Showing metabocard for 4-Amino-5-hydroxymethyl-2-methylpyrimidine (MMDBc0030014)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:50:42 UTC
Update Date2022-08-31 17:38:40 UTC
Metabolite IDMMDBc0030014
Metabolite Identification
Common Name4-Amino-5-hydroxymethyl-2-methylpyrimidine
Description4-amino-5-hydroxymethyl-2-methylpyrimidine is a member of the chemical class known as Pyrimidines and Pyrimidine Derivatives. These are compounds containing a pyrimidne ring, which is a six-member aromatic heterocycle which consists of two nitrogen atoms (at positions 1 and 3) and four carbon atoms. The conversion of 5-aminoimidazole ribonucleotide (AIR) into 4-amino-2-methyl-5-hydroxymethylpyrimidine (HMP) is a fascinating reaction on the thiamin biosynthetic pathway in bacteria and is probably the most complex unresolved rearrangement in primary metabolism. (PMID 15326535 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x000055c79a112490>


  Mrv0541 02231215542D          

 10 10  0  0  0  0            999 V2000
    2.1434   -0.4125    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
    0.7145   -0.4125    0.0000 N   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
    0.0000    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    0.8250    0.0000 O   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
    0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  2 10  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x000055c79a112490>

HMDB0247327
     RDKit          3D
4-Amino-5-hydroxymethyl-2-methylpyrimidine
 19 19  0  0  0  0  0  0  0  0999 V2000
   -3.4139   -0.0017    0.3196 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9531   -0.0019    0.0317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5209   -0.1065   -1.2300 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1716   -0.1304   -1.5340 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7855   -0.0444   -0.5563 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2249   -0.1178   -0.8991 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9393    0.9565   -0.3161 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3206    0.0648    0.7639 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2563    0.1828    1.8149 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0217    0.0792    0.9864 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6775   -0.7594    1.1285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7426    1.0123    0.6012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9743   -0.3606   -0.5627 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0537   -0.2217   -2.5778 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2891    0.0820   -2.0335 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6911   -1.1092   -0.7140 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6584    0.5643    0.3058 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3259    1.0522    2.4228 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9306   -0.5702    2.0488 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  2  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  8  9  1  0
  8 10  2  0
 10  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  4 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  9 18  1  0
  9 19  1  0
M  END
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3D SDF for #<Metabolite:0x000055c79a112490>


  Mrv0541 02231215542D          

 10 10  0  0  0  0            999 V2000
    2.1434   -0.4125    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
    0.7145   -0.4125    0.0000 N   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
    0.0000    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    0.8250    0.0000 O   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
    0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  2 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030014

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=NC=C(CO)C(N)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H9N3O/c1-4-8-2-5(3-10)6(7)9-4/h2,10H,3H2,1H3,(H2,7,8,9)

> <INCHI_KEY>
VUTBELPREDJDDH-UHFFFAOYSA-N

> <FORMULA>
C6H9N3O

> <MOLECULAR_WEIGHT>
139.1552

> <EXACT_MASS>
139.074561925

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
14.197332243457687

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4-amino-2-methylpyrimidin-5-yl)methanol

> <ALOGPS_LOGP>
-0.26

> <JCHEM_LOGP>
-0.36044671066666667

> <ALOGPS_LOGS>
-1.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.411032868169844

> <JCHEM_PKA_STRONGEST_BASIC>
6.17188544677804

> <JCHEM_POLAR_SURFACE_AREA>
72.03

> <JCHEM_REFRACTIVITY>
39.1765

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.20e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
toxopyrimidine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x000055c79a112490>

