Natural Product: NPC202433

Natural Product IDNPC202433
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 QPFBVCAQCZYOIT-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 9985405
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001586] Biflavonoids and polyflavonoids

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 QPFBVCAQCZYOIT-UHFFFAOYSA-N
Standard InCHI InChI=1S/C32H22O10/c1-39-24-13-20(36)27-19(35)11-23(16-5-9-18(34)10-6-16)42-32(27)30(24)29-25(40-2)14-26-28(31(29)38)21(37)12-22(41-26)15-3-7-17(33)8-4-15/h3-14,33-34,36,38H,1-2H3
SMILES COc1cc(c2c(=O)cc(c3ccc(cc3)O)oc2c1c1c(cc2c(c(=O)cc(c3ccc(cc3)O)o2)c1O)OC)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
NPO23434 Fissistigma latifolium Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[29160716]
NPO24272 Akania lucens Species Akaniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22365 Osbeckia chinensis Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23575 Aspergillus restrictus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22216 Chimonanthus fragrans Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23434 Fissistigma latifolium Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23814 Elsholtzia splendens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22216 Chimonanthus fragrans Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22216 Chimonanthus fragrans Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23814 Elsholtzia splendens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13513 Agathis palmerstonii Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20124 Xylopia discreta Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11353 Viscaria vulgaris Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22216 Chimonanthus fragrans Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22365 Osbeckia chinensis Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20124 Xylopia discreta Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24155 Nepeta annua Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23153 Eria smithii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24351 Sclerotinia libertiana Species Sclerotiniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23575 Aspergillus restrictus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11353 Viscaria vulgaris Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7689 Cota triumfettii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25084 Dasiphora fruticosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23814 Elsholtzia splendens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24234 Agrocybe aegerita Species Bolbitiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23434 Fissistigma latifolium Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13513 Agathis palmerstonii Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24272 Akania lucens Species Akaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22216 Chimonanthus fragrans Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24429 Cestrum pallidissimum Species Solanaceae 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

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 NPC202433 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
0.918 High Similarity NPC601984
0.7097 Intermediate Similarity NPC610914
0.6957 Remote Similarity NPC603508
0.6761 Remote Similarity NPC159707
0.6721 Remote Similarity NPC234133
0.6389 Remote Similarity NPC290830
0.629 Remote Similarity NPC52611
0.625 Remote Similarity NPC600972
0.6216 Remote Similarity NPC215203
0.6164 Remote Similarity NPC158027
0.5938 Remote Similarity NPC198826
0.5938 Remote Similarity NPC120163
0.589 Remote Similarity NPC248739
0.5867 Remote Similarity NPC194593
0.5846 Remote Similarity NPC78913
0.5714 Remote Similarity NPC205026
0.5714 Remote Similarity NPC601565
0.5641 Remote Similarity NPC265624
0.5606 Remote Similarity NPC108406
0.5538 Remote Similarity NPC241498
0.5538 Remote Similarity NPC127447
0.5538 Remote Similarity NPC47815
0.5538 Remote Similarity NPC29353
0.5507 Remote Similarity NPC67322
0.55 Remote Similarity NPC55443
0.5455 Remote Similarity NPC186227
0.5362 Remote Similarity NPC137062
0.5325 Remote Similarity NPC600396
0.5303 Remote Similarity NPC301323
0.5224 Remote Similarity NPC250266
0.5217 Remote Similarity NPC124784
0.519 Remote Similarity NPC121649
0.5156 Remote Similarity NPC222713
0.5152 Remote Similarity NPC607196
0.5128 Remote Similarity NPC71061
0.5128 Remote Similarity NPC72425
0.5075 Remote Similarity NPC71334
0.5075 Remote Similarity NPC275836

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC202433 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