Natural Product: NPC117609

Natural Product IDNPC117609
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-Hydroxy Plumbagin
IUPAC Name 5,6-dihydroxy-2-methylnaphthalene-1,4-dione
Synonyms 6-Hydroxy Plumbagin
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1094243
PubChem CID 13468231
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000023] Naphthalenes
        • [CHEMONTID:0000153] Naphthoquinones

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 HWWWTOHAFWXPCB-UHFFFAOYSA-N
Standard InCHI InChI=1S/C11H8O4/c1-5-4-8(13)9-6(10(5)14)2-3-7(12)11(9)15/h2-4,12,15H,1H3
SMILES CC1=CC(=O)c2c(C1=O)ccc(c2O)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
NPO6969 Triphyophyllum peltatum Species Dioncophyllaceae Eukaryota n.a. stem n.a. DOI[10.1007/s004360050318]
NPO6969 Triphyophyllum peltatum Species Dioncophyllaceae Eukaryota n.a. root n.a. DOI[10.1007/s004360050318]
NPO22192 Cribraria cancellata Species Cribrariaceae Eukaryota n.a. n.a. n.a. PMID[14695806]
NPO20721 Halichondria panicea Species Halichondriidae Eukaryota n.a. n.a. n.a. PMID[20695474]
NPO6969 Triphyophyllum peltatum Species Dioncophyllaceae Eukaryota n.a. n.a. n.a. PMID[22019229]
NPO22069 Persea major Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[2614421]
NPO20721 Halichondria panicea Species Halichondriidae Eukaryota n.a. n.a. n.a. PMID[27035556]
NPO6969 Triphyophyllum peltatum Species Dioncophyllaceae Eukaryota n.a. root n.a. PMID[9371362]
NPO6969 Triphyophyllum peltatum Species Dioncophyllaceae Eukaryota n.a. stem n.a. PMID[9371362]
NPO23517 Heterotropa aspera n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO18387 Sedum formosanum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22196 Kickxia ramosissima Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20721 Halichondria panicea Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21383 Cnicothamnus lorentzii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6969 Triphyophyllum peltatum Species Dioncophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23045 Lotus helleri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18256 Aconitum excelsum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23045 Lotus helleri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18256 Aconitum excelsum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6969 Triphyophyllum peltatum Species Dioncophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6969 Triphyophyllum peltatum Species Dioncophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21383 Cnicothamnus lorentzii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9038 Aconitum burnatii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13113 Ardisia kivuensis Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22999 Cussonia spicata Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22069 Persea major Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23045 Lotus helleri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23865 Scorzonera veratrifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19736 Haplopappus glutinosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23432 Viguiera oaxacana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22196 Kickxia ramosissima Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23517 Heterotropa aspera n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO20094 Loranthus micranthus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22831 Isodon angustifolius Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18256 Aconitum excelsum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18921 Athrixia phylicoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17645.1 Orobanche cernua var. cumana Varieties Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22192 Cribraria cancellata Species Cribrariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20721 Halichondria panicea Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18387 Sedum formosanum Species Crassulaceae 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
NPT927 Cell line PBMC Homo sapiens EC50 = 100000.0 nM PMID[22019229]
NPT1381 Organism Aedes aegypti Aedes aegypti Activity = 100.0 % PMID[20347303]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. EC50 = 75000.0 nM PMID[22019229]

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
- Aedes aegypti LC50 = 13.64 ug.mL-1 PMID[20347303]
- Aedes aegypti LC90 = 19.28 ug ml-1 PMID[20347303]

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 NPC117609 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
0.641 Remote Similarity NPC285829
0.6 Remote Similarity NPC55949
0.5854 Remote Similarity NPC58685
0.5854 Remote Similarity NPC168444
0.5789 Remote Similarity NPC609532
0.575 Remote Similarity NPC486398
0.5476 Remote Similarity NPC206778
0.5455 Remote Similarity NPC197864
0.5135 Remote Similarity NPC43945
0.5116 Remote Similarity NPC244699

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC117609 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
0.5135 Remote Similarity NPD650 Phase 4

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