Natural Product: NPC607242

Natural Product IDNPC607242
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 RYFAKJHWWSTDEJ-KWOXPHPHSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL513647
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey RYFAKJHWWSTDEJ-KWOXPHPHSA-N
Standard InCHI InChI=1S/C38H60O2/c1-3-37(39)35-33-31-29-27-25-23-21-19-17-15-13-11-9-7-5-6-8-10-12-14-16-18-20-22-24-26-28-30-32-34-36-38(40)4-2/h1-2,5-6,23-26,33-40H,7-22,27-32H2/b6-5-,25-23-,26-24-,35-33+,36-34+/t37-,38-/m1/s1
SMILES C#C[C@@H](O)/C=C/CCC/C=CCCCCCCCC/C=CCCCCCCCC/C=CCCC/C=C/[C@H](O)C#C

  Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO44987 Haliclona (Halichoclona) fulva Genus Chalinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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 Organism Name 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

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT139 Cell line HT-29 Homo sapiens ED50 = 1.0 ug ml-1 DOI[10.1021/np960436l]
NPT81 Cell line A549 Homo sapiens ED50 = 1.0 ug ml-1 DOI[10.1021/np960436l]
NPT168 Cell line P388 Mus musculus ED50 = 1.0 ug ml-1 DOI[10.1021/np960436l]
NPT170 Cell line SK-MEL-28 Homo sapiens ED50 = 1.0 ug ml-1 DOI[10.1021/np960436l]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC607242 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9545 High Similarity NPC170776
0.9545 High Similarity NPC9273
0.9545 High Similarity NPC165447
0.9545 High Similarity NPC471959
0.9545 High Similarity NPC199286
0.9545 High Similarity NPC489046
0.9545 High Similarity NPC76198
0.9545 High Similarity NPC610719
0.9091 High Similarity NPC125122
0.9091 High Similarity NPC471276
0.9091 High Similarity NPC471280
0.9091 High Similarity NPC471281
0.84 Intermediate Similarity NPC474642
0.84 Intermediate Similarity NPC473913
0.8 Intermediate Similarity NPC249670
0.7143 Intermediate Similarity NPC474644
0.7 Intermediate Similarity NPC161838
0.6774 Remote Similarity NPC471960
0.6774 Remote Similarity NPC477727
0.6452 Remote Similarity NPC471239
0.6452 Remote Similarity NPC474643
0.6452 Remote Similarity NPC473865
0.6452 Remote Similarity NPC55383
0.6176 Remote Similarity NPC197272
0.6 Remote Similarity NPC89824
0.6 Remote Similarity NPC475477
0.6 Remote Similarity NPC256656
0.6 Remote Similarity NPC294278
0.6 Remote Similarity NPC477723
0.5833 Remote Similarity NPC470966
0.5676 Remote Similarity NPC48058
0.5676 Remote Similarity NPC470963
0.5676 Remote Similarity NPC477661
0.5676 Remote Similarity NPC603233
0.5676 Remote Similarity NPC607245
0.55 Remote Similarity NPC473847
0.55 Remote Similarity NPC473721
0.55 Remote Similarity NPC473910
0.55 Remote Similarity NPC475384
0.5405 Remote Similarity NPC471278
0.5385 Remote Similarity NPC224148
0.5385 Remote Similarity NPC477726
0.5385 Remote Similarity NPC477725
0.5312 Remote Similarity NPC124183
0.5312 Remote Similarity NPC482802
0.525 Remote Similarity NPC473896
0.525 Remote Similarity NPC473735
0.525 Remote Similarity NPC146551
0.525 Remote Similarity NPC329608
0.5161 Remote Similarity NPC600749
0.5161 Remote Similarity NPC601019
0.5152 Remote Similarity NPC91226
0.5152 Remote Similarity NPC243546
0.5152 Remote Similarity NPC31194
0.5152 Remote Similarity NPC248884
0.5128 Remote Similarity NPC470970
0.5122 Remote Similarity NPC473725
0.5122 Remote Similarity NPC473532

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC607242 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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