NPASS Compound

Structure

NPC212495 OpenBabel06302215162D 23 22 0 0 0 0 0 0 0 0999 V2000 10.3923 14.0000 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 8.6603 14.0000 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 7.7942 12.5000 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 6.9282 11.0000 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 6.0622 9.5000 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 5.1962 8.0000 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 4.3301 6.5000 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 3.4641 5.0000 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 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 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 3 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 2 0 0 0 0 21 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	320.27
Volume:	378.807
LogP:	7.055
LogD:	3.335
LogS:	-5.776
# Rotatable Bonds:	16
TPSA:	37.3
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	0
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.2
Synthetic Accessibility Score:	2.422
Fsp3:	0.762
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:	-5.056
MDCK Permeability:	1.8387656382401474e-05
Pgp-inhibitor:	0.008
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.024
20% Bioavailability (F20%):	0.874
30% Bioavailability (F30%):	0.953

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.125
Plasma Protein Binding (PPB):	98.82971954345703%
Volume Distribution (VD):	0.754
Pgp-substrate:	0.6155366897583008%

ADMET: Metabolism

CYP1A2-inhibitor:	0.334
CYP1A2-substrate:	0.178
CYP2C19-inhibitor:	0.599
CYP2C19-substrate:	0.072
CYP2C9-inhibitor:	0.248
CYP2C9-substrate:	0.994
CYP2D6-inhibitor:	0.033
CYP2D6-substrate:	0.144
CYP3A4-inhibitor:	0.364
CYP3A4-substrate:	0.018

ADMET: Excretion

Clearance (CL):	2.75
Half-life (T1/2):	0.523

ADMET: Toxicity

hERG Blockers:	0.04
Human Hepatotoxicity (H-HT):	0.05
Drug-inuced Liver Injury (DILI):	0.012
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.016
Maximum Recommended Daily Dose:	0.068
Skin Sensitization:	0.966
Carcinogencity:	0.133
Eye Corrosion:	0.974
Eye Irritation:	0.967
Respiratory Toxicity:	0.818

Download Data

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

Natural Product: NPC212495

Natural Product ID:	NPC212495
*Common Name:**	FBZHCWZWZBCJJE-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FBZHCWZWZBCJJE-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C21H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21(22)23/h2H,1,3-14,17-20H2,(H,22,23)
SMILES:	C=CCCCCCCCCCCCCC#CCCCCC(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44203444
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000262] Fatty acids and conjugates [CHEMONTID:0002949] Long-chain fatty acids

*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
NPO12611	Lonicera korolkovii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11520235]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[1254564]
NPO26587	Croton steenkampianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18855442]
NPO2035	Daphne aurantiaca	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20192236]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[26195800]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8626242]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26587	Croton steenkampianus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11827	Zerynthia polyxena	Species	Papilionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10807	Melanothamnus somalensis	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23622	Pseudomonas putida	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6430	Cercosporina kikuchii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO10967	Parmelia gigas	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12611	Lonicera korolkovii	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11305	Garcinia cantleyana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18675	Pteris aquilina	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3376	Eriostemon brucei	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2035	Daphne aurantiaca	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7106	Talaromyces helicus	Species	Trichocomaceae	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 NPC212495 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	169
0.1-0.2	6034
0.2-0.3	20510
0.3-0.4	10632
0.4-0.5	4302
0.5-0.6	746
0.6-0.7	209
0.7-0.8	55
0.8-0.85	28
0.85-0.9	11
0.9-0.95	0
0.95-1	1

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 NPC212495 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	189
0.1-0.2	4635
0.2-0.3	3104
0.3-0.4	956
0.4-0.5	192
0.5-0.6	50
0.6-0.7	13
0.7-0.8	5
0.8-0.85	5
0.85-0.9	1
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