Natural Product: NPC306788

Natural Product IDNPC306788
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Lanceolatin B
IUPAC Name 2-phenylfuro[2,3-h]chromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL224157
PubChem CID 10978265
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001615] Flavones
          • [CHEMONTID:0001759] Furanoflavones

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 NQNOTBRHBRJKKH-UHFFFAOYSA-N
Standard InCHI InChI=1S/C17H10O3/c18-14-10-16(11-4-2-1-3-5-11)20-17-12(14)6-7-15-13(17)8-9-19-15/h1-10H
SMILES O=c1cc(oc2c1ccc1c2cco1)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
NPO21911 Tephrosia purpurea Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[10814365]
NPO30165 Pongamia pinnata Species Fabaceae Eukaryota stem bark Indonesia 1999-SEP PMID[14510596]
NPO30165 Pongamia pinnata Species Fabaceae Eukaryota n.a. stem n.a. PMID[14510596]
NPO30165 Pongamia pinnata Species Fabaceae Eukaryota dry stem n.a. n.a. PMID[25466192]
NPO19856 Millettia pulchra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25630222]
NPO21911 Tephrosia purpurea Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[26476665]
NPO30165 Pongamia pinnata Species Fabaceae Eukaryota Roots n.a. n.a. PMID[29482940]
NPO21911 Tephrosia purpurea Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9322358]
NPO30165 Pongamia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19856 Millettia pulchra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21911 Tephrosia purpurea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30165 Pongamia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21911 Tephrosia purpurea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21911 Tephrosia purpurea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21911 Tephrosia purpurea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21911 Tephrosia purpurea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19856 Millettia pulchra 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
NPT178 Individual protein Protein-tyrosine phosphatase 1B Homo sapiens Inhibition = 21.0 % DOI[10.1007/s00044-010-9338-x]
NPT1603 Individual protein Cytochrome P450 1A1 Homo sapiens Activity = 100.0 % PMID[30448188]
NPT1603 Individual protein Cytochrome P450 1A1 Homo sapiens EC50 = 14400.0 nM PMID[30448188]
NPT109 Individual protein Cytochrome P450 3A4 Homo sapiens IC50 > 20000.0 nM PMID[30448188]
NPT241 Individual protein Cytochrome P450 2E1 Homo sapiens IC50 > 20000.0 nM PMID[30448188]
NPT110 Individual protein Cytochrome P450 2D6 Homo sapiens IC50 > 20000.0 nM PMID[30448188]
NPT213 Individual protein Cytochrome P450 2C19 Homo sapiens IC50 > 20000.0 nM PMID[30448188]
NPT212 Individual protein Cytochrome P450 2C9 Homo sapiens IC50 > 20000.0 nM PMID[30448188]
NPT240 Individual protein Cytochrome P450 2A6 Homo sapiens IC50 > 20000.0 nM PMID[30448188]
NPT208 Individual protein Cytochrome P450 1A2 Homo sapiens IC50 = 187.0 nM PMID[30448188]
NPT1604 Individual protein Cytochrome P450 1B1 Homo sapiens IC50 = 390.0 nM PMID[30448188]
NPT1603 Individual protein Cytochrome P450 1A1 Homo sapiens IC50 = 20.0 nM PMID[30448188]
NPT1604 Individual protein Cytochrome P450 1B1 Homo sapiens IC50 = 290.0 nM PMID[30448188]
NPT1603 Individual protein Cytochrome P450 1A1 Homo sapiens IC50 = 76.0 nM PMID[30448188]
NPT365 Individual protein NAD(P)H dehydrogenase [quinone] 1 Mus musculus Ratio = 1.64 n.a. PMID[10560746]
NPT24960 Single protein Cytochrome P450 2C18 Homo sapiens IC50 > 20000.0 nM PMID[30448188]
NPT628 Individual protein Cytochrome P450 2C8 Homo sapiens IC50 > 20000.0 nM PMID[30448188]
NPT627 Individual protein Cytochrome P450 2B6 Homo sapiens IC50 > 20000.0 nM PMID[30448188]
NPT440 Individual protein Quinone oxidoreductase Mus musculus CD = 22.9 uM Open TG-GATES in vivo data: Hematology

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT34 Cell line BV-2 Mus musculus IC50 = 20590.0 nM PMID[25466192]
NPT83 Cell line MCF7 Homo sapiens Activity = 60.0 % PMID[30448188]
NPT83 Cell line MCF7 Homo sapiens Activity = 9.2 % PMID[30448188]
NPT83 Cell line MCF7 Homo sapiens Activity = 7.1 % PMID[30448188]
NPT83 Cell line MCF7 Homo sapiens Activity = 81.0 % PMID[30448188]
NPT83 Cell line MCF7 Homo sapiens EC50 = 700.0 nM PMID[30448188]
NPT115 Organism Mycobacterium tuberculosis H37Ra Mycobacterium tuberculosis H37Ra MIC = 50.0 ug.mL-1 Open TG-GATES in vivo data: Biochemistry
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 76300.0 nM PMID[9322358]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 100.0 % PMID[25630222]
NPT2 Others Unspecified n.a. Ratio > 3.3 n.a. DOI[10.6019/CHEMBL1201861]

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 NPC306788 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
0.7547 Intermediate Similarity NPC607647
0.7358 Intermediate Similarity NPC605336
0.717 Intermediate Similarity NPC38914
0.7143 Intermediate Similarity NPC130015
0.6852 Remote Similarity NPC38361
0.6545 Remote Similarity NPC41719
0.6364 Remote Similarity NPC135303
0.6333 Remote Similarity NPC167479
0.5833 Remote Similarity NPC472606
0.5833 Remote Similarity NPC233776
0.56 Remote Similarity NPC32298
0.5345 Remote Similarity NPC602791
0.5333 Remote Similarity NPC241820
0.5333 Remote Similarity NPC600870

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC306788 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