Structure

Physi-Chem Properties

Molecular Weight:  140.06
Volume:  177.721
LogP:  4.201
LogD:  3.129
LogS:  -4.144
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.45
Synthetic Accessibility Score:  4.454
Fsp3:  0.091
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -3.981
MDCK Permeability:  0.00011597310367505997
Pgp-inhibitor:  0.002
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.071
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.055

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  102.27318572998047%
Volume Distribution (VD):  1.185
Pgp-substrate:  2.7075719833374023%

ADMET: Metabolism

CYP1A2-inhibitor:  0.986
CYP1A2-substrate:  0.172
CYP2C19-inhibitor:  0.947
CYP2C19-substrate:  0.761
CYP2C9-inhibitor:  0.921
CYP2C9-substrate:  0.9
CYP2D6-inhibitor:  0.873
CYP2D6-substrate:  0.499
CYP3A4-inhibitor:  0.882
CYP3A4-substrate:  0.318

ADMET: Excretion

Clearance (CL):  7.418
Half-life (T1/2):  0.245

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.596
Drug-inuced Liver Injury (DILI):  0.991
AMES Toxicity:  0.669
Rat Oral Acute Toxicity:  0.828
Maximum Recommended Daily Dose:  0.795
Skin Sensitization:  0.977
Carcinogencity:  0.624
Eye Corrosion:  0.982
Eye Irritation:  0.993
Respiratory Toxicity:  0.865

Download Data

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

  Natural Product: NPC277244

Natural Product ID:  NPC277244
Common Name*:   CJFONSDZKXEVTQ-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CJFONSDZKXEVTQ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H8/c1-3-5-7-9-11-10-8-6-4-2/h3-4,6H,1H2,2H3
SMILES:  C=CC#CC#CC#CC=CC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004475] Unsaturated hydrocarbons
        • [CHEMONTID:0001566] Enynes

*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
NPO23086 Carex aridula Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25331 Sorgum bicolor n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24227 Blumea malcolmii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25112 Senecio glastifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20956 Bosistoa brassii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24990 Philodendron radiatum Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24567 Trifolium alpestre 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 NPC277244 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC277244 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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