Natural Product: NPC182421

Natural Product IDNPC182421
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 3',5,5',7-Tetrahydroxyflavanone
IUPAC Name (2S)-2-(3,5-dihydroxyphenyl)-5,7-dihydroxy-2,3-dihydrochromen-4-one
Synonyms 3',5,5',7-Tetrahydroxyflavanone
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1272251
PubChem CID 52945930
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 AYHOUUNTAVCXBN-ZDUSSCGKSA-N
Standard InCHI InChI=1S/C15H12O6/c16-8-1-7(2-9(17)3-8)13-6-12(20)15-11(19)4-10(18)5-14(15)21-13/h1-5,13,16-19H,6H2/t13-/m0/s1
SMILES c1c(cc(cc1O)O)[C@@H]1CC(=O)c2c(cc(cc2O1)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
NPO17675 Andira inermis Species Fabaceae Eukaryota n.a. leaf n.a. PMID[11025148]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. n.a. n.a. PMID[11473438]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota n.a. n.a. n.a. PMID[15787460]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota n.a. root n.a. PMID[15787460]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota n.a. n.a. n.a. PMID[16203143]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota n.a. n.a. n.a. PMID[16919944]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota root bark n.a. n.a. PMID[17608532]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota n.a. n.a. n.a. PMID[17950599]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota fruits n.a. n.a. PMID[19113968]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota Roots n.a. n.a. PMID[19191562]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota n.a. root n.a. PMID[19280148]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota n.a. n.a. n.a. PMID[19285413]
NPO17675 Andira inermis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO20289 Dracocephalum tanguticum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19499937]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota n.a. n.a. n.a. PMID[19660948]
NPO20289 Dracocephalum tanguticum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20932762]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota n.a. root n.a. PMID[21319773]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota heartwood n.a. n.a. PMID[23743282]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota Roots n.a. n.a. PMID[25322455]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota root barks purchased from the local herbal market, Chungbuk, Korea 2012-JUL PMID[26227773]
NPO40254 Opuntia humifusa Species Cactaceae Eukaryota Cladodes n.a. n.a. PMID[32118424]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. rhizome n.a. PMID[8281582]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9525107]
NPO17675 Andira inermis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20289 Dracocephalum tanguticum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40254 Opuntia humifusa Species Cactaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30804 Cudrania tricuspidata Species Moraceae 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]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17675 Andira inermis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30804 Cudrania tricuspidata Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17675 Andira inermis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18117 Dalbergia odorifera Species Fabaceae 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]
NPO30804 Cudrania tricuspidata Species Moraceae 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]
NPO20526 Menispermum dauricum Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21187 Leucanthemopsis pallida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26768 Lichtheimia blakesleeana Species Lichtheimiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20289 Dracocephalum tanguticum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17675 Andira inermis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20526 Menispermum dauricum Species Menispermaceae 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
NPT1120 Individual protein Pancreatic triacylglycerol lipase Sus scrofa IC50 = 81800.0 nM PMID[26227773]
NPT1120 Individual protein Pancreatic triacylglycerol lipase Sus scrofa Inhibition = 53.6 % PMID[26227773]

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 IC50 = 14000.0 nM PMID[27955927]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. EC50 = 161200000.0 nM PMID[20932762]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. EC50 = 16320.0 nM PMID[20932762]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 100000.0 nM PMID[23743282]
NPT1 Others Radical scavenging activity n.a. EC50 = 32150.0 nM PMID[20932762]

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 NPC182421 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
0.7609 Intermediate Similarity NPC32441
0.7609 Intermediate Similarity NPC243083
0.7609 Intermediate Similarity NPC13768
0.7609 Intermediate Similarity NPC287246
0.7609 Intermediate Similarity NPC79943
0.75 Intermediate Similarity NPC321011
0.75 Intermediate Similarity NPC294852
0.75 Intermediate Similarity NPC188679
0.7292 Intermediate Similarity NPC274784
0.7292 Intermediate Similarity NPC73028
0.7292 Intermediate Similarity NPC338131
0.7292 Intermediate Similarity NPC20709
0.72 Intermediate Similarity NPC302950
0.6875 Remote Similarity NPC295261
0.6875 Remote Similarity NPC296490
0.6875 Remote Similarity NPC12296
0.6604 Remote Similarity NPC236637
0.66 Remote Similarity NPC107586
0.6531 Remote Similarity NPC264083
0.6481 Remote Similarity NPC258630
0.6316 Remote Similarity NPC106976
0.625 Remote Similarity NPC477841
0.6207 Remote Similarity NPC174953
0.614 Remote Similarity NPC17170
0.614 Remote Similarity NPC109223
0.614 Remote Similarity NPC10937
0.6102 Remote Similarity NPC134783
0.6066 Remote Similarity NPC118256
0.6 Remote Similarity NPC470890
0.6 Remote Similarity NPC312973
0.5932 Remote Similarity NPC108456
0.5902 Remote Similarity NPC473990
0.5882 Remote Similarity NPC21835
0.5781 Remote Similarity NPC474038
0.5738 Remote Similarity NPC200761
0.5738 Remote Similarity NPC475790
0.5714 Remote Similarity NPC473272
0.5714 Remote Similarity NPC474021
0.5645 Remote Similarity NPC611447
0.5469 Remote Similarity NPC290133
0.5455 Remote Similarity NPC227579
0.5455 Remote Similarity NPC214166
0.5455 Remote Similarity NPC475784
0.541 Remote Similarity NPC85121
0.5373 Remote Similarity NPC74924
0.5373 Remote Similarity NPC111786
0.537 Remote Similarity NPC329203
0.537 Remote Similarity NPC324386
0.537 Remote Similarity NPC222342
0.5312 Remote Similarity NPC272502
0.5303 Remote Similarity NPC26195
0.5283 Remote Similarity NPC6407
0.5283 Remote Similarity NPC545184
0.5273 Remote Similarity NPC469764
0.5185 Remote Similarity NPC150648
0.5185 Remote Similarity NPC312391
0.5179 Remote Similarity NPC18727
0.5179 Remote Similarity NPC310135
0.5156 Remote Similarity NPC69531
0.5156 Remote Similarity NPC88964
0.5143 Remote Similarity NPC602605
0.5102 Remote Similarity NPC482958
0.5091 Remote Similarity NPC300668
0.5091 Remote Similarity NPC482119
0.5091 Remote Similarity NPC482120
0.5091 Remote Similarity NPC19721
0.5075 Remote Similarity NPC224851
0.5072 Remote Similarity NPC474023

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC182421 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
0.7609 Intermediate Similarity NPD1550 Phase 2
0.7609 Intermediate Similarity NPD1552 Clinical (unspecified phase)
0.72 Intermediate Similarity NPD1934 Phase 0

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