Hmdb loader

Showing metabocard for Crimidine (HMDB0250537)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 07:34:09 UTC
Update Date2021-09-26 23:02:03 UTC
HMDB IDHMDB0250537
Secondary Accession NumbersNone
Metabolite Identification
Common NameCrimidine
Description2-chloro-N,N,6-trimethylpyrimidin-4-amine belongs to the class of organic compounds known as dialkylarylamines. These are aliphatic aromatic amines in which the amino group is linked to two aliphatic chains and one aromatic group. Based on a literature review very few articles have been published on 2-chloro-N,N,6-trimethylpyrimidin-4-amine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Crimidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Crimidine 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0250537 (Crimidine)

  Mrv1572004191601152D          

 11 11  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
  8  7  1  0  0  0  0
  9  5  1  0  0  0  0
  9  7  2  0  0  0  0
 10  6  2  0  0  0  0
 10  7  1  0  0  0  0
 11  2  1  0  0  0  0
 11  3  1  0  0  0  0
 11  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0250537 (Crimidine)

HMDB0250537
     RDKit          3D
Crimidine
 21 21  0  0  0  0  0  0  0  0999 V2000
    3.3041    0.1236   -0.6805 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9913    0.5081   -0.1097 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8252   -0.2036   -0.3364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3843    0.1960    0.2269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6014   -0.4848    0.0164 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7579   -1.8441    0.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6930    0.1759   -0.6309 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3686    1.2923    0.9919 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7473    2.0049    1.2302 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7106    3.4334    2.2378 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.9119    1.5864    0.6646 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9106    0.9794   -1.0278 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8525   -0.4607    0.1137 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1916   -0.6155   -1.5187 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8461   -1.0806   -0.9544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8873   -2.5477   -0.4102 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8474   -2.2277    0.9844 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6036   -1.9928    1.1640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6741    0.0232   -0.0907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8888   -0.1537   -1.6668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5849    1.2881   -0.6664 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  4  8  2  0
  8  9  1  0
  9 10  1  0
  9 11  2  0
 11  2  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  6 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  7 21  1  0
M  END
Download

3D SDF for HMDB0250537 (Crimidine)

  Mrv1572004191601152D          

 11 11  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
  8  7  1  0  0  0  0
  9  5  1  0  0  0  0
  9  7  2  0  0  0  0
 10  6  2  0  0  0  0
 10  7  1  0  0  0  0
 11  2  1  0  0  0  0
 11  3  1  0  0  0  0
 11  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250537

> <DATABASE_NAME>
hmdb

> <SMILES>
CN(C)C1=NC(Cl)=NC(C)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C7H10ClN3/c1-5-4-6(11(2)3)10-7(8)9-5/h4H,1-3H3

> <INCHI_KEY>
HJIUPFPIEBPYIE-UHFFFAOYSA-N

> <FORMULA>
C7H10ClN3

> <MOLECULAR_WEIGHT>
171.63

> <EXACT_MASS>
171.056325

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
17.57656856101646

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-chloro-N,N,6-trimethylpyrimidin-4-amine

> <ALOGPS_LOGP>
2.07

> <JCHEM_LOGP>
1.7921573589999997

> <ALOGPS_LOGS>
-0.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
3.3340171842478936

> <JCHEM_POLAR_SURFACE_AREA>
29.020000000000003

> <JCHEM_REFRACTIVITY>
47.55449999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.10e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
crimidine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0250537 (Crimidine)

HMDB0250537
     RDKit          3D
Crimidine
 21 21  0  0  0  0  0  0  0  0999 V2000
    3.3041    0.1236   -0.6805 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9913    0.5081   -0.1097 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8252   -0.2036   -0.3364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3843    0.1960    0.2269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6014   -0.4848    0.0164 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7579   -1.8441    0.4625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6930    0.1759   -0.6309 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3686    1.2923    0.9919 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7473    2.0049    1.2302 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7106    3.4334    2.2378 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.9119    1.5864    0.6646 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9106    0.9794   -1.0278 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8525   -0.4607    0.1137 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1916   -0.6155   -1.5187 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8461   -1.0806   -0.9544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8873   -2.5477   -0.4102 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8474   -2.2277    0.9844 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6036   -1.9928    1.1640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6741    0.0232   -0.0907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8888   -0.1537   -1.6668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5849    1.2881   -0.6664 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  4  8  2  0
  8  9  1  0
  9 10  1  0
  9 11  2  0
 11  2  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  6 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  7 21  1  0
M  END
Download

