NPASS Compound

Structure

NPC281639 OpenBabel06302215212D 23 22 0 0 0 0 0 0 0 0999 V2000 16.4545 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.4545 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.5885 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.7224 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 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 2.0000 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 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 O 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 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 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 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 1 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 20 1 0 0 0 0 20 21 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:	324.3
Volume:	384.08
LogP:	7.075
LogD:	4.556
LogS:	-5.871
# Rotatable Bonds:	18
TPSA:	26.3
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.209
Synthetic Accessibility Score:	2.351
Fsp3:	0.857
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.738
MDCK Permeability:	1.4516578630718868e-05
Pgp-inhibitor:	0.019
Pgp-substrate:	0.003
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.912
30% Bioavailability (F30%):	0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.321
Plasma Protein Binding (PPB):	97.31429290771484%
Volume Distribution (VD):	1.072
Pgp-substrate:	1.633390188217163%

ADMET: Metabolism

CYP1A2-inhibitor:	0.258
CYP1A2-substrate:	0.198
CYP2C19-inhibitor:	0.351
CYP2C19-substrate:	0.056
CYP2C9-inhibitor:	0.238
CYP2C9-substrate:	0.912
CYP2D6-inhibitor:	0.024
CYP2D6-substrate:	0.127
CYP3A4-inhibitor:	0.369
CYP3A4-substrate:	0.048

ADMET: Excretion

Clearance (CL):	5.514
Half-life (T1/2):	0.274

ADMET: Toxicity

hERG Blockers:	0.132
Human Hepatotoxicity (H-HT):	0.025
Drug-inuced Liver Injury (DILI):	0.038
AMES Toxicity:	0.019
Rat Oral Acute Toxicity:	0.018
Maximum Recommended Daily Dose:	0.028
Skin Sensitization:	0.936
Carcinogencity:	0.066
Eye Corrosion:	0.916
Eye Irritation:	0.951
Respiratory Toxicity:	0.778

Download Data

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

Natural Product: NPC281639

Natural Product ID:	NPC281639
*Common Name:**	UTSWKGVXNYKHFW-ISLYRVAYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UTSWKGVXNYKHFW-ISLYRVAYSA-N
Standard InCHI:	InChI=1S/C21H40O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-21(22)19-20-23-2/h17-18H,3-16,19-20H2,1-2H3/b18-17+
SMILES:	CCCCCCCCCCCCCCC/C=C/C(=O)CCOC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	15458653
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0001831] Carbonyl compounds [CHEMONTID:0003131] Alpha,beta-unsaturated carbonyl compounds [CHEMONTID:0003672] Alpha,beta-unsaturated ketones [CHEMONTID:0001363] Enones

*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
NPO24496	Gymnopetalum integrifolium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22683	Pteris bella	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24576	Genista lydia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23300	Trichilia heudelotii	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23426	Andromeda polifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13008	Methanobrevibacter arboriphilus	Species	Methanobacteriaceae	Archaea	n.a.	n.a.	n.a.	Database[UNPD]
NPO25120	Vincetoxicum forrestii	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3711	Acalypha australis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24496	Gymnopetalum integrifolium	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24139	Calamus strictus	Species	Sparidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22683	Pteris bella	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24014	Scapania bolanderi	Species	Scapaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24184	Argyrochosma pilifera	Species	Pteridaceae	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 NPC281639 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	139
0.1-0.2	4945
0.2-0.3	20041
0.3-0.4	11231
0.4-0.5	4669
0.5-0.6	1359
0.6-0.7	285
0.7-0.8	28
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

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 NPC281639 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	138
0.1-0.2	4127
0.2-0.3	3949
0.3-0.4	705
0.4-0.5	176
0.5-0.6	48
0.6-0.7	7
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

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