NPASS Compound

Structure

NPC110105 OpenBabel06302215322D 57 57 0 0 0 0 0 0 0 0999 V2000 17.3205 25.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 17.3205 24.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.4545 23.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.5885 24.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7224 23.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7224 22.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 22.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 21.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 20.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 19.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 19.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 18.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 17.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 16.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 16.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 14.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 16.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 19.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.5885 22.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.1865 23.5000 0.0000 C 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 2 57 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 56 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 55 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 54 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 18 19 2 0 0 0 0 18 53 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 52 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 51 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 50 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 34 49 1 0 0 0 0 35 36 1 0 0 0 0 36 37 1 0 0 0 0 37 44 1 0 0 0 0 37 38 2 0 0 0 0 38 39 1 0 0 0 0 38 40 1 0 0 0 0 40 41 2 0 0 0 0 40 42 1 0 0 0 0 42 43 2 0 0 0 0 42 48 1 0 0 0 0 43 44 1 0 0 0 0 43 46 1 0 0 0 0 44 45 2 0 0 0 0 46 47 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	779.62
Volume:	919.781
LogP:	12.869
LogD:	7.962
LogS:	-3.499
# Rotatable Bonds:	26
TPSA:	75.71
# H-Bond Aceptor:	4
# H-Bond Donor:	4
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.029
Synthetic Accessibility Score:	4.143
Fsp3:	0.509
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.198
MDCK Permeability:	1.0504610145289917e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.792
Human Intestinal Absorption (HIA):	0.961
20% Bioavailability (F20%):	0.509
30% Bioavailability (F30%):	0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.015
Plasma Protein Binding (PPB):	103.63764953613281%
Volume Distribution (VD):	1.169
Pgp-substrate:	0.28397974371910095%

ADMET: Metabolism

CYP1A2-inhibitor:	0.063
CYP1A2-substrate:	0.161
CYP2C19-inhibitor:	0.085
CYP2C19-substrate:	0.072
CYP2C9-inhibitor:	0.081
CYP2C9-substrate:	0.994
CYP2D6-inhibitor:	0.133
CYP2D6-substrate:	0.916
CYP3A4-inhibitor:	0.3
CYP3A4-substrate:	0.088

ADMET: Excretion

Clearance (CL):	1.993
Half-life (T1/2):	0.059

ADMET: Toxicity

hERG Blockers:	0.165
Human Hepatotoxicity (H-HT):	0.758
Drug-inuced Liver Injury (DILI):	0.0
AMES Toxicity:	0.001
Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.984
Skin Sensitization:	0.996
Carcinogencity:	0.002
Eye Corrosion:	0.003
Eye Irritation:	0.452
Respiratory Toxicity:	0.016

Download Data

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

Natural Product: NPC110105

Natural Product ID:	NPC110105
*Common Name:**	GCQAFBRARRTBAO-NSCWJZNLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GCQAFBRARRTBAO-NSCWJZNLSA-N
Standard InCHI:	InChI=1S/C53H81NO3/c1-39(2)21-13-22-40(3)23-14-24-41(4)25-15-26-42(5)27-16-28-43(6)29-17-30-44(7)31-18-32-45(8)33-19-34-46(9)35-20-36-47(10)37-38-49-48(11)51(55)50(54)53(57-12)52(49)56/h21,23,25,27,29,31,33,35,37H,13-20,22,24,26,28,30,32,34,36,38,54H2,1-12H3/b40-23+,41-25+,42-27+,43-29+,44-31+,45-33+,46-35+,47-37+
SMILES:	CC(=CCC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C/CC1=C(C)C(=O)C(=C(C1=O)OC)N)/C)/C)/C)/C)/C)/C)/C)/C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	25246233
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001534] Quinone and hydroquinone lipids [CHEMONTID:0002802] Prenylquinones [CHEMONTID:0001294] Polyprenylbenzoquinones

*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
NPO18391	Tephrosia tepicana	Species	Geometridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18628	Lecidea ferax	Species	Lecideaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19049	Commiphora confusa	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15991	Laingia pacifica	Species	Aphididae	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 NPC110105 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	63
0.1-0.2	2198
0.2-0.3	25333
0.3-0.4	12067
0.4-0.5	2762
0.5-0.6	229
0.6-0.7	35
0.7-0.8	7
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
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 NPC110105 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	75
0.1-0.2	1695
0.2-0.3	5963
0.3-0.4	1267
0.4-0.5	128
0.5-0.6	17
0.6-0.7	4
0.7-0.8	0
0.8-0.85	1
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