Natural Product: NPC607644

Natural Product IDNPC607644
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XZQLSABETMKIGG-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL137586
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 XZQLSABETMKIGG-UHFFFAOYSA-N
Standard InCHI InChI=1S/C16H12O3/c1-18-12-7-8-15-13(9-12)14(17)10-16(19-15)11-5-3-2-4-6-11/h2-10H,1H3
SMILES COc1ccc2oc(-c3ccccc3)cc(=O)c2c1

  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
NPO19812 Pimelea simplex Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[21049973]
NPO49034 Pimelea decora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19812 Pimelea simplex Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19812 Pimelea simplex Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19812 Pimelea simplex Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19812 Pimelea simplex Species Thymelaeaceae 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 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
NPT249 Individual protein Glucocorticoid receptor Homo sapiens Ratio = 1400.0 n.a. PMID[19592245]
NPT249 Individual protein Glucocorticoid receptor Homo sapiens EC150 = 0.7 uM PMID[19592245]
NPT153 Individual protein Androgen Receptor Homo sapiens Ratio = 1400.0 n.a. PMID[19592245]
NPT249 Individual protein Glucocorticoid receptor Homo sapiens Ratio = 3.6 n.a. PMID[19592245]
NPT1422 Individual protein ATP-binding cassette sub-family G member 2 Homo sapiens IC50 = 10000.0 nM PMID[21354800]
NPT153 Individual protein Androgen Receptor Homo sapiens Ratio = 3.6 n.a. PMID[19592245]
NPT1422 Individual protein ATP-binding cassette sub-family G member 2 Homo sapiens IC50 = 3400.0 nM PMID[21354800]
NPT153 Individual protein Androgen Receptor Homo sapiens EC150 = 0.7 uM PMID[19592245]
NPT249 Individual protein Glucocorticoid receptor Homo sapiens Activity n.a. n.a. n.a. PMID[19592245]
NPT28926 Protein complex group GABA-A receptor; anion channel Rattus norvegicus Ki = 570.0 nM PMID[10543878]
NPT28926 Protein complex group GABA-A receptor; anion channel Rattus norvegicus GABA ratio = 1.51 n.a. PMID[10543878]
NPT588 Individual protein Tankyrase-1 Homo sapiens IC50 > 10000.0 nM PMID[24116873]
NPT668 Individual protein P-glycoprotein 1 Homo sapiens IC50 = 15000.0 nM PMID[21354800]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT113 Cell line RAW264.7 Mus musculus Activity = 115.93 % PMID[28408221]
NPT113 Cell line RAW264.7 Mus musculus Inhibition = 22.17 % PMID[28408221]
NPT83 Cell line MCF7 Homo sapiens Activity n.a. n.a. n.a. PMID[21354800]
NPT179 Cell line A2780 Homo sapiens Activity n.a. n.a. n.a. PMID[21354800]
NPT28438 Unchecked Unchecked n.a. logKi = -0.066 n.a. PMID[18158201]
NPT28438 Unchecked Unchecked n.a. Max_Activity n.a. 0.9 uM PubChem BioAssay data set
NPT28438 Unchecked Unchecked n.a. AbsAC35 = 8.22 uM PubChem BioAssay data set
NPT28438 Unchecked Unchecked n.a. AC50 = 6500.0 nM PubChem BioAssay data set
NPT28438 Unchecked Unchecked n.a. Inhibition n.a. n.a. % PMID[21354800]
NPT28438 Unchecked Unchecked n.a. AC50 = 5460.0 nM PubChem BioAssay data set
NPT28438 Unchecked Unchecked n.a. log(ratio) = -0.05 n.a. PMID[35576701]
NPT28438 Unchecked Unchecked n.a. IC50 = 13000.0 nM PMID[21354800]
NPT29337 Protein family Cytochrome P450 Homo sapiens Inhibition = 16.0 % PMID[35576701]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. AC50 > 52000.0 nM PubChem BioAssay data set
NPT29337 Protein family Cytochrome P450 Homo sapiens Inhibition < 15.0 % PMID[35576701]
NPT1175 Organism Spodoptera litura Spodoptera litura ED50 = 0.15 umol/cm2 PMID[12517100]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT29 Organism Rattus norvegicus Rattus norvegicus Protection = 29.0 % PMID[8523407]





 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
- Mus musculus LD50 = 1.799803894 mg/kg TOXRIC
- Mus musculus LD50 > 4000.0 mg/kg ToxVal

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 NPC607644 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
0.8085 Intermediate Similarity NPC599976
0.6939 Remote Similarity NPC284424
0.66 Remote Similarity NPC2771
0.66 Remote Similarity NPC93653
0.6531 Remote Similarity NPC41721
0.6226 Remote Similarity NPC608264
0.617 Remote Similarity NPC32298
0.5962 Remote Similarity NPC278556
0.5962 Remote Similarity NPC602026
0.5926 Remote Similarity NPC125887
0.5818 Remote Similarity NPC604085
0.5769 Remote Similarity NPC604293
0.566 Remote Similarity NPC106461
0.566 Remote Similarity NPC483772
0.5636 Remote Similarity NPC77955
0.5636 Remote Similarity NPC127447
0.549 Remote Similarity NPC602460
0.5455 Remote Similarity NPC293183
0.5455 Remote Similarity NPC601286
0.5455 Remote Similarity NPC608669
0.537 Remote Similarity NPC603094
0.5357 Remote Similarity NPC275722
0.5357 Remote Similarity NPC239128
0.5357 Remote Similarity NPC194281
0.5357 Remote Similarity NPC609062
0.5273 Remote Similarity NPC333230
0.5263 Remote Similarity NPC18260
0.5263 Remote Similarity NPC250266
0.5263 Remote Similarity NPC266597
0.5172 Remote Similarity NPC148423
0.5094 Remote Similarity NPC197425
0.5091 Remote Similarity NPC101294
0.5091 Remote Similarity NPC299582
0.5088 Remote Similarity NPC113089
0.5088 Remote Similarity NPC483774
0.5085 Remote Similarity NPC292460

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC607644 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