 40 41 1 0 39 42 1 0 38 43 1 0 40 3 1 0 12 7 1 0 23 17 1 0 18 10 1 0 27 22 1 0 1 44 1 0 2 45 1 0 2 46 1 0 3 47 1 1 5 48 1 6 7 49 1 6 8 50 1 0 8 51 1 0 9 52 1 0 9 53 1 0 11 54 1 6 13 55 1 0 13 56 1 0 13 57 1 0 14 58 1 0 14 59 1 0 14 60 1 0 15 61 1 0 15 62 1 0 16 63 1 0 16 64 1 0 18 65 1 6 19 66 1 0 19 67 1 0 20 68 1 6 21 69 1 0 22 70 1 1 24 71 1 0 24 72 1 0 24 73 1 0 25 74 1 0 25 75 1 0 26 76 1 0 26 77 1 0 27 78 1 6 29 79 1 0 29 80 1 0 30 81 1 0 30 82 1 0 31 83 1 0 31 84 1 0 32 85 1 0 34 86 1 0 34 87 1 0 34 88 1 0 35 89 1 0 35 90 1 0 35 91 1 0 36 92 1 0 36 93 1 0 36 94 1 0 37 95 1 0 37 96 1 0 37 97 1 0 38 98 1 1 39 99 1 6 40100 1 1 41101 1 0 42102 1 0 43103 1 0 M END

Standard InCHIKey	WMGBQZAELMGYNO-YMWSGFAJSA-N
Standard InCHI	InChI=1S/C36H60O7/c1-20(2)10-9-11-21(3)22-12-16-36(8)28(22)23(38)18-26-34(6)15-14-27(33(4,5)25(34)13-17-35(26,36)7)43-32-31(41)30(40)29(39)24(19-37)42-32/h10,22-32,37-41H,3,9,11-19H2,1-2,4-8H3/t22-,23-,24-,25+,26-,27+,28+,29-,30+,31-,32+,34+,35-,36-/m1/s1
SMILES	OC[C@H]1O[C@@H](O[C@H]2CC[C@]3([C@H](C2(C)C)CC[C@@]2([C@@H]3C[C@@H](O)[C@H]3[C@@]2(C)CC[C@@H]3C(=C)CCC=C(C)C)C)C)[C@@H]([C@H]([C@@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	604.43	Volume:	644.688 ? Van der Waals volume.
Dense:	0.938	LogP:	3.981 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.943 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.771 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	28.0
TPSA:	119.61 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	5.0	Rings:	5.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.202	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.289	Fsp³:	0.889
MCE-18:	105.882 ? 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:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.96	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:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.288	Promiscuous compounds:	0.286

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.752	MDCK Permeability:	-5.173
Pgp-inhibitor:	0.944	Pgp-substrate:	0.014
PAMPA:	0.166 ? 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):	0.007
20% Bioavailability (F20%):	0.124	30% Bioavailability (F30%):	0.717
50% Bioavailability (F50%):	0.951

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.058	MRP1:	0.839
Plasma Protein Binding (PPB):	90.081%	Volume Distribution (VD):	-0.359
Fu:	7.613% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.021
BSEP inhibitor:	0.562

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.48	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.01
CYP3A4-inhibitor:	0.002	CYP3A4-substrate:	0.887
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.836
HLM stability:	0.45 ? 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):

2.23

Half-life (T1/2):

