Natural Product: NPC310340

Natural Product IDNPC310340
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Lichexanthone
IUPAC Name 1-hydroxy-3,6-dimethoxy-8-methylxanthen-9-one
Synonyms Lichexanthone
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL470650
PubChem CID 5358904
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0002817] Dibenzopyrans
            • [CHEMONTID:0000200] Xanthenes
              • [CHEMONTID:0000204] Xanthones

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 QDLAGTHXVHQKRE-UHFFFAOYSA-N
Standard InCHI InChI=1S/C16H14O5/c1-8-4-9(19-2)6-12-14(8)16(18)15-11(17)5-10(20-3)7-13(15)21-12/h4-7,17H,1-3H3
SMILES Cc1cc(cc2c1c(=O)c1c(cc(cc1o2)OC)O)OC

  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
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. n.a. n.a. PMID[12662092]
NPO20214 Ruprechtia tangarana Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[12932125]
NPO13075 Gustavia hexapetala Species Lecythidaceae Eukaryota n.a. Peru 1979 PMID[15217278]
NPO8520 Mucor spinosus Species Mucoraceae Eukaryota n.a. n.a. n.a. PMID[15844967]
NPO14038 Oriciopsis glaberrima n.a. n.a. n.a. n.a. stem n.a. PMID[16508179]
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. Caribbean n.a. PMID[1686898]
NPO31410 Cupania cinerea Species Sapindaceae Eukaryota n.a. bark n.a. PMID[21438586]
NPO4424 Salvia amplexicaulis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38611827]
NPO18894 Karenia mikimotoi Species Kareniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13009 Laurencia saitoi Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17495 Isodon amethystoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14236 Physalis coztomatl Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1787 Agathis lanceolata Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14567 Ursinia anethoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14407 Stachyurus praecox Species Stachyuraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13075 Gustavia hexapetala Species Lecythidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10765 Dracaena concinna Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota Leaf Diffusate n.a. n.a. Database[FooDB]
NPO14407 Stachyurus praecox Species Stachyuraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29532 Vigna angularis Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO3998 Neolitsea pulchella Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14038 Oriciopsis glaberrima n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO14407 Stachyurus praecox Species Stachyuraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17495 Isodon amethystoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14038 Oriciopsis glaberrima n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO4424 Salvia amplexicaulis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13075 Gustavia hexapetala Species Lecythidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14236 Physalis coztomatl Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3426 Pseudocyphellaria hirsuta Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15020 Flindersia amboinensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17495 Isodon amethystoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2360 Jatropha mahafalensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18894 Karenia mikimotoi Species Kareniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10765 Dracaena concinna Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10542 Liparis keitaoensis Species Liparidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14335 Ophiorrhiza kuroiwae Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15862 Eminium lehmannii Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1787 Agathis lanceolata Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13009 Laurencia saitoi Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13389 Cystoseira barbatula Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14407 Stachyurus praecox Species Stachyuraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3998 Neolitsea pulchella Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13247 Stevia pilosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20214 Ruprechtia tangarana Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10423 Sibthorpia europaea Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14567 Ursinia anethoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8520 Mucor spinosus Species Mucoraceae 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
