Structure

Physi-Chem Properties

Molecular Weight:  83.05
Volume:  79.605
LogP:  -2.095
LogD:  -1.277
LogS:  -0.401
# Rotatable Bonds:  0
TPSA:  55.43
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.39
Synthetic Accessibility Score:  4.456
Fsp3:  0.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.965
MDCK Permeability:  0.00014367944095283747
Pgp-inhibitor:  0.0
Pgp-substrate:  0.066
Human Intestinal Absorption (HIA):  0.051
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.71
Plasma Protein Binding (PPB):  6.688029766082764%
Volume Distribution (VD):  0.892
Pgp-substrate:  85.28807830810547%

ADMET: Metabolism

CYP1A2-inhibitor:  0.015
CYP1A2-substrate:  0.841
CYP2C19-inhibitor:  0.052
CYP2C19-substrate:  0.045
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.03
CYP2D6-inhibitor:  0.017
CYP2D6-substrate:  0.106
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.135

ADMET: Excretion

Clearance (CL):  5.452
Half-life (T1/2):  0.918

ADMET: Toxicity

hERG Blockers:  0.058
Human Hepatotoxicity (H-HT):  0.985
Drug-inuced Liver Injury (DILI):  0.659
AMES Toxicity:  0.468
Rat Oral Acute Toxicity:  0.82
Maximum Recommended Daily Dose:  0.444
Skin Sensitization:  0.897
Carcinogencity:  0.856
Eye Corrosion:  0.047
Eye Irritation:  0.947
Respiratory Toxicity:  0.909

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC31657

Natural Product ID:  NPC31657
Common Name*:   2-Aminoimidazole
IUPAC Name:   1H-imidazol-2-amine
Synonyms:   2-Aminoimidazole
Standard InCHIKey:  DEPDDPLQZYCHOH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C3H5N3/c4-3-5-1-2-6-3/h1-2H,(H3,4,5,6)
SMILES:  N=c1[nH]cc[nH]1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL291627
PubChem CID:   82140
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000436] Azoles
        • [CHEMONTID:0000078] Imidazoles
          • [CHEMONTID:0002310] Substituted imidazoles
            • [CHEMONTID:0001225] Aminoimidazoles

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO6975 Spina gleditsiae n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO6975 Spina gleditsiae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]

☑ 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 NP ID 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT2542 Individual Protein Arginase-1 Homo sapiens Ki = 3600000.0 nM PMID[476473]
NPT269 Individual Protein Nitric-oxide synthase, brain Rattus norvegicus IC50 = 65000.0 nM PMID[476473]
NPT270 Individual Protein Nitric oxide synthase, inducible Mus musculus IC50 = 65000.0 nM PMID[476473]
NPT35 Others n.a. pKa = 8.46 n.a. PMID[476469]
NPT35 Others n.a. pKa = 8.46 n.a. PMID[476470]
NPT805 Protein Complex GABA-A receptor; anion channel Rattus norvegicus Inhibition = 0.0 % PMID[476471]
NPT35 Others n.a. pKa = 8.46 n.a. PMID[476472]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC31657 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.6735 Remote Similarity NPC39250
0.6122 Remote Similarity NPC230087

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC31657 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

  Bioactivity similarity: Similar Natural Products in NPASS

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