NPASS Compound

Structure

NPC208965 OpenBabel06302215552D 23 25 0 0 0 0 0 0 0 0999 V2000 2.5097 -1.0703 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8116 -1.0652 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2097 -0.7117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2133 -0.0063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6090 0.3432 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6127 1.0486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0080 1.3977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0116 2.1035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2009 2.1098 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2046 1.4040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8128 1.0611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4854 1.4565 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8164 0.3557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4243 0.0125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4280 -0.6929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8237 -1.0424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2154 -0.6992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6111 -1.0486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9915 -0.3177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8001 -0.1594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0029 -0.7054 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6018 -1.0549 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 22 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 23 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 21 1 0 0 0 0 19 20 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	308.14
Volume:	334.086
LogP:	3.382
LogD:	3.231
LogS:	-4.335
# Rotatable Bonds:	1
TPSA:	35.53
# H-Bond Aceptor:	3
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.759
Synthetic Accessibility Score:	4.405
Fsp3:	0.25
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:	-4.962
MDCK Permeability:	1.4424206710828003e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.102
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.025

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.346
Plasma Protein Binding (PPB):	96.05030059814453%
Volume Distribution (VD):	0.494
Pgp-substrate:	0.6874300837516785%

ADMET: Metabolism

CYP1A2-inhibitor:	0.971
CYP1A2-substrate:	0.946
CYP2C19-inhibitor:	0.95
CYP2C19-substrate:	0.365
CYP2C9-inhibitor:	0.867
CYP2C9-substrate:	0.963
CYP2D6-inhibitor:	0.58
CYP2D6-substrate:	0.926
CYP3A4-inhibitor:	0.734
CYP3A4-substrate:	0.55

ADMET: Excretion

Clearance (CL):	8.927
Half-life (T1/2):	0.636

ADMET: Toxicity

hERG Blockers:	0.753
Human Hepatotoxicity (H-HT):	0.491
Drug-inuced Liver Injury (DILI):	0.645
AMES Toxicity:	0.88
Rat Oral Acute Toxicity:	0.106
Maximum Recommended Daily Dose:	0.869
Skin Sensitization:	0.9
Carcinogencity:	0.909
Eye Corrosion:	0.003
Eye Irritation:	0.147
Respiratory Toxicity:	0.83

Download Data

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

Natural Product: NPC208965

Natural Product ID:	NPC208965
*Common Name:**	QOGTVHQGZNQSJZ-DUXPYHPUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QOGTVHQGZNQSJZ-DUXPYHPUSA-N
Standard InCHI:	InChI=1S/C20H20O3/c1-22-19-13-9-16-4-2-3-5-17(21)10-6-15-7-11-18(12-8-15)23-20(19)14-16/h2,4,7-9,11-14H,3,5-6,10H2,1H3/b4-2+
SMILES:	COc1ccc2/C=C/CCC(=O)CCc3ccc(cc3)Oc1c2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10913866
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002650] Diarylheptanoids [CHEMONTID:0002652] Cyclic diarylheptanoids [CHEMONTID:0003523] Meta,para-diphenylether diarylheptanoids

*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
NPO28138	Burkea africana	Species	Fabaceae	Eukaryota	Bark	n.a.	n.a.	PMID[29394063]
NPO27547	Laminaria digitata	Species	Laminariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28438	Dipterocarpus hasseltii	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27723	Artemisia rothrockii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27767	Artemisia turcomanica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28188	Rindera echinata	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27898	Ormosia stipitata	Species	Limoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28046	Lotus hispidus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20701	Leonotis leonurus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28138	Burkea africana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28002	Lupinus kingii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28294	Astragalus tomentosus	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

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 NPC208965 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	341
0.1-0.2	1586
0.2-0.3	4448
0.3-0.4	13395
0.4-0.5	4635
0.5-0.6	4695
0.6-0.7	9905
0.7-0.8	3466
0.8-0.85	186
0.85-0.9	37
0.9-0.95	3
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 NPC208965 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	331
0.1-0.2	1024
0.2-0.3	1277
0.3-0.4	2677
0.4-0.5	1896
0.5-0.6	1101
0.6-0.7	683
0.7-0.8	156
0.8-0.85	3
0.85-0.9	2
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