Natural Product: NPC607934

Natural Product IDNPC607934
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 IUGYQRQAERSCNH-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL322719
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 IUGYQRQAERSCNH-UHFFFAOYSA-N
Standard InCHI InChI=1S/C5H10O2/c1-5(2,3)4(6)7/h1-3H3,(H,6,7)
SMILES CC(C)(C)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
NPO46321 Streptomyces avermitilis Species Streptomycetaceae Bacteria 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
NPT705 Individual protein Solute carrier family 22 member 5 Homo sapiens Activity n.a. n.a. n.a. PMID[10525100]
NPT21289 Single protein Free fatty acid receptor 3 Rattus norvegicus EC50 = 500000.0 nM WO-2001061359-A2

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT111 Cell line K562 Homo sapiens IC50 = 4500000.0 nM PMID[10560743]
NPT111 Cell line K562 Homo sapiens Erythroid induction = 6.0 % PMID[10560743]
NPT111 Cell line K562 Homo sapiens Erythroid induction = 12.0 % PMID[10560743]
NPT111 Cell line K562 Homo sapiens Erythroid induction = 11.0 % PMID[10560743]
NPT111 Cell line K562 Homo sapiens Erythroid induction = 4.0 % PMID[10560743]
NPT111 Cell line K562 Homo sapiens Erythroid induction = 9.0 % PMID[10560743]
NPT28438 Unchecked Unchecked n.a. EC50 = 5530.0 nM PMID[33848153]
NPT28438 Unchecked Unchecked n.a. Activity = 77.0 % PMID[33848153]

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
- Rattus norvegicus NOAEL = 30.0 mg/kg-day ToxVal
- Rattus norvegicus NOAEL = 300.0 mg/kg-day ToxVal
- Rattus norvegicus NOAEL = 125.0 mg/kg-day ToxVal
- Rattus norvegicus NOAEL = 75.0 mg/kg-day ToxVal
- Rattus norvegicus LD50 < 2.0 mL/kg bw ToxVal
- Rattus norvegicus LD50 > 1.0 mL/kg bw ToxVal
- Rattus norvegicus LD50 = 2000.0 mg/kg ToxVal
- Rattus norvegicus LC50 > 5300.0 mg/m3 ToxVal
- Rattus norvegicus LD50 <= 4.0 mL/kg bw ToxVal
- Rattus norvegicus LD50 >= 2.0 mL/kg bw ToxVal
- Rattus norvegicus LD50 = 900.0 mg/kg ToxVal
- Rattus norvegicus LD50 <= 4820.0 mg/kg ToxVal
- Rattus norvegicus LD50 >= 830.0 mg/kg ToxVal
- Rattus norvegicus LC50 > 4.0 mg/L ToxVal
- Rattus norvegicus LC50 < 4.0 mg/L ToxVal
- Rattus norvegicus LD50 = 1900.0 mg/kg ToxVal
- Mus musculus LC50 < 4.0 mg/L ToxVal
- Mus musculus LC50 > 4.0 mg/L ToxVal
- Oryctolagus cuniculus NOAEL = 12.5 mg/kg-day ToxVal
- Oryctolagus cuniculus NOAEL = 50.0 mg/kg-day ToxVal
- Oryctolagus cuniculus LD50 = 3160.0 mg/kg ToxVal
- Oryctolagus cuniculus NOAEL = 300.0 mg/kg-day ToxVal
- Homo sapiens DNEL systemic = 0.44 mg/m3 ToxVal
- Homo sapiens PAC-3 = 180.0 mg/m3 ToxVal
- Homo sapiens PAC-2 = 30.0 mg/m3 ToxVal
- Homo sapiens PAC-1 = 2.7 mg/m3 ToxVal
- Homo sapiens MEG = 10.0 mg/m3 ToxVal
- Homo sapiens MEG = 75.0 mg/m3 ToxVal
- Homo sapiens MEG = 400.0 mg/m3 ToxVal

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 NPC607934 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
0.75 Intermediate Similarity NPC604184
0.6667 Remote Similarity NPC230726
0.6667 Remote Similarity NPC181153
0.6364 Remote Similarity NPC68873
0.6154 Remote Similarity NPC286233
0.6154 Remote Similarity NPC241404
0.6154 Remote Similarity NPC328569
0.5714 Remote Similarity NPC9294
0.5714 Remote Similarity NPC307739
0.5714 Remote Similarity NPC116709
0.5714 Remote Similarity NPC76217
0.5714 Remote Similarity NPC212144
0.5714 Remote Similarity NPC21290
0.5714 Remote Similarity NPC272614
0.5714 Remote Similarity NPC178595
0.5385 Remote Similarity NPC3343
0.5385 Remote Similarity NPC20903
0.5385 Remote Similarity NPC307812
0.5333 Remote Similarity NPC104195
0.5333 Remote Similarity NPC149209
0.5333 Remote Similarity NPC61066
0.5333 Remote Similarity NPC308418
0.5333 Remote Similarity NPC60675
0.5333 Remote Similarity NPC151140
0.5333 Remote Similarity NPC122768
0.5333 Remote Similarity NPC297363

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC607934 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
0.6667 Remote Similarity NPD8201 Phase 2
0.6667 Remote Similarity NPD8213 Pre-clinical
0.6364 Remote Similarity NPD7364 Phase 4
0.6154 Remote Similarity NPD8189 Phase 2
0.6 Remote Similarity NPD9411 Phase 1
0.5714 Remote Similarity NPD8202 Phase 4
0.5714 Remote Similarity NPD8205 Phase 4
0.5714 Remote Similarity NPD8210 Phase 3
0.5714 Remote Similarity NPD8211 Approved
0.5385 Remote Similarity NPD8187 Phase 3

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