Natural Product: NPC91492

Natural Product IDNPC91492
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.
 Dalbergin
IUPAC Name 6-hydroxy-7-methoxy-4-phenylchromen-2-one
Synonyms Dalbergin
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1829658
PubChem CID 442768
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0001614] Neoflavonoids
        • [CHEMONTID:0001389] Neoflavones

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 AZELSOYQOIUPBZ-UHFFFAOYSA-N
Standard InCHI InChI=1S/C16H12O4/c1-19-15-9-14-12(7-13(15)17)11(8-16(18)20-14)10-5-3-2-4-6-10/h2-9,17H,1H3
SMILES COc1cc2c(cc1O)c(cc(=O)o2)c1ccccc1

  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
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. seed n.a. DOI[10.1016/S0031-9422(98)00552-4]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[12932142]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18154272]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota Heartwood India n.a. PMID[21488654]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. heartwood n.a. PMID[21488654]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota heartwood n.a. n.a. PMID[21784631]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota leaves n.a. n.a. PMID[22212722]
NPO26331 Plumbago auriculata Species Plumbaginaceae Eukaryota n.a. flower n.a. PMID[22260638]
NPO20876 Arnica longifolia Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota heartwood n.a. n.a. PMID[23743282]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9525107]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22848 Kaempferia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3982 Dalbergia stevensonii 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]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7149 Dalbergia melanoxylon Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17889 Clerodendrum indicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23269 Spodoptera exigua Species Noctuidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20876 Arnica longifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26897 Dalbergia riparia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26331 Plumbago auriculata Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2732 Dalbergia cearensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22848 Kaempferia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26897 Dalbergia riparia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3982 Dalbergia stevensonii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23821 Rubus rigidus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26897 Dalbergia riparia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2732 Dalbergia cearensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7149 Dalbergia melanoxylon Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12433 Dalbergia cultrata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23821 Rubus rigidus Species Rosaceae 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]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3982 Dalbergia stevensonii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22848 Kaempferia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7149 Dalbergia melanoxylon Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30891 Dalbergia cultrate Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2732 Dalbergia cearensis 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]
NPO26897 Dalbergia riparia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22848 Kaempferia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22848 Kaempferia galanga Species Zingiberaceae 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]
NPO6173 Senegalia caesia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12433 Dalbergia cultrata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3982 Dalbergia stevensonii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23821 Rubus rigidus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26897 Dalbergia riparia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26331 Plumbago auriculata Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22848 Kaempferia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20888 Paraderris canarensis 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]
NPO1830 Dalbergia sissoo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7149 Dalbergia melanoxylon Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23269 Spodoptera exigua Species Noctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17889 Clerodendrum indicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20876 Arnica longifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29428 Dalbergia cochinchinensis 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
NPT81 Cell line A549 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[21784631]
NPT90 Cell line DU-145 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[21784631]
NPT91 Cell line KB Homo sapiens IC50 > 10.0 ug.mL-1 PMID[21784631]
NPT23156 Cell line Calvarial osteoblast n.a. Emax = 1.0 pM PMID[24803361]
NPT23156 Cell line Calvarial osteoblast n.a. EC50 = 1.015 nM PMID[24803361]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 10.0 ug.mL-1 PMID[21784631]

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 NPC91492 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
0.8367 Intermediate Similarity NPC256555
0.7843 Intermediate Similarity NPC7439
0.7843 Intermediate Similarity NPC34245
0.7115 Intermediate Similarity NPC110067
0.6667 Remote Similarity NPC234865
0.6275 Remote Similarity NPC38874
0.5636 Remote Similarity NPC603727
0.5283 Remote Similarity NPC139548
0.5091 Remote Similarity NPC168259
0.5091 Remote Similarity NPC608413

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC91492 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