NPASS Compound

Structure

NPC289764 OpenBabel06302215412D 30 29 0 0 0 0 0 0 0 0999 V2000 12.9904 20.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 21.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 20.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 19.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 19.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 18.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 17.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 16.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 16.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 14.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 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 0.0000 1.0000 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 2 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 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 21 22 1 0 0 0 0 22 23 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 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 M END $$$$

Physi-Chem Properties

Molecular Weight:	420.47
Volume:	524.8
LogP:	13.593
LogD:	5.121
LogS:	-7.998
# Rotatable Bonds:	27
TPSA:	0.0
# H-Bond Aceptor:	0
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	0

MedChem Properties

QED Drug-Likeness Score:	0.091
Synthetic Accessibility Score:	1.718
Fsp3:	0.933
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.313
MDCK Permeability:	3.0649373456981266e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.044
30% Bioavailability (F30%):	0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004
Plasma Protein Binding (PPB):	102.0426254272461%
Volume Distribution (VD):	5.271
Pgp-substrate:	0.5135000944137573%

ADMET: Metabolism

CYP1A2-inhibitor:	0.034
CYP1A2-substrate:	0.124
CYP2C19-inhibitor:	0.108
CYP2C19-substrate:	0.049
CYP2C9-inhibitor:	0.016
CYP2C9-substrate:	0.976
CYP2D6-inhibitor:	0.05
CYP2D6-substrate:	0.044
CYP3A4-inhibitor:	0.176
CYP3A4-substrate:	0.014

ADMET: Excretion

Clearance (CL):	4.165
Half-life (T1/2):	0.005

ADMET: Toxicity

hERG Blockers:	0.358
Human Hepatotoxicity (H-HT):	0.004
Drug-inuced Liver Injury (DILI):	0.177
AMES Toxicity:	0.014
Rat Oral Acute Toxicity:	0.011
Maximum Recommended Daily Dose:	0.068
Skin Sensitization:	0.986
Carcinogencity:	0.02
Eye Corrosion:	0.997
Eye Irritation:	0.931
Respiratory Toxicity:	0.123

Download Data

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

Natural Product: NPC289764

Natural Product ID:	NPC289764
*Common Name:**	WMZHDICSCDKPFS-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WMZHDICSCDKPFS-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C30H60/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h3H,1,4-30H2,2H3
SMILES:	C=CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	87639
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002837] Hydrocarbons [CHEMONTID:0004475] Unsaturated hydrocarbons [CHEMONTID:0004476] Unsaturated aliphatic hydrocarbons

*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
NPO8286	Porophyllum ruderale	Species	Asteraceae	Eukaryota	n.a.	Along the Valencian coast, Spain	2020-Jun&Jul	PMID[35161358]
NPO11719	Lamellomorpha strongylata	Species	Vulcanellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9644054]
NPO13613	Lophophora williamsii	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13613	Lophophora williamsii	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11719	Lamellomorpha strongylata	Species	Vulcanellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4236	Microscleroderma spirophora	Species	Scleritodermidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13613	Lophophora williamsii	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4964	Traversia baccharoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14610	Ophiopogon intermedius	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8286	Porophyllum ruderale	Species	Asteraceae	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 NPC289764 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	1486
0.1-0.2	28643
0.2-0.3	10089
0.3-0.4	1791
0.4-0.5	530
0.5-0.6	121
0.6-0.7	20
0.7-0.8	7
0.8-0.85	1
0.85-0.9	1
0.9-0.95	2
0.95-1	6

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 NPC289764 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1394
0.1-0.2	6748
0.2-0.3	873
0.3-0.4	103
0.4-0.5	28
0.5-0.6	4
0.6-0.7	0
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