Natural Product: NPC183959

Natural Product IDNPC183959
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 3',4',7-Trihydroxyflavaonone
IUPAC Name 2-(3,4-dihydroxyphenyl)-7-hydroxy-2,3-dihydrochromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3401430
PubChem CID 3496769
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0001632] Flavanones

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 MJBPUQUGJNAPAZ-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H12O5/c16-9-2-3-10-12(18)7-14(20-15(10)6-9)8-1-4-11(17)13(19)5-8/h1-6,14,16-17,19H,7H2
SMILES Oc1ccc2c(c1)OC(CC2=O)c1ccc(c(c1)O)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
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[11551759]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. whole plant n.a. PMID[21214467]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota heartwood n.a. n.a. PMID[23743282]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[26690274]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9525107]
NPO2340 Caulis spatholobi n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO277 Caulis millettiae n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22420 Lignum dalbergiae odoriferae rosewood n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2340 Caulis spatholobi n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO277 Caulis millettiae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22420 Lignum dalbergiae odoriferae rosewood n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO10587 Herba inulae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO2340 Caulis spatholobi n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18117 Dalbergia odorifera 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 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
NPT169 Cell line B16-F10 Mus musculus Activity = 136.83 % PMID[25748162]

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 NPC183959 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
1.0 High Similarity NPC1612
0.8182 Intermediate Similarity NPC329225
0.8182 Intermediate Similarity NPC147686
0.766 Intermediate Similarity NPC264083
0.7447 Intermediate Similarity NPC476480
0.7447 Intermediate Similarity NPC84585
0.6863 Remote Similarity NPC321011
0.6863 Remote Similarity NPC294852
0.6863 Remote Similarity NPC188679
0.6735 Remote Similarity NPC103991
0.6607 Remote Similarity NPC221432
0.6607 Remote Similarity NPC257097
0.66 Remote Similarity NPC472460
0.6545 Remote Similarity NPC143896
0.6346 Remote Similarity NPC610021
0.6207 Remote Similarity NPC68104
0.6167 Remote Similarity NPC23728
0.6038 Remote Similarity NPC246328
0.6038 Remote Similarity NPC27532
0.6 Remote Similarity NPC474033
0.5818 Remote Similarity NPC474208
0.5806 Remote Similarity NPC291508
0.5769 Remote Similarity NPC225153
0.5769 Remote Similarity NPC479876
0.5714 Remote Similarity NPC474034
0.566 Remote Similarity NPC32441
0.566 Remote Similarity NPC79943
0.5636 Remote Similarity NPC192083
0.5636 Remote Similarity NPC210084
0.5593 Remote Similarity NPC39329
0.5593 Remote Similarity NPC51032
0.5455 Remote Similarity NPC300668
0.5455 Remote Similarity NPC325028
0.5455 Remote Similarity NPC256346
0.5455 Remote Similarity NPC324386
0.5455 Remote Similarity NPC606550
0.5441 Remote Similarity NPC209040
0.5441 Remote Similarity NPC110303
0.5441 Remote Similarity NPC601247
0.5357 Remote Similarity NPC486095
0.5323 Remote Similarity NPC480158
0.5224 Remote Similarity NPC170475
0.5179 Remote Similarity NPC329203
0.5179 Remote Similarity NPC222342
0.5167 Remote Similarity NPC169591
0.5167 Remote Similarity NPC298223
0.5167 Remote Similarity NPC604412
0.5147 Remote Similarity NPC224851
0.5094 Remote Similarity NPC603336
0.5088 Remote Similarity NPC469764
0.5088 Remote Similarity NPC606248

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC183959 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
0.8182 Intermediate Similarity NPD1549 Phase 2
0.566 Remote Similarity NPD1552 Clinical (unspecified phase)
0.5636 Remote Similarity NPD2393 Clinical (unspecified phase)

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