NPASS Compound

Natural Product: NPC88744

Natural Product ID	NPC88744
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-O-Beta-D-Glucopyranosyl 3Alpha,11Alpha-Dihydroxylup-20(29)-En-28-Oic Acid
IUPAC Name	(1R,3aS,5aR,5bR,7aR,9R,11aS,11bR,12R,13aR,13bR)-12-hydroxy-5a,5b,8,8,11a-pentamethyl-1-prop-1-en-2-yl-9-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,2,3,4,5,6,7,7a,9,10,11,11b,12,13,13a,13b-hexadecahydrocyclopenta[a]chrysene-3a-carboxylic acid
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1269326
PubChem CID	52949152
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

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 103108 0 0 0 0 0 0 0 0999 V2000 8.8159 1.8156 -2.7771 O 0 0 0 0 0 0 0 0 0 0 0 0 8.0788 0.7075 -2.4158 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2248 1.0138 -1.2247 C 0 0 1 0 0 0 0 0 0 0 0 0 6.4983 -0.1278 -0.8957 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7437 0.0889 0.2360 C 0 0 1 0 0 0 0 0 0 0 0 0 4.5888 -0.6047 0.3292 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4058 0.0638 0.3527 C 0 0 2 0 0 0 0 0 0 0 0 0 2.6156 -0.1686 1.5599 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1722 0.1080 1.5663 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5371 0.3607 0.1897 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2334 -0.5465 -0.7386 C 0 0 2 0 0 0 0 0 0 0 0 0 2.6952 -0.3119 -0.9561 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2182 -1.6848 -1.4358 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0930 0.6726 -1.9898 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5454 -0.8045 -2.0470 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8750 -1.2027 -1.9214 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6487 -0.3842 -0.8967 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9119 -0.0532 0.3327 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6901 0.8481 1.2166 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3869 0.6186 2.5939 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1524 0.7573 1.1361 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8352 -0.0305 0.0652 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8858 -1.1330 -0.4466 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6424 -2.0681 0.6890 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5033 -1.9247 -1.5554 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8565 -2.4222 -1.2071 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7513 -1.4320 -0.5852 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.0490 -0.6857 0.5629 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.2398 0.0529 1.0463 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.0750 -1.2533 1.3922 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8567 -2.1332 0.2165 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2259 0.8011 2.2782 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7160 0.3763 3.4418 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7616 2.2369 2.3202 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3435 -0.5060 -1.5421 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6246 -0.4540 -1.6210 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6237 0.3033 -2.3572 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1244 0.8031 -1.7075 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7083 1.8365 -0.0545 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6544 -0.0234 1.4286 C 0 0 1 0 0 0 0 0 0 0 0 0 7.9340 0.6691 1.1562 C 0 0 2 0 0 0 0 0 0 0 0 0 8.0088 1.5352 -0.0488 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7204 2.8795 0.1958 O 0 0 0 0 0 0 0 0 0 0 0 0 8.9877 -0.2505 1.1701 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9718 0.5629 2.5182 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6765 2.5200 -2.1143 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7523 -0.1655 -2.2104 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4834 0.4027 -3.3030 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4910 1.7927 -1.5130 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4507 1.1841 0.1924 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6468 1.1676 0.2912 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0601 0.4775 2.3806 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8636 -1.2129 1.9273 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6584 -0.8178 1.9454 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8764 0.9832 2.1814 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2000 -1.5617 -0.2160 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6450 -2.5032 -0.9778 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2131 -1.7199 -2.5449 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2773 -1.8060 -1.1327 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7193 1.5200 -1.5547 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8365 0.1969 -2.6783 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3249 1.0708 -2.6459 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5832 0.1184 -2.6612 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0625 -1.5721 -2.6598 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9032 -2.2802 -1.6537 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3473 -1.1374 -2.9244 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8370 -1.0186 0.9292 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3150 1.9298 1.1438 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0619 1.1301 3.1077 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6344 0.4492 2.0947 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5022 1.8269 0.9656 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1158 0.6337 -0.7782 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7698 -2.7481 0.5295 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6694 -1.6096 1.6969 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4949 -2.8135 0.7292 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8561 -2.8286 -1.7015 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5305 -1.4149 -2.5283 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3431 -2.7341 -2.1873 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8538 -3.3859 -0.6257 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8228 -1.4406 1.3832 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8044 0.5691 0.2343 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5898 -1.7590 2.2536 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0726 -0.9265 1.5878 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5389 -3.1536 0.4349 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7647 -2.1085 -0.4137 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6761 0.9937 4.3554 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1847 -0.5690 3.5671 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8317 2.3401 2.8848 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7136 2.5963 1.2925 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5826 2.8042 2.8268 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9792 0.8897 -3.1060 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2796 1.1427 -2.3865 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9205 0.5293 -2.4175 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4175 1.6769 -1.1539 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1593 2.2548 -0.6050 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5990 2.1064 -0.6171 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6617 2.3777 0.9401 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7987 -1.0938 1.6857 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1471 1.3415 2.0408 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0906 1.5298 -0.3810 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9084 3.0056 0.7494 H 0 0 0 0 0 0 0 0 0 0 0 0 9.6335 -0.0994 0.4342 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2408 0.1011 3.3362 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 19 21 1 0 21 22 1 0 22 23 1 0 23 24 1 1 23 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 29 32 1 0 32 33 2 0 32 34 1 0 27 35 1 6 35 36 2 0 35 37 1 0 17 38 1 6 10 39 1 6 5 40 1 0 40 41 1 0 41 42 1 0 42 43 1 0 41 44 1 0 40 45 1 0 42 3 1 0 12 7 1 0 23 17 1 0 31 27 1 0 18 10 1 0 28 22 1 0 1 46 1 0 2 47 1 0 2 48 1 0 3 49 1 6 5 50 1 6 7 51 1 6 8 52 1 0 8 53 1 0 9 54 1 0 9 55 1 0 11 56 1 1 13 57 1 0 13 58 1 0 13 59 1 0 14 60 1 0 14 61 1 0 14 62 1 0 15 63 1 0 15 64 1 0 16 65 1 0 16 66 1 0 18 67 1 1 19 68 1 6 20 69 1 0 21 70 1 0 21 71 1 0 22 72 1 6 24 73 1 0 24 74 1 0 24 75 1 0 25 76 1 0 25 77 1 0 26 78 1 0 26 79 1 0 28 80 1 1 29 81 1 6 30 82 1 0 30 83 1 0 31 84 1 0 31 85 1 0 33 86 1 0 33 87 1 0 34 88 1 0 34 89 1 0 34 90 1 0 37 91 1 0 38 92 1 0 38 93 1 0 38 94 1 0 39 95 1 0 39 96 1 0 39 97 1 0 40 98 1 1 41 99 1 1 42100 1 6 43101 1 0 44102 1 0 45103 1 0 M END