NPT168 Cell line P388 Mus musculus GI50 > 10.0 ug.mL-1 PMID[15217278]
NPT1081 Cell line BXPC-3 Homo sapiens GI50 = 2.5 ug.mL-1 PMID[15217278]
NPT83 Cell line MCF7 Homo sapiens GI50 = 4.1 ug.mL-1 PMID[15217278]
NPT395 Cell line SF-268 Homo sapiens GI50 = 3.0 ug.mL-1 PMID[15217278]
NPT397 Cell line NCI-H460 Homo sapiens GI50 = 7.1 ug.mL-1 PMID[15217278]
NPT575 Cell line KM-20L2 Homo sapiens GI50 = 2.0 ug.mL-1 PMID[15217278]
NPT90 Cell line DU-145 Homo sapiens GI50 = 3.7 ug.mL-1 PMID[15217278]
NPT839 Cell line L6 Rattus norvegicus IC50 = 52100.0 nM PMID[21438586]
NPT113 Cell line RAW264.7 Mus musculus Inhibition = 32.02 % PMID[31255927]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 19500.0 nM PMID[35007071]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense IC50 > 90000.0 nM PMID[21438586]
NPT529 Organism Rhizoctonia solani Rhizoctonia solani ED50 = 202.5 ug ml-1 PMID[21351753]
NPT722 Organism Athelia rolfsii Athelia rolfsii ED50 = 273.33 ug ml-1 PMID[21351753]
NPT529 Organism Rhizoctonia solani Rhizoctonia solani Inhibition = 19.63 % PMID[21351753]
NPT529 Organism Rhizoctonia solani Rhizoctonia solani Inhibition = 29.36 % PMID[21351753]
NPT529 Organism Rhizoctonia solani Rhizoctonia solani Inhibition = 41.0 % PMID[21351753]
NPT722 Organism Athelia rolfsii Athelia rolfsii Inhibition = 16.67 % PMID[21351753]
NPT722 Organism Athelia rolfsii Athelia rolfsii Inhibition = 23.2 % PMID[21351753]
NPT722 Organism Athelia rolfsii Athelia rolfsii Inhibition = 37.33 % PMID[21351753]
NPT2701 Organism Pythium debaryanum Pythium debaryanum ED50 = 148.95 ug ml-1 PMID[21351753]
NPT2703 Organism Rhizoctonia bataticola Rhizoctonia bataticola ED50 = 133.76 ug ml-1 PMID[21351753]
NPT2701 Organism Pythium debaryanum Pythium debaryanum Inhibition = 9.03 % PMID[21351753]
NPT2701 Organism Pythium debaryanum Pythium debaryanum Inhibition = 28.4 % PMID[21351753]
NPT2701 Organism Pythium debaryanum Pythium debaryanum Inhibition = 42.03 % PMID[21351753]
NPT2703 Organism Rhizoctonia bataticola Rhizoctonia bataticola Inhibition = 11.43 % PMID[21351753]
NPT2703 Organism Rhizoctonia bataticola Rhizoctonia bataticola Inhibition = 30.26 % PMID[21351753]
NPT2703 Organism Rhizoctonia bataticola Rhizoctonia bataticola Inhibition = 50.0 % PMID[21351753]
NPT965 Organism Amaranthus hypochondriacus Amaranthus hypochondriacus IC50 > 2000000.0 nM PMID[11076561]
NPT117 Organism Echinochloa crus-galli Echinochloa crus-galli IC50 > 2000000.0 nM PMID[11076561]
NPT961 Organism Pythium aphanidermatum Pythium aphanidermatum ED50 = 174.14 ug ml-1 PMID[21351753]
NPT961 Organism Pythium aphanidermatum Pythium aphanidermatum Inhibition = 13.03 % PMID[21351753]
NPT961 Organism Pythium aphanidermatum Pythium aphanidermatum Inhibition = 23.4 % PMID[21351753]
NPT961 Organism Pythium aphanidermatum Pythium aphanidermatum Inhibition = 42.66 % PMID[21351753]
NPT485 Organism Plasmodium falciparum (isolate K1 / Thailand) Plasmodium falciparum K1 IC50 > 20000.0 nM PMID[21438586]
NPT2702 Organism Fusarium udum Fusarium udum ED50 = 151.03 ug ml-1 PMID[21351753]
NPT2702 Organism Fusarium udum Fusarium udum Inhibition = 20.33 % PMID[21351753]
NPT2702 Organism Fusarium udum Fusarium udum Inhibition = 24.53 % PMID[21351753]
NPT2702 Organism Fusarium udum Fusarium udum Inhibition = 53.33 % PMID[21351753]

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 NPC310340 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
0.74 Intermediate Similarity NPC141285
0.72 Intermediate Similarity NPC604712
0.6604 Remote Similarity NPC486841
0.6154 Remote Similarity NPC180234
0.6038 Remote Similarity NPC62042
0.5926 Remote Similarity NPC188167
0.5926 Remote Similarity NPC120537
0.5926 Remote Similarity NPC117579
0.5882 Remote Similarity NPC31872
0.5849 Remote Similarity NPC199100
0.5741 Remote Similarity NPC609936
0.5536 Remote Similarity NPC29231
0.5231 Remote Similarity NPC245975
0.5179 Remote Similarity NPC223457
0.5091 Remote Similarity NPC473584
0.5091 Remote Similarity NPC25937

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC310340 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