Natural Product: NPC36852

Natural Product IDNPC36852
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Cratoxyarborenone E
IUPAC Name 1,3,7-trihydroxy-6-methoxy-4,5-bis(3-methylbut-2-enyl)xanthen-9-one
Synonyms cratoxyarborenone E
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL462716
PubChem CID 5323543
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
                • [CHEMONTID:0003518] 4-prenylated 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 CJBZJZGULKATPY-UHFFFAOYSA-N
Standard InCHI InChI=1S/C24H26O6/c1-12(2)6-8-14-17(25)11-18(26)20-21(28)16-10-19(27)23(29-5)15(9-7-13(3)4)22(16)30-24(14)20/h6-7,10-11,25-27H,8-9H2,1-5H3
SMILES COc1c(O)cc2c(c1CC=C(C)C)oc1c(c2=O)c(O)cc(c1CC=C(C)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
NPO9520 Cratoxylum sumatranum Species Hypericaceae Eukaryota n.a. leaf n.a. PMID[11908969]
NPO9520 Cratoxylum sumatranum Species Hypericaceae Eukaryota n.a. stem n.a. PMID[11908969]
NPO9520 Cratoxylum sumatranum Species Hypericaceae Eukaryota n.a. twig n.a. PMID[11908969]
NPO16745 Scorzonera judaica Species Asteraceae Eukaryota n.a. tuberous root n.a. PMID[21650157]
NPO16745 Scorzonera judaica Species Asteraceae Eukaryota roots Daba desert reserve (50 km South of Amman), Jordan 2009-APR PMID[21650157]
NPO13263 Verbena brasiliensis Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19227 Hippoglossus hippoglossus Species Pleuronectidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16038 Ribes rubrum Species Grossulariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6106 Hymeniacidon perlevis Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17438 Polygala virgata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9520 Cratoxylum sumatranum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16745 Scorzonera judaica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18657 Galanthus gracilis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18005 Artemisia leucodes Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11770 Amphicome emodi n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO14950 Ardisia polycephala Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18995 Gaultheria itoana Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19359 Parmotrema delicatulum Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19560 Populus italica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19501 Pseudosuberites hyalinus Species Suberitidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19227 Hippoglossus hippoglossus Species Pleuronectidae Eukaryota n.a. n.a. Database[FooDB]
NPO19227 Hippoglossus hippoglossus Species Pleuronectidae Eukaryota n.a. n.a. Database[FooDB]
NPO16038 Ribes rubrum Species Grossulariaceae Eukaryota Fruits n.a. Database[FooDB]
NPO16038 Ribes rubrum Species Grossulariaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16038 Ribes rubrum Species Grossulariaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16038 Ribes rubrum Species Grossulariaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO11770 Amphicome emodi n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14950 Ardisia polycephala Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6106 Hymeniacidon perlevis Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16745 Scorzonera judaica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18995 Gaultheria itoana Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19227 Hippoglossus hippoglossus Species Pleuronectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17438 Polygala virgata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19560 Populus italica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18657 Galanthus gracilis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18005 Artemisia leucodes Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19359 Parmotrema delicatulum Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13263 Verbena brasiliensis Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16038 Ribes rubrum Species Grossulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9520 Cratoxylum sumatranum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19501 Pseudosuberites hyalinus Species Suberitidae 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
NPT91 Cell line KB Homo sapiens EC50 = 4.3 ug.mL-1 PMID[11908969]

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 NPC36852 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
0.6324 Remote Similarity NPC479160
0.589 Remote Similarity NPC603436
0.5821 Remote Similarity NPC70433
0.5733 Remote Similarity NPC83922
0.5513 Remote Similarity NPC206153
0.5513 Remote Similarity NPC271629
0.5362 Remote Similarity NPC227122
0.5205 Remote Similarity NPC303460
0.52 Remote Similarity NPC471982
0.5139 Remote Similarity NPC273538
0.5135 Remote Similarity NPC130589
0.5067 Remote Similarity NPC220313

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC36852 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
0.5139 Remote Similarity NPD4378 Phase 3

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