PDB for HMDB0250537 (Crimidine)

HEADER    PROTEIN                                 19-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-16         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8 Cl   UNK     0      -1.334  -0.770   0.000  0.00  0.00          Cl+0
HETATM    9  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       4.001  -0.770   0.000  0.00  0.00           N+0
CONECT    1    5                                                            
CONECT    2   11                                                            
CONECT    3   11                                                            
CONECT    4    5    6                                                       
CONECT    5    1    4    9                                                  
CONECT    6    4   10   11                                                  
CONECT    7    8    9   10                                                  
CONECT    8    7                                                            
CONECT    9    5    7                                                       
CONECT   10    6    7                                                       
CONECT   11    2    3    6                                                  
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
Download

3D PDB for HMDB0250537 (Crimidine)

COMPND    HMDB0250537
HETATM    1  C1  UNL     1       3.304   0.124  -0.681  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.991   0.508  -0.110  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.825  -0.204  -0.336  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.384   0.196   0.227  1.00  0.00           C  
HETATM    5  N1  UNL     1      -1.601  -0.485   0.016  1.00  0.00           N  
HETATM    6  C5  UNL     1      -1.758  -1.844   0.462  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.693   0.176  -0.631  1.00  0.00           C  
HETATM    8  N2  UNL     1      -0.369   1.292   0.992  1.00  0.00           N  
HETATM    9  C7  UNL     1       0.747   2.005   1.230  1.00  0.00           C  
HETATM   10 CL1  UNL     1       0.711   3.433   2.238  1.00  0.00          CL  
HETATM   11  N3  UNL     1       1.912   1.586   0.665  1.00  0.00           N  
HETATM   12  H1  UNL     1       3.911   0.979  -1.028  1.00  0.00           H  
HETATM   13  H2  UNL     1       3.852  -0.461   0.114  1.00  0.00           H  
HETATM   14  H3  UNL     1       3.192  -0.616  -1.519  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.846  -1.081  -0.954  1.00  0.00           H  
HETATM   16  H5  UNL     1      -1.887  -2.548  -0.410  1.00  0.00           H  
HETATM   17  H6  UNL     1      -0.847  -2.228   0.984  1.00  0.00           H  
HETATM   18  H7  UNL     1      -2.604  -1.993   1.164  1.00  0.00           H  
HETATM   19  H8  UNL     1      -3.674   0.023  -0.091  1.00  0.00           H  
HETATM   20  H9  UNL     1      -2.889  -0.154  -1.667  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.585   1.288  -0.666  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    3   11
CONECT    3    4   15
CONECT    4    5    8    8
CONECT    5    6    7
CONECT    6   16   17   18
CONECT    7   19   20   21
CONECT    8    9
CONECT    9   10   11   11
END
Download

SMILES for HMDB0250537 (Crimidine)

CN(C)C1=NC(Cl)=NC(C)=C1
Download

INCHI for HMDB0250537 (Crimidine)

InChI=1S/C7H10ClN3/c1-5-4-6(11(2)3)10-7(8)9-5/h4H,1-3H3
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
CastrixMeSH
CrimidineMeSH
Chemical FormulaC7H10ClN3
Average Molecular Weight171.63
Monoisotopic Molecular Weight171.056325
IUPAC Name2-chloro-N,N,6-trimethylpyrimidin-4-amine
Traditional Namecrimidine
CAS Registry NumberNot Available
SMILES
CN(C)C1=NC(Cl)=NC(C)=C1
InChI Identifier
InChI=1S/C7H10ClN3/c1-5-4-6(11(2)3)10-7(8)9-5/h4H,1-3H3
InChI KeyHJIUPFPIEBPYIE-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dialkylarylamines. These are aliphatic aromatic amines in which the amino group is linked to two aliphatic chains and one aromatic group.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct ParentDialkylarylamines
Alternative Parents
Substituents
  • Dialkylarylamine
  • Aminopyrimidine
  • 2-halopyrimidine
  • Halopyrimidine
  • Aryl chloride
  • Aryl halide
  • Pyrimidine
  • Imidolactam
  • Heteroaromatic compound
  • Organoheterocyclic compound
  • Azacycle
  • Organopnictogen compound
  • Organochloride
  • Organohalogen compound
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic 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 ID10356
KEGG Compound IDC19138
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
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 ]