Standard InCHIKey	WRJZIYSNFOGUAQ-ZEJDLYSXSA-N
Standard InCHI	InChI=1S/C36H58O9/c1-18(2)19-8-13-36(31(42)43)15-14-34(6)20(25(19)36)16-21(38)29-33(5)11-10-24(32(3,4)23(33)9-12-35(29,34)7)45-30-28(41)27(40)26(39)22(17-37)44-30/h19-30,37-41H,1,8-17H2,2-7H3,(H,42,43)/t19-,20+,21+,22+,23-,24+,25+,26+,27-,28+,29+,30-,33-,34+,35+,36-/m0/s1
SMILES	OC[C@H]1O[C@@H](O[C@@H]2CC[C@]3([C@H](C2(C)C)CC[C@@]2([C@@H]3[C@H](O)C[C@H]3[C@@]2(C)CC[C@@]2([C@@H]3[C@@H](CC2)C(=C)C)C(=O)O)C)C)[C@@H]([C@H]([C@@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	634.41	Volume:	653.712 ? Van der Waals volume.
Dense:	0.97	LogP:	2.467 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.841 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.486 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	33.0
TPSA:	156.91 ? Topological Polar Surface Area.	H-Bond Acceptor:	9.0
H-Bond Donor:	6.0	Rings:	6.0
Heavy Atoms:	9.0