HMDB0247327
     RDKit          3D
4-Amino-5-hydroxymethyl-2-methylpyrimidine
 19 19  0  0  0  0  0  0  0  0999 V2000
   -3.4139   -0.0017    0.3196 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9531   -0.0019    0.0317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5209   -0.1065   -1.2300 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1716   -0.1304   -1.5340 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7855   -0.0444   -0.5563 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2249   -0.1178   -0.8991 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9393    0.9565   -0.3161 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3206    0.0648    0.7639 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2563    0.1828    1.8149 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0217    0.0792    0.9864 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6775   -0.7594    1.1285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7426    1.0123    0.6012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9743   -0.3606   -0.5627 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0537   -0.2217   -2.5778 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2891    0.0820   -2.0335 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6911   -1.1092   -0.7140 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6584    0.5643    0.3058 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3259    1.0522    2.4228 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9306   -0.5702    2.0488 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  2  0
  5  6  1  0
  6  7  1  0
  5  8  1  0
  8  9  1  0
  8 10  2  0
 10  2  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  4 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
  9 18  1  0
  9 19  1  0
M  END
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PDB for #<Metabolite:0x000055c79a112490>

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    2                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for #<Metabolite:0x000055c79a112490>

COMPND    HMDB0247327
HETATM    1  C1  UNL     1      -3.414  -0.002   0.320  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.953  -0.002   0.032  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.521  -0.107  -1.230  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.172  -0.130  -1.534  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.786  -0.044  -0.556  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.225  -0.118  -0.899  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.939   0.957  -0.316  1.00  0.00           O  
HETATM    8  C6  UNL     1       0.321   0.065   0.764  1.00  0.00           C  
HETATM    9  N2  UNL     1       1.256   0.183   1.815  1.00  0.00           N  
HETATM   10  N3  UNL     1      -1.022   0.079   0.986  1.00  0.00           N  
HETATM   11  H1  UNL     1      -3.677  -0.759   1.128  1.00  0.00           H  
HETATM   12  H2  UNL     1      -3.743   1.012   0.601  1.00  0.00           H  
HETATM   13  H3  UNL     1      -3.974  -0.361  -0.563  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.054  -0.222  -2.578  1.00  0.00           H  
HETATM   15  H5  UNL     1       2.289   0.082  -2.034  1.00  0.00           H  
HETATM   16  H6  UNL     1       2.691  -1.109  -0.714  1.00  0.00           H  
HETATM   17  H7  UNL     1       3.658   0.564   0.306  1.00  0.00           H  
HETATM   18  H8  UNL     1       1.326   1.052   2.423  1.00  0.00           H  
HETATM   19  H9  UNL     1       1.931  -0.570   2.049  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    3   10
CONECT    3    4
CONECT    4    5    5   14
CONECT    5    6    8
CONECT    6    7   15   16
CONECT    7   17
CONECT    8    9   10   10
CONECT    9   18   19
END
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SMILES for #<Metabolite:0x000055c79a112490>

CC1=NC=C(CO)C(N)=N1
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INCHI for #<Metabolite:0x000055c79a112490>

InChI=1S/C6H9N3O/c1-4-8-2-5(3-10)6(7)9-4/h2,10H,3H2,1H3,(H2,7,8,9)
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Synonyms
ValueSource
2-Methyl-4-amino-5-hydroxymethylpyrimidineChEBI
4-Amino-2-methyl-5-hydroxymethylpyrimidineChEBI
4-Amino-2-methyl-5-pyrimidinemethanolChEBI
AtoxopyrimidineChEBI
PyraminChEBI
PyramineChEBI
ToxopyrimidineChEBI
HMPKegg
HMP CPDHMDB
Molecular FormulaC6H9N3O
Average Mass139.1552
Monoisotopic Mass139.074561925
IUPAC Name(4-amino-2-methylpyrimidin-5-yl)methanol
Traditional Nametoxopyrimidine
CAS Registry Number73-67-6
SMILES
CC1=NC=C(CO)C(N)=N1
InChI Identifier
InChI=1S/C6H9N3O/c1-4-8-2-5(3-10)6(7)9-4/h2,10H,3H2,1H3,(H2,7,8,9)
InChI KeyVUTBELPREDJDDH-UHFFFAOYSA-N