1.632

ADMET: Toxicity

hERG Blockers:	0.042	hERG Blockers (10um):	0.099
Human Hepatotoxicity (H-HT):	0.6	Drug-induced Liver Injury (DILI):	0.446
AMES Toxicity:	0.737	Rat Oral Acute Toxicity:	0.049
Maximum Recommended Daily Dose:	0.105	Skin Sensitization:	1.0
Carcinogencity:	0.531	Eye Corrosion:	0.001
Eye Irritation:	0.216	Respiratory Toxicity:	0.484
Drug-induced Neurotoxicity:	0.027	Ototoxicity:	0.922
Hematotoxicity:	0.721	Drug-induced Nephrotoxicity:	0.889
Genotoxicity:	0.121	RPMI-8226 Immunitoxicity:	0.109
A549 Cytotoxicity:	0.668	Hek293 Cytotoxicity:	0.394
BCF:	2.132 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	4.106 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.208 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.758 ? 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]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Flower buds	n.a.	n.a.	PMID[12880307]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Stems	n.a.	n.a.	PMID[17663584]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Roots	n.a.	n.a.	PMID[18186611]
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]
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]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	Steamed Roots	n.a.	n.a.	PMID[26200131]
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]
NPO21891	Panax notoginseng	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]
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]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21891	Panax notoginseng	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[TCM_Taiwan]
NPO29141	Panax ginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21891	Panax notoginseng	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29141	Panax ginseng	Species	Araliaceae	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
Activity	1
IC50	5

Activity Type	# Activity
Cell line	5
Non-molecular	1

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
NPT681	Cell line	PC-12	Rattus norvegicus	Activity	=	8.9	%	PMID[26200131]
NPT116	Cell line	HL-60	Homo sapiens	IC50	>	10000.0	nM	PMID[26200131]
NPT81	Cell line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[26200131]
NPT83	Cell line	MCF7	Homo sapiens	IC50	>	10000.0	nM	PMID[26200131]
NPT660	Cell line	SW480	Homo sapiens	IC50	>	10000.0	nM	PMID[26200131]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	>	10000.0	nM	PMID[26200131]

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 NPC234287 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	19829
0.1-0.2	23795
0.2-0.3	4948
0.3-0.4	1073
0.4-0.5	166
0.5-0.6	30
0.6-0.7	8
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.863	High Similarity	NPC312553
0.7746	Intermediate Similarity	NPC280825
0.7746	Intermediate Similarity	NPC473198
0.7342	Intermediate Similarity	NPC16573
0.7297	Intermediate Similarity	NPC88000
0.7297	Intermediate Similarity	NPC4831
0.7297	Intermediate Similarity	NPC472023
0.7105	Intermediate Similarity	NPC31907
0.6795	Remote Similarity	NPC609286
0.675	Remote Similarity	NPC159036
0.6548	Remote Similarity	NPC69737
0.6386	Remote Similarity	NPC8039
0.6386	Remote Similarity	NPC120123
0.6329	Remote Similarity	NPC473200
0.6235	Remote Similarity	NPC208477
0.6118	Remote Similarity	NPC472987
0.5949	Remote Similarity	NPC607273
0.587	Remote Similarity	NPC208650
0.5833	Remote Similarity	NPC157659
0.5783	Remote Similarity	NPC470312
0.5761	Remote Similarity	NPC234160
0.5745	Remote Similarity	NPC220427
0.5714	Remote Similarity	NPC601606
0.5567	Remote Similarity	NPC14946
0.5567	Remote Similarity	NPC63368
0.5517	Remote Similarity	NPC472897
0.5517	Remote Similarity	NPC472896
0.5488	Remote Similarity	NPC66654
0.5476	Remote Similarity	NPC472989
0.5474	Remote Similarity	NPC472988
0.5474	Remote Similarity	NPC38217
0.5435	Remote Similarity	NPC194842
0.5412	Remote Similarity	NPC473844
0.5408	Remote Similarity	NPC159005
0.54	Remote Similarity	NPC135369
0.5393	Remote Similarity	NPC165033
0.5393	Remote Similarity	NPC273879
0.5275	Remote Similarity	NPC181467
0.5256	Remote Similarity	NPC477927
0.5227	Remote Similarity	NPC611039
0.5176	Remote Similarity	NPC7341
0.5161	Remote Similarity	NPC269627
0.5094	Remote Similarity	NPC488292
0.5094	Remote Similarity	NPC146868
0.5063	Remote Similarity	NPC90583
0.5048	Remote Similarity	NPC241381

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC234287 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7467
0.1-0.2	1595
0.2-0.3	75
0.3-0.4	13
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	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

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