Natural Product: NPC107109

Natural Product IDNPC107109
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.
 6-O-Methylalaternin
IUPAC Name 1,2,8-trihydroxy-6-methoxy-3-methylanthracene-9,10-dione
Synonyms 6-O-Methylalaternin
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL556684
PubChem CID 177458
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000018] Anthracenes
        • [CHEMONTID:0000151] Anthraquinones
          • [CHEMONTID:0001598] Hydroxyanthraquinones

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 IOPGGNYCFGEWPF-UHFFFAOYSA-N
Standard InCHI InChI=1S/C16H12O6/c1-6-3-8-12(16(21)13(6)18)15(20)11-9(14(8)19)4-7(22-2)5-10(11)17/h3-5,17-18,21H,1-2H3
SMILES COc1cc(O)c2c(c1)C(=O)c1c(C2=O)c(O)c(c(c1)C)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
NPO17255 Chondrosia corticata Species Chondrillidae Eukaryota n.a. n.a. n.a. PMID[15568783]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota Mentha pulegium n.a. n.a. PMID[19271717]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[19271717]
NPO22865 Neopetrosia proxima Species Petrosiidae Eukaryota n.a. Caribbean sea n.a. PMID[20727745]
NPO22865 Neopetrosia proxima Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[21341726]
NPO17255 Chondrosia corticata Species Chondrillidae Eukaryota n.a. reef slopes on the south side of Cocos Lagoon, Guam n.a. PMID[21550239]
NPO18542 Salvia sahendica Species Lamiaceae Eukaryota n.a. collected from the plants natural habitat in Tabriz, Northwestern Iran, at an altitude of 1400 m n.a. PMID[21775156]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota Stems n.a. n.a. PMID[23664494]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota isolated from fresh Juncus acutus Lake Wadi el Natrun, Egypt 2012-NOV PMID[25010124]
NPO18279 Paraconiothyrium brasiliense Species Didymosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[25760674]
NPO18279 Paraconiothyrium brasiliense Species Didymosphaeriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18194 Primula modesta Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17255 Chondrosia corticata Species Chondrillidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19321 Notholaena californica Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22865 Neopetrosia proxima Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18194 Primula modesta Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18194 Primula modesta Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19101 Deutzia gracilis Species Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19321 Notholaena californica Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19726 Limnatis nilotica Species Hirudinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18542 Salvia sahendica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15888 Streptogonopus phipsoni n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13444 Centaurea ptosimopappoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17255 Chondrosia corticata Species Chondrillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18080 Peltophorum ferrugineum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18687 Pterocarpus gracilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18279 Paraconiothyrium brasiliense Species Didymosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22865 Neopetrosia proxima Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14894 Udotea conglutinata Species Udoteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18194 Primula modesta Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19382 Corallina elongata Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18944 Vernonia filigera Species Asteraceae 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
NPT1598 Individual protein Casein kinase II alpha Homo sapiens IC50 > 10.0 ug.mL-1 PMID[19271717]
NPT2575 Individual protein Platelet-derived growth factor receptor beta Homo sapiens IC50 > 10.0 ug.mL-1 PMID[19271717]
NPT1436 Individual protein Focal adhesion kinase 1 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[19271717]
NPT286 Individual protein Receptor protein-tyrosine kinase erbB-2 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[19271717]
NPT2572 Individual protein Ephrin type-B receptor 4 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[19271717]
NPT1371 Individual protein Cyclin-dependent kinase 2 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[19271717]
NPT1434 Individual protein Serine/threonine-protein kinase B-raf Homo sapiens IC50 > 10.0 ug.mL-1 PMID[19271717]
NPT1660 Individual protein NUAK family SNF1-like kinase 1 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[19271717]
NPT2571 Individual protein Mitogen-activated protein kinase kinase kinase 8 Homo sapiens IC50 = 7.3 ug.mL-1 PMID[19271717]
NPT2576 Individual protein Tyrosine-protein kinase TIE-2 Homo sapiens IC50 = 4.5 ug.mL-1 PMID[19271717]
NPT1702 Individual protein Serine/threonine-protein kinase PLK4 Homo sapiens IC50 = 4.4 ug.mL-1 PMID[19271717]
NPT1337 Individual protein Hepatocyte growth factor receptor Homo sapiens IC50 = 4.3 ug.mL-1 PMID[19271717]
NPT285 Individual protein Epidermal growth factor receptor erbB1 Homo sapiens IC50 = 4.0 ug.mL-1 PMID[19271717]
NPT2574 Individual protein Insulin receptor Homo sapiens IC50 = 3.9 ug.mL-1 PMID[19271717]
NPT1432 Individual protein Serine/threonine-protein kinase Aurora-A Homo sapiens IC50 = 3.0 ug.mL-1 PMID[19271717]
NPT1438 Individual protein Insulin-like growth factor I receptor Homo sapiens IC50 = 2.8 ug.mL-1 PMID[19271717]
NPT2573 Individual protein Vascular endothelial growth factor receptor 3 Homo sapiens IC50 = 2.7 ug.mL-1 PMID[19271717]
NPT1650 Individual protein Tyrosine-protein kinase receptor FLT3 Homo sapiens IC50 = 2.5 ug.mL-1 PMID[19271717]
NPT1433 Individual protein Serine/threonine-protein kinase Aurora-B Homo sapiens IC50 = 1.8 ug.mL-1 PMID[19271717]
NPT1478 Individual protein Vascular endothelial growth factor receptor 2 Homo sapiens IC50 = 1.2 ug.mL-1 PMID[19271717]
NPT1560 Protein complex Cyclin-dependent kinase 4/cyclin D1 Homo sapiens IC50 = 3.6 ug.mL-1 PMID[19271717]
NPT831 Individual protein Serine/threonine-protein kinase PLK1 Homo sapiens IC50 > 10.0 ug.mL-1 PMID[19271717]
NPT36 Individual protein Tyrosine-protein kinase SRC Homo sapiens IC50 = 1.8 ug.mL-1 PMID[19271717]
NPT728 Individual protein Serine/threonine-protein kinase AKT Homo sapiens IC50 > 10.0 ug.mL-1 PMID[19271717]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1864 Cell line L5178Y Mus musculus Activity = 4.9 % PMID[19271717]
NPT1864 Cell line L5178Y Mus musculus EC50 = 4.2 ug.mL-1 PMID[19271717]

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 NPC107109 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
0.6977 Remote Similarity NPC312929
0.6818 Remote Similarity NPC126767
0.6818 Remote Similarity NPC294646
0.6383 Remote Similarity NPC472052
0.6364 Remote Similarity NPC56433
0.6 Remote Similarity NPC19896
0.5957 Remote Similarity NPC118027
0.5778 Remote Similarity NPC416
0.5714 Remote Similarity NPC77807
0.5652 Remote Similarity NPC134191
0.5581 Remote Similarity NPC258502
0.5306 Remote Similarity NPC489035
0.5294 Remote Similarity NPC155030
0.5091 Remote Similarity NPC470568

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC107109 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