Natural Product: NPC280638

Natural Product IDNPC280638
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 5-[5-(4-Hydroxy-Benzyl)-4-(4-Methoxy-Benzyl)-1-Methyl-1H-Imidazol-2-Ylamino]-3-Methyl-Imidazole-2,4-Dione
IUPAC Name 5-[[5-[(4-hydroxyphenyl)methyl]-4-[(4-methoxyphenyl)methyl]-1-methylimidazol-2-yl]amino]-3-methylimidazole-2,4-dione
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL339727
PubChem CID 188306
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids 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 REQFUGYVPAQCTH-UHFFFAOYSA-N
Standard InCHI InChI=1S/C23H23N5O4/c1-27-19(13-15-4-8-16(29)9-5-15)18(12-14-6-10-17(32-3)11-7-14)24-22(27)25-20-21(30)28(2)23(31)26-20/h4-11,29H,12-13H2,1-3H3,(H,24,25,26,31)
SMILES COc1ccc(cc1)Cc1nc(n(c1Cc1ccc(cc1)O)C)N=C1N=C(N(C1=O)C)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
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO29509 Leucetta chagosensis Species Leucettidae Eukaryota n.a. n.a. n.a. PMID[12193030]
NPO29509 Leucetta chagosensis Species Leucettidae Eukaryota n.a. n.a. n.a. PMID[15165143]
NPO29509 Leucetta chagosensis Species Leucettidae Eukaryota n.a. n.a. n.a. PMID[17822294]
NPO25094 Artemisia princeps Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[17996677]
NPO29473 Amycolatopsis mediterranei Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. PMID[25256628]
NPO644 Pestalotiopsis theae Species Sporocadaceae Eukaryota n.a. n.a. n.a. PMID[27731995]
NPO29509 Leucetta chagosensis Species Leucettidae Eukaryota n.a. n.a. n.a. PMID[29648818]
NPO29255 Salvia chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30370766]
NPO28968 Teucrium flavum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[33530639]
NPO17683 Cryptocarya moschata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28968 Teucrium flavum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29025 Streptomyces nojiriensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO29255 Salvia chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25094 Artemisia princeps Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29509 Leucetta chagosensis Species Leucettidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29043 Hypoxylon oceanicum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24421.1 Agave salmiana var. ferox Varieties Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29473 Amycolatopsis mediterranei Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO29470 Anhalonium fissuratum n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO29124 Argemone squarrosa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29434 Centaurea involucrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28861 Cladonia graciliformis Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29238 Heterocondylus vitalbae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29065 Hypoxis rooperi Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24342 Lupinus albus Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25094 Artemisia princeps Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25094 Artemisia princeps Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25094 Artemisia princeps Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25094 Artemisia princeps Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29043 Hypoxylon oceanicum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29473 Amycolatopsis mediterranei Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29124 Argemone squarrosa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24421.1 Agave salmiana var. ferox Varieties Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29470 Anhalonium fissuratum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO29025 Streptomyces nojiriensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24342 Lupinus albus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28861 Cladonia graciliformis Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29065 Hypoxis rooperi Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29509 Leucetta chagosensis Species Leucettidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28968 Teucrium flavum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29434 Centaurea involucrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29255 Salvia chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29238 Heterocondylus vitalbae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17683 Cryptocarya moschata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO644 Pestalotiopsis theae Species Sporocadaceae 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
NPT1556 Individual protein Epidermal growth factor receptor erbB1 Mus musculus IC50 = 11300.0 nM PMID[9748366]
NPT4142 Individual protein Insulin receptor Mus musculus IC50 = 242000.0 nM PMID[9748366]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT762 Cell line A-431 Homo sapiens Inhibition = 96.4 % PMID[9748366]
NPT762 Cell line A-431 Homo sapiens Inhibition = 87.4 % PMID[9748366]
NPT762 Cell line A-431 Homo sapiens Inhibition = 52.0 % PMID[9748366]
NPT762 Cell line A-431 Homo sapiens Inhibition = 35.0 % PMID[9748366]
NPT2 Others Unspecified n.a. IC50 = 3000.0 nM PMID[17462892]

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 NPC280638 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 NPC136924
0.806 Intermediate Similarity NPC489314
0.7671 Intermediate Similarity NPC46970
0.641 Remote Similarity NPC242923
0.506 Remote Similarity NPC308906

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC280638 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