Natural Product: NPC609532

Natural Product IDNPC609532
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YKPXIWHBRBFRQM-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL11475
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 YKPXIWHBRBFRQM-UHFFFAOYSA-N
Standard InCHI InChI=1S/C11H8O4/c1-5-4-8(14)9-6(12)2-3-7(13)10(9)11(5)15/h2-4,12-13H,1H3
SMILES CC1=CC(=O)c2c(O)ccc(O)c2C1=O

  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
NPO1448 Diospyros lycioides Species Ebenaceae Eukaryota n.a. n.a. n.a. PMID[9644074]
NPO1448 Diospyros lycioides Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10145 Diospyros heterotricha Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10145 Diospyros heterotricha Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1448 Diospyros lycioides Species Ebenaceae 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
NPT105 Individual protein Muscleblind-like protein 1 Homo sapiens Potency n.a. 28183.8 nM PubChem BioAssay data set
NPT1416 Individual protein Neuropeptide S receptor Homo sapiens Potency = 5011.9 nM PubChem BioAssay data set
NPT1038 Individual protein Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 31622.8 nM PubChem BioAssay data set
NPT3 Individual protein Thioredoxin glutathione reductase Schistosoma mansoni Potency = 631.0 nM PubChem BioAssay data set
NPT282 Individual protein MAP kinase ERK2 Homo sapiens Potency = 39810.7 nM PubChem BioAssay data set
NPT537 Individual protein Ras-related protein Rab-9A Homo sapiens Potency = 1122.0 nM PubChem BioAssay data set
NPT58 Individual protein Bloom syndrome protein Homo sapiens Potency = 17782.8 nM PubChem BioAssay data set
NPT55 Individual protein Putative fructose-1,6-bisphosphate aldolase Giardia intestinalis Potency = 8891.4 nM PubChem BioAssay data set
NPT484 Individual protein Luciferin 4-monooxygenase Photinus pyralis Potency n.a. 23934.1 nM PubChem BioAssay data set
NPT7 Individual protein Thioredoxin reductase 1, cytoplasmic Rattus norvegicus IC50 = 700.0 nM PMID[28987605]
NPT7 Individual protein Thioredoxin reductase 1, cytoplasmic Rattus norvegicus Inhibition n.a. n.a. % PMID[28987605]
NPT94 Individual protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 31622.8 nM PubChem BioAssay data set
NPT4035 Individual protein Female germline-specific tumor suppressor gld-1 Caenorhabditis elegans IC50 = 5581.0 nM PubChem BioAssay data set
NPT538 Individual protein Niemann-Pick C1 protein Homo sapiens Potency = 1584.9 nM PubChem BioAssay data set
NPT48 Individual protein Lysine-specific demethylase 4D-like Homo sapiens Potency = 25118.9 nM PubChem BioAssay data set
NPT6255 Individual protein Thioredoxin reductase 1 Homo sapiens Inhibition n.a. n.a. % PMID[28987605]
NPT6255 Individual protein Thioredoxin reductase 1 Homo sapiens IC50 = 2400.0 nM PMID[28987605]
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 17782.8 nM PubChem BioAssay data set
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens Potency = 11220.2 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 31622.8 nM PubChem BioAssay data set
NPT29280 Single protein Genome polyprotein Hepatitis C virus IC50 > 49751.0 nM PubChem BioAssay data set
NPT3725 Individual protein Eukaryotic translation initiation factor 4E Mus musculus IC50 n.a. 10270.0 nM PubChem BioAssay data set
NPT28586 Single protein Glutathione reductase Rattus norvegicus Inhibition n.a. n.a. % PMID[28987605]
NPT59 Individual protein DNA polymerase beta Homo sapiens Potency = 1778.3 nM PubChem BioAssay data set
NPT63 Individual protein Bromodomain adjacent to zinc finger domain protein 2B Homo sapiens Potency n.a. 3548.1 nM PubChem BioAssay data set
NPT51 Individual protein Microtubule-associated protein tau Homo sapiens Potency = 1000.0 nM PubChem BioAssay data set
NPT46 Individual protein Thyroid hormone receptor beta-1 Homo sapiens Potency = 22387.2 nM PubChem BioAssay data set
NPT4033 Individual protein Protein Rev Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)(HIV-1) IC50 > 75414.0 nM PubChem BioAssay data set
