NPASS Compound

Structure

NPC250498 OpenBabel06302215232D 26 29 0 0 1 0 0 0 0 0999 V2000 1.3273 -2.2964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8418 -1.4560 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8415 -0.4855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6816 0.0005 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.6813 0.9714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9709 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8418 1.4564 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8421 2.4279 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6836 2.9134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5248 2.4274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3657 2.9129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2064 2.4269 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -4.2061 1.4555 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -3.3652 0.9699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5245 1.4559 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.5242 0.4525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6830 0.9704 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.6827 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8412 -0.4860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.0003 -1.0035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0751 0.9536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0475 2.9121 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.3480 3.8355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6969 2.1902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5479 -0.4990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 20 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 26 1 0 0 0 0 5 6 1 0 0 0 0 6 20 1 0 0 0 0 6 7 1 0 0 0 0 7 17 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 15 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 23 1 0 0 0 0 13 14 1 0 0 0 0 13 22 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	359.28
Volume:	395.443
LogP:	3.606
LogD:	4.027
LogS:	-4.171
# Rotatable Bonds:	1
TPSA:	43.7
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.701
Synthetic Accessibility Score:	4.929
Fsp3:	0.826
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.756
MDCK Permeability:	9.387221325596329e-06
Pgp-inhibitor:	0.001
Pgp-substrate:	0.007
Human Intestinal Absorption (HIA):	0.079
20% Bioavailability (F20%):	0.013
30% Bioavailability (F30%):	0.015

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.937
Plasma Protein Binding (PPB):	52.240997314453125%
Volume Distribution (VD):	1.703
Pgp-substrate:	50.76567459106445%

ADMET: Metabolism

CYP1A2-inhibitor:	0.021
CYP1A2-substrate:	0.287
CYP2C19-inhibitor:	0.021
CYP2C19-substrate:	0.976
CYP2C9-inhibitor:	0.035
CYP2C9-substrate:	0.188
CYP2D6-inhibitor:	0.796
CYP2D6-substrate:	0.899
CYP3A4-inhibitor:	0.067
CYP3A4-substrate:	0.83

ADMET: Excretion

Clearance (CL):	16.851
Half-life (T1/2):	0.074

ADMET: Toxicity

hERG Blockers:	0.022
Human Hepatotoxicity (H-HT):	0.266
Drug-inuced Liver Injury (DILI):	0.06
AMES Toxicity:	0.018
Rat Oral Acute Toxicity:	0.183
Maximum Recommended Daily Dose:	0.87
Skin Sensitization:	0.014
Carcinogencity:	0.737
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.971

Download Data

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

Natural Product: NPC250498

Natural Product ID:	NPC250498
*Common Name:**	LWZNDYKDUGVSBN-OMCISZLKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	LWZNDYKDUGVSBN-OMCISZLKSA-N
Standard InCHI:	InChI=1S/C23H37NO2/c1-6-16-20(25)12-18-15-8-7-14-11-19(24(4)5)21(26)13-23(14,3)17(15)9-10-22(16,18)2/h6-7,15,17-21,25-26H,8-13H2,1-5H3/b16-6+
SMILES:	C/C=C/1C(CC2C3CC=C4CC(C(CC4(C)C3CCC12C)O)N(C)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5318883
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003568] Androstane steroids

*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
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	root	n.a.	PMID[16335823]
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	root	n.a.	PMID[9397205]
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30941	Holarrhena antidysenterica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO765	Holarrhena pubescens	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO765	Holarrhena pubescens	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO30941	Holarrhena antidysenterica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO765	Holarrhena pubescens	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22686	Gentiana macrophylla	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO765	Holarrhena pubescens	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22686	Gentiana macrophylla	Species	Gentianaceae	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC250498 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	83
0.1-0.2	741
0.2-0.3	7735
0.3-0.4	17094
0.4-0.5	9368
0.5-0.6	6044
0.6-0.7	1400
0.7-0.8	222
0.8-0.85	7
0.85-0.9	2
0.9-0.95	1
0.95-1	0

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 NPC250498 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	88
0.1-0.2	449
0.2-0.3	3203
0.3-0.4	3703
0.4-0.5	1191
0.5-0.6	390
0.6-0.7	121
0.7-0.8	5
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

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