Natural Product: NPC607543

Natural Product IDNPC607543
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 CIBNJPPYSPYHDB-UEBIAWITSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL225817
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0002321] Cycloartanols 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 CIBNJPPYSPYHDB-UEBIAWITSA-N
Standard InCHI InChI=1S/C31H52O/c1-20(2)21(3)9-10-22(4)23-13-15-29(8)25-12-11-24-27(5,6)26(32)14-16-30(24)19-31(25,30)18-17-28(23,29)7/h22-26,32H,9-19H2,1-8H3/t22-,23-,24+,25+,26+,28-,29+,30-,31+/m1/s1
SMILES CC(C)=C(C)CC[C@@H](C)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@H]4C(C)(C)[C@@H](O)CC[C@@]45C[C@@]35CC[C@]12C

  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
NPO1099 Capparis spinosa Species Capparaceae Eukaryota aerial parts and buds Cagliari, Sardinia 2012-FEB PMID[22769561]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]

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
NPT80 Cell line Raji Homo sapiens Activity = 70.0 % PMID[17503850]
NPT29358 Organism Human gammaherpesvirus 4 Human gammaherpesvirus 4 Inhibition = 0.0 % PMID[17503850]
NPT29358 Organism Human gammaherpesvirus 4 Human gammaherpesvirus 4 Inhibition = 30.5 % PMID[17503850]
NPT28438 Unchecked Unchecked n.a. Activity = 1.9 n.a. PMID[17503850]
NPT29358 Organism Human gammaherpesvirus 4 Human gammaherpesvirus 4 Inhibition = 94.5 % PMID[17503850]
NPT29358 Organism Human gammaherpesvirus 4 Human gammaherpesvirus 4 IC50 = 9.4 nM PMID[17503850]
NPT29358 Organism Human gammaherpesvirus 4 Human gammaherpesvirus 4 Inhibition = 71.3 % PMID[17503850]
NPT28438 Unchecked Unchecked n.a. Kcat = 0.006 /min PMID[18590960]
NPT28438 Unchecked Unchecked n.a. Ki = 100000.0 nM PMID[18590960]
NPT28438 Unchecked Unchecked n.a. Ki = 25000.0 nM PMID[18590960]
NPT28438 Unchecked Unchecked n.a. Ratio = 0.04 n.a. PMID[18590960]

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 NPC607543 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
0.8261 Intermediate Similarity NPC254509
0.8085 Intermediate Similarity NPC472342
0.8 Intermediate Similarity NPC41577
0.766 Intermediate Similarity NPC331618
0.766 Intermediate Similarity NPC257191
0.766 Intermediate Similarity NPC196358
0.75 Intermediate Similarity NPC200243
0.75 Intermediate Similarity NPC85346
0.75 Intermediate Similarity NPC65897
0.75 Intermediate Similarity NPC80237
0.7447 Intermediate Similarity NPC299948
0.7447 Intermediate Similarity NPC241085
0.7143 Intermediate Similarity NPC604180
0.7059 Intermediate Similarity NPC76518
0.7037 Intermediate Similarity NPC483817
0.7 Intermediate Similarity NPC470830
0.7 Intermediate Similarity NPC195530
0.7 Intermediate Similarity NPC479659
0.7 Intermediate Similarity NPC273366
0.68 Remote Similarity NPC82623
0.6792 Remote Similarity NPC89747
0.6731 Remote Similarity NPC472341
0.6538 Remote Similarity NPC70982
0.6538 Remote Similarity NPC473279
0.6538 Remote Similarity NPC22133
0.6481 Remote Similarity NPC473238
0.625 Remote Similarity NPC18384
0.625 Remote Similarity NPC110923
0.625 Remote Similarity NPC74296
0.6226 Remote Similarity NPC49168
0.6226 Remote Similarity NPC5046
0.6182 Remote Similarity NPC134481
0.6111 Remote Similarity NPC67872
0.6034 Remote Similarity NPC195366
0.6034 Remote Similarity NPC114743
0.6 Remote Similarity NPC12722
0.6 Remote Similarity NPC195489
0.5893 Remote Similarity NPC606508
0.5763 Remote Similarity NPC85379
0.5763 Remote Similarity NPC144909
0.5763 Remote Similarity NPC476304
0.5741 Remote Similarity NPC145552
0.5741 Remote Similarity NPC69149
0.569 Remote Similarity NPC476186
0.5636 Remote Similarity NPC302041
0.5593 Remote Similarity NPC307776
0.5263 Remote Similarity NPC113978
0.5238 Remote Similarity NPC146937
0.5172 Remote Similarity NPC477858
0.5077 Remote Similarity NPC603266

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC607543 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