Natural Product: NPC39265

Natural Product IDNPC39265
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PQZHRNHSIAKVKG-JACXBSBZSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101673972
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0004081] Iridoid O-glycosides

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 PQZHRNHSIAKVKG-JACXBSBZSA-N
Standard InCHI InChI=1S/C17H24O11/c1-25-15(24)7-3-2-6-8(14(22)23)5-26-16(10(6)7)28-17-13(21)12(20)11(19)9(4-18)27-17/h5-7,9-13,16-21H,2-4H2,1H3,(H,22,23)/t6-,7+,9-,10+,11-,12+,13-,16+,17+/m1/s1
SMILES COC(=O)[C@H]1CC[C@@H]2C(=CO[C@H]([C@H]12)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)C(=O)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
NPO1766 Hymenaea courbaril Species Fabaceae Eukaryota n.a. Suriname rain forest n.a. PMID[11809056]
NPO6779 Sutherlandia frutescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18808182]
NPO5985 Klebsiella pneumoniae Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24572278]
NPO6381 Dendrobium crepidatum Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[26710212]
NPO5985 Klebsiella pneumoniae Species Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO5039 Cryptomonas ovata Species Cryptomonadaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8175 Acacia kempeana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5235 Laburnum watereri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO850 Metatrichia vesparium Species Trichiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2366 Diospyros buxifolia Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7812 Alhagi persarum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1766 Hymenaea courbaril Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6979 Baillonella toxisperma Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4271 Dendrobium thyrsiflorum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4271 Dendrobium thyrsiflorum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4271 Dendrobium thyrsiflorum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2218 Aframomum sulcatum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26373.1 Microbispora rosea subsp. aerata Subspecies Streptosporangiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO22995 Oophaga histrionica Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7601 Centaurea cana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3944 Senecio variabilis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4096 Acanthias vulgaris n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO8175 Acacia kempeana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2525 Castanopsis cuspidata Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8476 Teucrium lanigerum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6381 Dendrobium crepidatum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5039 Cryptomonas ovata Species Cryptomonadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4271 Dendrobium thyrsiflorum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5235 Laburnum watereri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6979 Baillonella toxisperma Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4644 Pteris pacifica Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7812 Alhagi persarum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3672 Montanoa guatemalensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1766 Hymenaea courbaril Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO720 Badilloa salicina n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6779 Sutherlandia frutescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2011 Decaisnea fargesii Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8312 Polygonatum stenophyllum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5985 Klebsiella pneumoniae Species Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2366 Diospyros buxifolia Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO850 Metatrichia vesparium Species Trichiidae 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 NPC39265 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
0.6719 Remote Similarity NPC287539
0.6719 Remote Similarity NPC3488
0.6119 Remote Similarity NPC161293
0.6119 Remote Similarity NPC241911
0.5588 Remote Similarity NPC600174
0.5333 Remote Similarity NPC28304
0.5333 Remote Similarity NPC77262
0.5263 Remote Similarity NPC474285
0.5181 Remote Similarity NPC17567
0.5128 Remote Similarity NPC484096
0.5116 Remote Similarity NPC322503
0.507 Remote Similarity NPC606871

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC39265 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