NPT49 Individual protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 1995.3 nM PubChem BioAssay data set
NPT864 Individual protein Lethal(3)malignant brain tumor-like protein 1 Homo sapiens Potency = 794.3 nM PubChem BioAssay data set
NPT47 Individual protein ATP-dependent DNA helicase Q1 Homo sapiens Potency = 3548.1 nM PubChem BioAssay data set
NPT45 Individual protein Ubiquitin carboxyl-terminal hydrolase 2 Homo sapiens Potency = 22387.2 nM PubChem BioAssay data set
NPT62 Individual protein 6-phospho-1-fructokinase Trypanosoma brucei Potency n.a. 30131.3 nM PubChem BioAssay data set
NPT53 Individual protein 4'-phosphopantetheinyl transferase ffp Bacillus subtilis Potency = 25118.9 nM PubChem BioAssay data set
NPT443 Individual protein Histone acetyltransferase GCN5 Homo sapiens Potency n.a. 12589.3 nM PubChem BioAssay data set
NPT56 Individual protein Beta-lactamase AmpC Escherichia coli K-12 Potency = 56234.1 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT393 Cell line HCT-116 Homo sapiens IC50 = 1190.0 nM PMID[17949858]
NPT116 Cell line HL-60 Homo sapiens Activity n.a. n.a. n.a. PMID[28987605]
NPT65 Cell line HepG2 Homo sapiens Activity n.a. n.a. n.a. PMID[28987605]
NPT165 Cell line HeLa Homo sapiens Activity n.a. n.a. n.a. PMID[28987605]
NPT116 Cell line HL-60 Homo sapiens Activity = 0.0 % PMID[28987605]
NPT116 Cell line HL-60 Homo sapiens IC50 = 860.0 nM PMID[28987605]
NPT81 Cell line A549 Homo sapiens Activity n.a. n.a. n.a. PMID[28987605]
NPT2615 Cell line HEK-293T Homo sapiens Activity n.a. n.a. n.a. PMID[28987605]
NPT116 Cell line HL-60 Homo sapiens Activity = 56.0 % PMID[28987605]
NPT116 Cell line HL-60 Homo sapiens IC50 = 640.0 nM PMID[28987605]
NPT65 Cell line HepG2 Homo sapiens IC50 = 2340.0 nM PMID[17949858]
NPT116 Cell line HL-60 Homo sapiens Activity = 42.0 % PMID[28987605]
NPT116 Cell line HL-60 Homo sapiens IC50 = 720.0 nM PMID[28987605]
NPT116 Cell line HL-60 Homo sapiens Activity = 10.0 % PMID[28987605]
NPT116 Cell line HL-60 Homo sapiens Activity = 23.0 % PMID[28987605]
NPT116 Cell line HL-60 Homo sapiens Activity = 27.0 % PMID[28987605]
NPT116 Cell line HL-60 Homo sapiens Activity > 43.0 % PMID[28987605]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 827.5 nM PubChem BioAssay data set
NPT28438 Unchecked Unchecked n.a. IC50 = 8020.0 nM PubChem BioAssay data set
NPT28438 Unchecked Unchecked n.a. IC50 = 5640.0 nM PubChem BioAssay data set
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 1471.6 nM PubChem BioAssay data set
NPT28438 Unchecked Unchecked n.a. CC50 = 12896.0 nM PubChem BioAssay data set
NPT21742 Cell line L02 Homo sapiens Activity n.a. n.a. n.a. PMID[28987605]
NPT29533 Protein-protein interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 7943.3 nM PubChem BioAssay data set
NPT29533 Protein-protein interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 31622.8 nM PubChem BioAssay data set

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT29 Organism Rattus norvegicus Rattus norvegicus T/C = 23.0 % PMID[14980639]
NPT29 Organism Rattus norvegicus Rattus norvegicus Survivors = 4.0 ug ml-1 PMID[14980639]





 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 NPC609532 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
0.6667 Remote Similarity NPC285829
0.6486 Remote Similarity NPC244699
0.6486 Remote Similarity NPC206778
0.6 Remote Similarity NPC246693
0.6 Remote Similarity NPC242358
0.6 Remote Similarity NPC306765
0.6 Remote Similarity NPC110609
0.5806 Remote Similarity NPC232178
0.5789 Remote Similarity NPC55949
0.5789 Remote Similarity NPC117609
0.5556 Remote Similarity NPC1991
0.5526 Remote Similarity NPC486398
0.525 Remote Similarity NPC58685
0.5238 Remote Similarity NPC481949
0.5217 Remote Similarity NPC216312
0.5217 Remote Similarity NPC299405
0.5106 Remote Similarity NPC256463

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC609532 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