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Showing metabocard for Imidazolidine (HMDB0253420)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 11:51:31 UTC
Update Date2021-09-26 23:06:37 UTC
HMDB IDHMDB0253420
Secondary Accession NumbersNone
Metabolite Identification
Common NameImidazolidine
DescriptionImidazolidine belongs to the class of organic compounds known as imidazolidines. These are organic compounds containing an imidazolidine ring, which is a saturated ring (derived from imidazole) with two nitrogen atoms at positions 1 and 3 respectively, and containing only single bonds. Based on a literature review a significant number of articles have been published on Imidazolidine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Imidazolidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Imidazolidine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0253420 (Imidazolidine)

  Mrv1652309112113512D          

  5  5  0  0  0  0            999 V2000
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
M  END
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3D MOL for HMDB0253420 (Imidazolidine)

HMDB0253420
     RDKit          3D
Imidazolidine
 13 13  0  0  0  0  0  0  0  0999 V2000
   -0.6834   -0.9268   -0.3209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9258    0.5647   -0.3288 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3726    1.1497   -0.2043 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2972    0.1317    0.1955 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5325   -1.0780    0.4475 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5381   -1.4367    0.1647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6012   -1.3354   -1.3361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6406    0.8413    0.4537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3345    0.8643   -1.3249 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4162    2.0210    0.3374 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9989   -0.0369   -0.6436 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8742    0.3605    1.0994 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2317   -1.1193    1.4604 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  1  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
M  END
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3D SDF for HMDB0253420 (Imidazolidine)

  Mrv1652309112113512D          

  5  5  0  0  0  0            999 V2000
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253420

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CNCN1

> <INCHI_IDENTIFIER>
InChI=1S/C3H8N2/c1-2-5-3-4-1/h4-5H,1-3H2

> <INCHI_KEY>
WRYCSMQKUKOKBP-UHFFFAOYSA-N

> <FORMULA>
C3H8N2

> <MOLECULAR_WEIGHT>
72.111

> <EXACT_MASS>
72.068748266

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
7.970772799383743

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
imidazolidine

> <ALOGPS_LOGP>
-1.78

> <JCHEM_LOGP>
-0.6187058876666667

> <ALOGPS_LOGS>
0.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
8.699373581408292

> <JCHEM_POLAR_SURFACE_AREA>
24.06

> <JCHEM_REFRACTIVITY>
20.258300000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.70e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
imidazolidine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0253420 (Imidazolidine)

HMDB0253420
     RDKit          3D
Imidazolidine
 13 13  0  0  0  0  0  0  0  0999 V2000
   -0.6834   -0.9268   -0.3209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9258    0.5647   -0.3288 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3726    1.1497   -0.2043 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2972    0.1317    0.1955 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5325   -1.0780    0.4475 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5381   -1.4367    0.1647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6012   -1.3354   -1.3361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6406    0.8413    0.4537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3345    0.8643   -1.3249 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4162    2.0210    0.3374 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9989   -0.0369   -0.6436 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8742    0.3605    1.0994 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2317   -1.1193    1.4604 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  1  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  2  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
M  END
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PDB for HMDB0253420 (Imidazolidine)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.830  -0.290   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
MASTER        0    0    0    0    0    0    0    0    5    0   10    0
END
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3D PDB for HMDB0253420 (Imidazolidine)

COMPND    HMDB0253420
HETATM    1  C1  UNL     1      -0.683  -0.927  -0.321  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.926   0.565  -0.329  1.00  0.00           C  
HETATM    3  N1  UNL     1       0.373   1.150  -0.204  1.00  0.00           N  
HETATM    4  C3  UNL     1       1.297   0.132   0.196  1.00  0.00           C  
HETATM    5  N2  UNL     1       0.533  -1.078   0.447  1.00  0.00           N  
HETATM    6  H1  UNL     1      -1.538  -1.437   0.165  1.00  0.00           H  
HETATM    7  H2  UNL     1      -0.601  -1.335  -1.336  1.00  0.00           H  
HETATM    8  H3  UNL     1      -1.641   0.841   0.454  1.00  0.00           H  
HETATM    9  H4  UNL     1      -1.334   0.864  -1.325  1.00  0.00           H  
HETATM   10  H5  UNL     1       0.416   2.021   0.337  1.00  0.00           H  
HETATM   11  H6  UNL     1       1.999  -0.037  -0.644  1.00  0.00           H  
HETATM   12  H7  UNL     1       1.874   0.361   1.099  1.00  0.00           H  
HETATM   13  H8  UNL     1       0.232  -1.119   1.460  1.00  0.00           H  
CONECT    1    2    5    6    7
CONECT    2    3    8    9
CONECT    3    4   10
CONECT    4    5   11   12
CONECT    5   13
END
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SMILES for HMDB0253420 (Imidazolidine)

C1CNCN1
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INCHI for HMDB0253420 (Imidazolidine)

InChI=1S/C3H8N2/c1-2-5-3-4-1/h4-5H,1-3H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
ImidazolidinesHMDB
Chemical FormulaC3H8N2
Average Molecular Weight72.111
Monoisotopic Molecular Weight72.068748266
IUPAC Nameimidazolidine
Traditional Nameimidazolidine
CAS Registry NumberNot Available
SMILES
C1CNCN1
InChI Identifier
InChI=1S/C3H8N2/c1-2-5-3-4-1/h4-5H,1-3H2
InChI KeyWRYCSMQKUKOKBP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as imidazolidines. These are organic compounds containing an imidazolidine ring, which is a saturated ring (derived from imidazole) with two nitrogen atoms at positions 1 and 3 respectively, and containing only single bonds.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzolidines
Sub ClassImidazolidines
Direct ParentImidazolidines
Alternative Parents
Substituents
  • Imidazolidine
  • Azacycle
  • Secondary amine
  • Secondary aliphatic amine
  • Aminal
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID396007
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkImidazolidine
METLIN IDNot Available
PubChem Compound449488
PDB IDNot Available
ChEBI ID33137
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]