NPASS Compound

Structure

NPC488519 OpenBabel06302215542D 35 39 0 0 1 0 0 0 0 0999 V2000 -0.6726 3.5263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.8537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8788 3.2177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8238 2.3780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8238 1.4268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.9512 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8238 1.4268 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8238 2.3780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6476 0.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4713 1.4268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2951 0.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2951 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1189 -0.4756 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1189 0.4756 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9427 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7665 -0.4756 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7665 -1.4268 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9427 -1.9024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4183 -2.7262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4671 -2.7262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1189 -1.4268 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2951 -1.9024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4713 -1.4268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4713 -0.4756 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8238 -1.4268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6476 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6476 -0.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8238 -0.4756 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8238 -0.4756 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5902 -1.9024 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6476 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6476 -0.9512 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4713 0.4756 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4713 1.4268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 8 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 29 1 0 0 0 0 6 7 1 0 0 0 0 6 32 1 1 0 0 0 7 8 1 1 0 0 0 7 9 1 0 0 0 0 9 26 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 12 11 1 1 0 0 0 12 13 1 0 0 0 0 12 24 1 0 0 0 0 13 21 1 0 0 0 0 13 14 1 1 0 0 0 13 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 31 1 1 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 18 21 1 0 0 0 0 21 22 1 1 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 1 0 0 0 24 26 1 0 0 0 0 26 27 1 6 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 6 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 34 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	486.37
Volume:	531.838
LogP:	5.885
LogD:	4.881
LogS:	-5.406
# Rotatable Bonds:	2
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.337
Synthetic Accessibility Score:	4.803
Fsp3:	0.903
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.138
MDCK Permeability:	3.542946433299221e-05
Pgp-inhibitor:	0.4
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.489
30% Bioavailability (F30%):	0.809

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.275
Plasma Protein Binding (PPB):	94.1834945678711%
Volume Distribution (VD):	1.134
Pgp-substrate:	4.271261215209961%

ADMET: Metabolism

CYP1A2-inhibitor:	0.011
CYP1A2-substrate:	0.283
CYP2C19-inhibitor:	0.074
CYP2C19-substrate:	0.926
CYP2C9-inhibitor:	0.253
CYP2C9-substrate:	0.585
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.612
CYP3A4-inhibitor:	0.749
CYP3A4-substrate:	0.337

ADMET: Excretion

Clearance (CL):	5.845
Half-life (T1/2):	0.134

ADMET: Toxicity

hERG Blockers:	0.474
Human Hepatotoxicity (H-HT):	0.234
Drug-inuced Liver Injury (DILI):	0.026
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.977
Maximum Recommended Daily Dose:	0.993
Skin Sensitization:	0.69
Carcinogencity:	0.035
Eye Corrosion:	0.025
Eye Irritation:	0.225
Respiratory Toxicity:	0.97

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC488519

Natural Product ID:	NPC488519
*Common Name:**	ZSRIUUWYDGCPHU-HPXKIVQKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZSRIUUWYDGCPHU-HPXKIVQKSA-N
Standard InCHI:	InChI=1S/C31H50O4/c1-26(2)15-16-31(25(34)35-8)20(17-26)19-9-10-22-28(5)13-12-23(32)27(3,4)21(28)11-14-29(22,6)30(19,7)18-24(31)33/h9,20-24,32-33H,10-18H2,1-8H3/t20-,21+,22-,23+,24-,28+,29-,30-,31-/m1/s1
SMILES:	CC1(C)CC[C@]2([C@H](C1)C1=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]1(C)C[C@H]2O)O)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44584184
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO27443	Gymnocladus chinensis	Species	Fabaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[7494144]
NPO7631	Gleditsia japonica	Species	Fabaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[7494144]
NPO7631	Gleditsia japonica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27443	Gymnocladus chinensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7631	Gleditsia japonica	Species	Fabaceae	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	NP ID	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
EC50	1
IC50	1

Activity Type	# Activity
Cell Line	1
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT759	Cell Line	H9	Homo sapiens	IC50	=	4900.0	nM	PMID[7494144]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	3100.0	nM	PMID[7494144]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC488519 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	214
0.1-0.2	1346
0.2-0.3	4740
0.3-0.4	12552
0.4-0.5	10400
0.5-0.6	5671
0.6-0.7	4722
0.7-0.8	2286
0.8-0.85	422
0.85-0.9	126
0.9-0.95	166
0.95-1	52

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC488519 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	185
0.1-0.2	1678
0.2-0.3	3770
0.3-0.4	2323
0.4-0.5	727
0.5-0.6	220
0.6-0.7	174
0.7-0.8	66
0.8-0.85	3
0.85-0.9	2
0.9-0.95	2
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

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