Natural Product: NPC39250

Natural Product IDNPC39250
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 3-Amino-1-(2-Aminoimidazoyl)-Prop-1-Ene
IUPAC Name 5-[(E)-3-aminoprop-1-enyl]-1H-imidazol-2-amine
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL240306
PubChem CID 10820593
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000436] Azoles
        • [CHEMONTID:0000078] Imidazoles
          • [CHEMONTID:0002310] Substituted imidazoles
            • [CHEMONTID:0001225] Aminoimidazoles

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 YFJXNGUQXKFQAO-OWOJBTEDSA-N
Standard InCHI InChI=1S/C6H10N4/c7-3-1-2-5-4-9-6(8)10-5/h1-2,4H,3,7H2,(H3,8,9,10)/b2-1+
SMILES NC/C=C/c1c[nH]c(=N)[nH]1

  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
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota leaves n.a. n.a. PMID[11170659]
NPO27012 Laurencia pannosa Species Rhodomelaceae Eukaryota n.a. Malaysian n.a. PMID[11374951]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota leaves n.a. n.a. PMID[12502329]
NPO27072 Monochaetum vulcanicum Species Melastomataceae Eukaryota n.a. n.a. n.a. PMID[15165161]
NPO40426 Agelas oroides enoyl Strain Agelasidae Eukaryota Tubers n.a. n.a. PMID[17765547]
NPO17223 Agelas oroides Species Agelasidae Eukaryota n.a. n.a. n.a. PMID[32072810]
NPO27707 Soja hispida Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20208 Rhinogobius brunneus Species Gobiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27688 Aeonium goochiae Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17223 Agelas oroides Species Agelasidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40426 Agelas oroides enoyl Strain Agelasidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27740 Alcantara ekmaniana n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO27569 Archangelica officinalis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27725 Artemisia vestita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16500 Byssochlamys spectabilis Species Thermoascaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27191 Schistochila appendiculata Species Schistochilaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27773 Rhododendron ovatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27072 Monochaetum vulcanicum Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22488 Leptosphaeria oraemaris Species Leptosphaeriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27012 Laurencia pannosa Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7497 Guatteria blepharophylla Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27262 Dryopteris inaequalis Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11140 Coprinopsis cinerea Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27648 Cereus aethiops Species Cactaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26895 Baccharis bigelovii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27725 Artemisia vestita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27725 Artemisia vestita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27773 Rhododendron ovatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27725 Artemisia vestita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27725 Artemisia vestita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27569 Archangelica officinalis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27707 Soja hispida Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17223 Agelas oroides Species Agelasidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27072 Monochaetum vulcanicum Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27773 Rhododendron ovatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27262 Dryopteris inaequalis Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27191 Schistochila appendiculata Species Schistochilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27740 Alcantara ekmaniana n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO7497 Guatteria blepharophylla Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26895 Baccharis bigelovii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11140 Coprinopsis cinerea Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27012 Laurencia pannosa Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27648 Cereus aethiops Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27688 Aeonium goochiae Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20208 Rhinogobius brunneus Species Gobiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16500 Byssochlamys spectabilis Species Thermoascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22488 Leptosphaeria oraemaris Species Leptosphaeriaceae 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
NPT1333 Individual protein Enoyl-acyl-carrier protein reductase Plasmodium falciparum IC50 > 100.0 ug.mL-1 PMID[17765547]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT839 Cell line L6 Rattus norvegicus IC50 = 0.7 ug.mL-1 PMID[17765547]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 7.4 ug.mL-1 PMID[17765547]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense IC50 = 2.4 ug.mL-1 PMID[17765547]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi IC50 = 2.5 ug.mL-1 PMID[17765547]
NPT633 Organism Leishmania donovani Leishmania donovani IC50 = 13.1 ug.mL-1 PMID[17765547]

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 NPC39250 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
NPC

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC39250 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