MedChem Properties

QED Drug-Likeness Score:	0.195	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.412	Fsp³:	0.917
MCE-18:	129.42 ? 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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.941	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.009 ? 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:	0.196	Promiscuous compounds:	0.204

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.678	MDCK Permeability:	-5.143
Pgp-inhibitor:	0.0	Pgp-substrate:	0.056
PAMPA:	0.983 ? 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%):	0.015	30% Bioavailability (F30%):	0.622
50% Bioavailability (F50%):	0.834

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.067	MRP1:	0.765
Plasma Protein Binding (PPB):	84.258%	Volume Distribution (VD):	-0.516
Fu:	11.959% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.997	BCRP inhibitor:	0.024
BSEP inhibitor:	0.005

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.027	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.235	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
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):

2.24

Half-life (T1/2):

2.364

ADMET: Toxicity

hERG Blockers:	0.016	hERG Blockers (10um):	0.02
Human Hepatotoxicity (H-HT):	0.676	Drug-induced Liver Injury (DILI):	0.906
AMES Toxicity:	0.554	Rat Oral Acute Toxicity:	0.019
Maximum Recommended Daily Dose:	0.032	Skin Sensitization:	0.998
Carcinogencity:	0.639	Eye Corrosion:	0.0
Eye Irritation:	0.084	Respiratory Toxicity:	0.122
Drug-induced Neurotoxicity:	0.002	Ototoxicity:	0.98
Hematotoxicity:	0.478	Drug-induced Nephrotoxicity:	0.898
Genotoxicity:	0.293	RPMI-8226 Immunitoxicity:	0.028
A549 Cytotoxicity:	0.075	Hek293 Cytotoxicity:	0.109
BCF:	0.801 ? 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:	3.383 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.856 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.117 ? 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
NPO29834	Acanthopanax koreanum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[20621475]
NPO29834	Acanthopanax koreanum	n.a.	n.a.	n.a.	steamed leaves	n.a.	n.a.	PMID[20932756]
NPO29834	Acanthopanax koreanum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29834	Acanthopanax koreanum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]

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
Inhibition	1

Activity Type	# Activity
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
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Inhibition	<	50.0	%	PMID[20932756]

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 NPC88744 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	20796
0.1-0.2	23587
0.2-0.3	4401
0.3-0.4	889
0.4-0.5	153
0.5-0.6	23
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	0

Similarity Score	Similarity Level	Natural Product ID
0.6556	Remote Similarity	NPC51947
0.6458	Remote Similarity	NPC204392
0.6364	Remote Similarity	NPC2783
0.6282	Remote Similarity	NPC269360
0.6263	Remote Similarity	NPC275668
0.5957	Remote Similarity	NPC488208
0.5934	Remote Similarity	NPC224414
0.5926	Remote Similarity	NPC169933
0.5859	Remote Similarity	NPC240734
0.5686	Remote Similarity	NPC91838
0.5612	Remote Similarity	NPC488205
0.5604	Remote Similarity	NPC606107
0.5556	Remote Similarity	NPC57954
0.5366	Remote Similarity	NPC4309
0.5361	Remote Similarity	NPC473481
0.5326	Remote Similarity	NPC274507
0.5244	Remote Similarity	NPC271974
0.5244	Remote Similarity	NPC247312
0.5238	Remote Similarity	NPC160506
0.5196	Remote Similarity	NPC488207
0.5165	Remote Similarity	NPC473844
0.5158	Remote Similarity	NPC31839
0.5149	Remote Similarity	NPC108748
0.514	Remote Similarity	NPC488206
0.5106	Remote Similarity	NPC57362
0.5059	Remote Similarity	NPC482135
0.5056	Remote Similarity	NPC253586
0.5052	Remote Similarity	NPC471967

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC88744 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6284
0.1-0.2	2761
0.2-0.3	94
0.3-0.4	8
0.4-0.5	0
0.5-0.6	2
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
0.5238	Remote Similarity	NPD8035	Phase 2
0.5155	Remote Similarity	NPD8034	Phase 2

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