Natural Product: NPC258366

Natural Product IDNPC258366
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Calicoferol A
IUPAC Name (1R,3aS,4S,7aR)-4-[2-(5-hydroxy-2-methylphenyl)ethyl]-7a-methyl-1-[(E,2R)-6-methylhept-3-en-2-yl]-2,3,3a,4,6,7-hexahydro-1H-inden-5-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL518060
PubChem CID 9547698
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

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 MDPPOIXSNMVHOD-FBPKMIEBSA-N
Standard InCHI InChI=1S/C27H40O2/c1-18(2)7-6-8-20(4)24-13-14-25-23(26(29)15-16-27(24,25)5)12-10-21-17-22(28)11-9-19(21)3/h6,8-9,11,17-18,20,23-25,28H,7,10,12-16H2,1-5H3/b8-6+/t20-,23+,24-,25+,27-/m1/s1
SMILES CC(C)C/C=C/[C@@H](C)[C@H]1CC[C@H]2[C@H](CCc3cc(ccc3C)O)C(=O)CC[C@]12C

  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
NPO32924 gorgonian astrogorgia sp. Species n.a. n.a. n.a. Chinese n.a. PMID[21982797]

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
NPT1661 Individual protein ALK tyrosine kinase receptor Homo sapiens IC50 = 4160.0 nM PubChem BioAssay data set
NPT1660 Individual protein NUAK family SNF1-like kinase 1 Homo sapiens IC50 > 100000.0 nM PMID[15165136]
NPT1433 Individual protein Serine/threonine-protein kinase Aurora-B Homo sapiens IC50 > 100000.0 nM PMID[15270556]
NPT1659 Individual protein Tyrosine-protein kinase receptor UFO Homo sapiens IC50 = 14700.0 nM PMID[19319825]
NPT1436 Individual protein Focal adhesion kinase 1 Homo sapiens IC50 = 9920.0 nM PMID[19319825]
NPT1438 Individual protein Insulin-like growth factor I receptor Homo sapiens IC50 = 2420.0 nM PMID[23347584]
NPT1337 Individual protein Hepatocyte growth factor receptor Homo sapiens IC50 = 47600.0 nM PMID[21142112]
NPT1658 Individual protein Serine/threonine-protein kinase NEK2 Homo sapiens IC50 > 100000.0 nM PMID[18591275]
NPT1657 Individual protein Serine/threonine-protein kinase NEK6 Homo sapiens IC50 > 100000.0 nM PMID[19778089]
NPT1265 Individual protein Serine/threonine-protein kinase PIM1 Homo sapiens IC50 > 100000.0 nM PMID[15974616]
NPT1656 Individual protein Protein kinase N1 Homo sapiens IC50 > 100000.0 nM PMID[10075777]
NPT1478 Individual protein Vascular endothelial growth factor receptor 2 Homo sapiens IC50 = 4600.0 nM PMID[22931300]
NPT491 Individual protein Dual specificity mitogen-activated protein kinase kinase 1 Homo sapiens IC50 > 100000.0 nM PMID[20421396]
NPT831 Individual protein Serine/threonine-protein kinase PLK1 Homo sapiens IC50 > 100000.0 nM PMID[15921411]
NPT36 Individual protein Tyrosine-protein kinase SRC Homo sapiens IC50 = 2240.0 nM PMID[10840050]
NPT728 Individual protein Serine/threonine-protein kinase AKT Homo sapiens IC50 > 100000.0 nM PMID[15270571]

In vitro activity

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

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
- Artemia LD50 = 1.8 ppm PMID[21377877]

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 NPC258366 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
0.8448 Intermediate Similarity NPC473974
0.7541 Intermediate Similarity NPC79933
0.7143 Intermediate Similarity NPC31296
0.6765 Remote Similarity NPC611852
0.6719 Remote Similarity NPC154511
0.6719 Remote Similarity NPC608033
0.6377 Remote Similarity NPC269598
0.5775 Remote Similarity NPC611179
0.5634 Remote Similarity NPC611030
0.5522 Remote Similarity NPC474358
0.5522 Remote Similarity NPC474387
0.5522 Remote Similarity NPC601488

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC258366 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