Natural Product: NPC134725

Natural Product IDNPC134725
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XYPJAWWDSQFSQA-VMCYIVQPSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001543] Sesquiterpene lactones
            • [CHEMONTID:0001771] Germacranolides and derivatives

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 XYPJAWWDSQFSQA-VMCYIVQPSA-N
Standard InCHI InChI=1S/C22H28O8/c1-12-5-6-17(28-15(4)25)13(2)10-19-20(14(3)21(26)29-19)18(9-12)30-22(27)16(11-24)7-8-23/h5,7,10,17-20,23-24H,3,6,8-9,11H2,1-2,4H3/b12-5+,13-10-,16-7-/t17-,18+,19+,20+/m0/s1
SMILES C/C/1=CC[C@@H](/C(=C[C@@H]2[C@H](C(=C)C(=O)O2)[C@@H](C1)OC(=O)/C(=CCO)/CO)/C)OC(=O)C

  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
NPO2440 Schkuhria pinnata Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[29244495]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[29244495]
NPO2440 Schkuhria pinnata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2440 Schkuhria pinnata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2440 Schkuhria pinnata Species Asteraceae 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
NPT839 Cell line L6 Rattus norvegicus IC50 = 54600.0 nM PMID[29244495]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense IC50 = 1700.0 nM PMID[29244495]
NPT2 Others Unspecified n.a. Ratio IC50 = 31.1 n.a. PMID[29244495]

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 NPC134725 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
1.0 High Similarity NPC48657
0.902 High Similarity NPC482128
0.902 High Similarity NPC482129
0.8491 Intermediate Similarity NPC269509
0.8421 Intermediate Similarity NPC486033
0.8393 Intermediate Similarity NPC486037
0.7843 Intermediate Similarity NPC476028
0.7636 Intermediate Similarity NPC482130
0.7143 Intermediate Similarity NPC482126
0.7143 Intermediate Similarity NPC482131
0.7018 Intermediate Similarity NPC470755
0.7018 Intermediate Similarity NPC298801
0.6984 Remote Similarity NPC59330
0.6885 Remote Similarity NPC486034
0.6885 Remote Similarity NPC482132
0.6842 Remote Similarity NPC266957
0.678 Remote Similarity NPC486031
0.6613 Remote Similarity NPC96018
0.65 Remote Similarity NPC482133
0.6333 Remote Similarity NPC482127
0.5873 Remote Similarity NPC230800
0.5714 Remote Similarity NPC482134
0.5625 Remote Similarity NPC488118
0.5588 Remote Similarity NPC486035
0.5574 Remote Similarity NPC158756
0.5574 Remote Similarity NPC601035
0.5469 Remote Similarity NPC488120
0.5455 Remote Similarity NPC288876
0.541 Remote Similarity NPC473321
0.5345 Remote Similarity NPC603669
0.5312 Remote Similarity NPC471141
0.5312 Remote Similarity NPC469910
0.5246 Remote Similarity NPC250940
0.5246 Remote Similarity NPC169575
0.5172 Remote Similarity NPC171204
0.5172 Remote Similarity NPC606745
0.5085 Remote Similarity NPC611318
0.5079 Remote Similarity NPC481909
0.5068 Remote Similarity NPC486032
0.5067 Remote Similarity NPC486036

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC134725 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