Natural Product: NPC610778

Natural Product IDNPC610778
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 HYZRWYQBGNTGTK-LNLATYFQSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL5396597
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic 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 HYZRWYQBGNTGTK-LNLATYFQSA-N
Standard InCHI InChI=1S/C13H14O5/c1-16-11-4-7(2-3-10(11)14)12-8-5-18-13(15)9(8)6-17-12/h2-4,8-9,12,14H,5-6H2,1H3/t8-,9-,12+/m1/s1
SMILES COc1cc([C@@H]2OC[C@H]3C(=O)OC[C@H]32)ccc1O

  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
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota leaves n.a. n.a. PMID[16933890]
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota n.a. root n.a. PMID[19052526]
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[28817274]
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[31967821]
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[32649211]
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[9548837]
NPO30295 Calotropis gigantea Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT71 Cell line HEK293 Homo sapiens Activity n.a. n.a. n.a. PMID[38528772]

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 NPC610778 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
0.7551 Intermediate Similarity NPC27159
0.7551 Intermediate Similarity NPC186220
0.7234 Intermediate Similarity NPC115207
0.7234 Intermediate Similarity NPC158079
0.7234 Intermediate Similarity NPC228346
0.7234 Intermediate Similarity NPC40432
0.7234 Intermediate Similarity NPC161557
0.6667 Remote Similarity NPC126409
0.6667 Remote Similarity NPC223185
0.6667 Remote Similarity NPC99572
0.6667 Remote Similarity NPC488505
0.6604 Remote Similarity NPC27843
0.6604 Remote Similarity NPC7171
0.6552 Remote Similarity NPC67247
0.6364 Remote Similarity NPC473236
0.629 Remote Similarity NPC281780
0.6275 Remote Similarity NPC209229
0.6034 Remote Similarity NPC88640
0.6034 Remote Similarity NPC101153
0.6034 Remote Similarity NPC193666
0.6034 Remote Similarity NPC123526
0.6034 Remote Similarity NPC608725
0.6 Remote Similarity NPC478955
0.6 Remote Similarity NPC478700
0.5849 Remote Similarity NPC147379
0.5849 Remote Similarity NPC469480
0.5714 Remote Similarity NPC14022
0.5714 Remote Similarity NPC601703
0.5588 Remote Similarity NPC67467
0.5577 Remote Similarity NPC142985
0.549 Remote Similarity NPC282703
0.549 Remote Similarity NPC184733
0.549 Remote Similarity NPC128208
0.549 Remote Similarity NPC129570
0.549 Remote Similarity NPC63238
0.549 Remote Similarity NPC602603
0.5469 Remote Similarity NPC265154
0.5385 Remote Similarity NPC487682
0.5362 Remote Similarity NPC252402
0.5362 Remote Similarity NPC102934
0.5357 Remote Similarity NPC479434
0.5333 Remote Similarity NPC471942
0.5303 Remote Similarity NPC267091
0.5283 Remote Similarity NPC242807
0.5283 Remote Similarity NPC153739
0.5246 Remote Similarity NPC272
0.5246 Remote Similarity NPC187998
0.5246 Remote Similarity NPC77040
0.5246 Remote Similarity NPC257582
0.5246 Remote Similarity NPC241522
0.5246 Remote Similarity NPC485398
0.5231 Remote Similarity NPC471988
0.5167 Remote Similarity NPC181049
0.5167 Remote Similarity NPC480701
0.5098 Remote Similarity NPC141765
0.5098 Remote Similarity NPC34103
0.5088 Remote Similarity NPC11258
0.5088 Remote Similarity NPC21867
0.5088 Remote Similarity NPC487683
0.5088 Remote Similarity NPC45774
0.5088 Remote Similarity NPC74914
0.5079 Remote Similarity NPC282833
0.5079 Remote Similarity NPC145144
0.5072 Remote Similarity NPC243891

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC610778 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