Natural Product: NPC114096

Natural Product IDNPC114096
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Prupersin D
IUPAC Name [(2R,3S,4S,5R,6R)-6-[[(2R,3S,4S,5R,6S)-6-benzoyloxy-3,4,5-trihydroxyoxan-2-yl]methoxy]-3,4,5-trihydroxyoxan-2-yl]methyl benzoate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2419611
PubChem CID 73355242
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002207] O-glycosyl compounds

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 NMJQZNCXSRWPAF-GXMBHZMLSA-N
Standard InCHI InChI=1S/C26H30O13/c27-17-15(11-35-23(33)13-7-3-1-4-8-13)37-25(21(31)19(17)29)36-12-16-18(28)20(30)22(32)26(38-16)39-24(34)14-9-5-2-6-10-14/h1-10,15-22,25-32H,11-12H2/t15-,16-,17-,18-,19+,20+,21-,22-,25-,26+/m1/s1
SMILES O[C@@H]1[C@@H](O)[C@H](OC[C@H]2O[C@@H](OC(=O)c3ccccc3)[C@@H]([C@H]([C@@H]2O)O)O)O[C@@H]([C@H]1O)COC(=O)c1ccccc1

  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
NPO4446 Prunus davidiana Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[2045817]
NPO4446 Prunus davidiana Species Rosaceae Eukaryota seeds n.a. n.a. PMID[23985009]
NPO4446 Prunus davidiana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4446 Prunus davidiana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4446 Prunus davidiana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4446 Prunus davidiana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]

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
NPT179 Cell line A2780 Homo sapiens IC50 > 10000.0 nM PMID[17220404]
NPT81 Cell line A549 Homo sapiens IC50 > 10000.0 nM PMID[17220404]
NPT547 Cell line BGC-823 Homo sapiens IC50 > 10000.0 nM PMID[23999041]
NPT181 Cell line Bel-7402 Homo sapiens IC50 > 10000.0 nM PMID[19654408]
NPT180 Cell line HCT-8 Homo sapiens IC50 > 10000.0 nM PMID[25316317]
NPT1084 Subcellular Liver microsomes Rattus norvegicus Inhibition = 56.0 % DrugMatrix in vitro pharmacology data
NPT1084 Subcellular Liver microsomes Rattus norvegicus Inhibition = 66.0 % PMID[18088097]

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 NPC114096 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
0.7925 Intermediate Similarity NPC148026
0.6557 Remote Similarity NPC471345
0.6481 Remote Similarity NPC92117
0.6441 Remote Similarity NPC301857
0.5738 Remote Similarity NPC65833
0.5652 Remote Similarity NPC478832
0.5625 Remote Similarity NPC473867
0.5556 Remote Similarity NPC323574
0.5517 Remote Similarity NPC30563
0.5507 Remote Similarity NPC478831
0.5455 Remote Similarity NPC485233
0.5429 Remote Similarity NPC309498
0.541 Remote Similarity NPC469527
0.5397 Remote Similarity NPC479469
0.5362 Remote Similarity NPC471028
0.5342 Remote Similarity NPC469399
0.5303 Remote Similarity NPC111785
0.5238 Remote Similarity NPC470825
0.5224 Remote Similarity NPC140151
0.5161 Remote Similarity NPC266389
0.5161 Remote Similarity NPC122245
0.5161 Remote Similarity NPC216605
0.5161 Remote Similarity NPC264784
0.5147 Remote Similarity NPC215811
0.5147 Remote Similarity NPC4958
0.5143 Remote Similarity NPC197708
0.5135 Remote Similarity NPC469448
0.5077 Remote Similarity NPC57607
0.5067 Remote Similarity NPC469417

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC114096 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