Natural Product: NPC607953

Natural Product IDNPC607953
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 DGYHPLMPMRKMPD-BYPYZUCNSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL50483
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 DGYHPLMPMRKMPD-BYPYZUCNSA-N
Standard InCHI InChI=1S/C5H7NO2/c1-2-3-4(6)5(7)8/h1,4H,3,6H2,(H,7,8)/t4-/m0/s1
SMILES C#CC[C@H](N)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
NPO52746 Streptomyces sp. # 8-4 (HLR-599A) Genus 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
NPT24914 Single protein Cystathionine gamma-lyase Homo sapiens IC50 = 40000.0 nM PMID[29259741]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1122 Organism Haemophilus influenzae Haemophilus influenzae MIC > 100.0 ug.mL-1 PMID[6417332]
NPT1033 Organism Enterobacter cloacae Enterobacter cloacae MIC > 100.0 ug.mL-1 PMID[6417332]
NPT172 Organism Proteus mirabilis Proteus mirabilis MIC > 100.0 ug.mL-1 PMID[6417332]
NPT2909 Organism Shigella flexneri Shigella flexneri MIC > 100.0 ug.mL-1 PMID[6417332]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium MIC > 100.0 ug.mL-1 PMID[6417332]
NPT2710 Organism Streptococcus agalactiae Streptococcus agalactiae MIC > 100.0 ug.mL-1 PMID[6417332]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC > 100.0 ug.mL-1 PMID[6417332]
NPT1228 Organism Streptococcus pyogenes Streptococcus pyogenes MIC > 100.0 ug.mL-1 PMID[6417332]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis MIC > 100.0 ug.mL-1 PMID[6417332]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 100.0 ug.mL-1 PMID[6417332]
NPT19 Organism Escherichia coli Escherichia coli MIC > 100.0 ug.mL-1 PMID[6417332]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC > 100.0 ug.mL-1 PMID[6417332]
NPT3495 Organism Morganella morganii Morganella morganii MIC > 100.0 ug.mL-1 PMID[6417332]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 100.0 ug.mL-1 PMID[6417332]
NPT29356 Organism Klebsiella aerogenes Klebsiella aerogenes MIC > 100.0 ug.mL-1 PMID[6417332]
NPT1248 Organism Serratia marcescens Serratia marcescens MIC > 100.0 ug.mL-1 PMID[6417332]

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 NPC607953 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 NPC604272
0.6842 Remote Similarity NPC63621
0.6842 Remote Similarity NPC326992
0.6842 Remote Similarity NPC121517
0.6842 Remote Similarity NPC168375
0.6842 Remote Similarity NPC600066
0.619 Remote Similarity NPC329263
0.619 Remote Similarity NPC118459
0.619 Remote Similarity NPC309658
0.619 Remote Similarity NPC327698
0.619 Remote Similarity NPC53449
0.6111 Remote Similarity NPC116709
0.6111 Remote Similarity NPC21290
0.6111 Remote Similarity NPC272614
0.6087 Remote Similarity NPC137958
0.6087 Remote Similarity NPC273330
0.5909 Remote Similarity NPC245027
0.5909 Remote Similarity NPC162620
0.5909 Remote Similarity NPC62045
0.5909 Remote Similarity NPC601942
0.5714 Remote Similarity NPC208793
0.5714 Remote Similarity NPC285322
0.5714 Remote Similarity NPC118187
0.5652 Remote Similarity NPC49952
0.5652 Remote Similarity NPC153370
0.5652 Remote Similarity NPC34908
0.5652 Remote Similarity NPC136476
0.56 Remote Similarity NPC279661
0.56 Remote Similarity NPC183845
0.55 Remote Similarity NPC237525
0.55 Remote Similarity NPC326212
0.5417 Remote Similarity NPC167986
0.5417 Remote Similarity NPC140872
0.5417 Remote Similarity NPC93081
0.5417 Remote Similarity NPC291186
0.5417 Remote Similarity NPC600338
0.5238 Remote Similarity NPC132307
0.5238 Remote Similarity NPC126925
0.5217 Remote Similarity NPC84636
0.5217 Remote Similarity NPC226027
0.5217 Remote Similarity NPC174246
0.5217 Remote Similarity NPC43204
0.52 Remote Similarity NPC322532
0.52 Remote Similarity NPC50047
0.52 Remote Similarity NPC608987

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC607953 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
0.6111 Remote Similarity NPD8210 Phase 3
0.6111 Remote Similarity NPD8211 Approved
0.6087 Remote Similarity NPD8872 Phase 3
0.5909 Remote Similarity NPD9018 Phase 3
0.5833 Remote Similarity NPD8871 Phase 4
0.5714 Remote Similarity NPD8610 Phase 3
0.5652 Remote Similarity NPD8614 Pre-clinical
0.5417 Remote Similarity NPD8804 Phase 4
0.5417 Remote Similarity NPD8805 Approved
0.5417 Remote Similarity NPD8809 Phase 3
0.5417 Remote Similarity NPD9016 Phase 1
0.5238 Remote Similarity NPD8798 Phase 2
0.5217 Remote Similarity NPD9017 Phase 2
0.52 Remote Similarity NPD9021 Pre-clinical

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