Showing metabocard for 4-Amino-2-methyl-5-phosphomethylpyrimidine (MMDBc0030012)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:50:38 UTC
Update Date2022-08-31 17:38:39 UTC
MiMeDB IDMMDBc0030012
Metabolite Identification
Common Name4-Amino-2-methyl-5-phosphomethylpyrimidine
Description4-amino-2-methyl-5-phosphomethylpyrimidine 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. Tomato LeTHIC is an Fe-requiring HMP-P synthase involved in thiamine synthesis and regulated by multiple factors. (PMID 21511719 ) Although each isoform independently can synthesize HMP pyrophosphate (HMP-PP) from HMP, there is a marked difference in efficiency between the two proteins. (PMID 15614489 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000564abd861b78>


  Mrv0541 01211515292D          

 14 14  0  0  0  0            999 V2000
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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
    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 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.1250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.2539    3.3000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.6039    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  2  0  0  0  0
  8  2  1  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
  9  6  1  0  0  0  0
 13  3  1  0  0  0  0
 14 10  1  0  0  0  0
 14 11  1  0  0  0  0
 14 12  2  0  0  0  0
 14 13  1  0  0  0  0
M  CHG  2  10  -1  11  -1
M  END
Download

3D MOL for #<Metabolite:0x0000564abd861b78>

HMDB0304169
     RDKit          3D
4-amino-2-methyl-5-phosphomethylpyrimidine
 22 22  0  0  0  0  0  0  0  0999 V2000
   -3.9596   -0.2883    0.8085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5062   -0.1051    0.5877 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8449    1.0304    0.8675 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5246    1.1766    0.6596 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1926    0.1347    0.1415 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6428    0.1607   -0.1354 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2388    1.3583    0.1797 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8816    1.2565   -0.1815 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.1621    2.1443   -1.3643 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3060   -0.3310   -0.6418 O   0  0  0  0  0  1  0  0  0  0  0  0
    4.8190    1.6545    1.1570 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.4852   -1.0371   -0.1481 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1059   -2.0740   -0.6395 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8182   -1.1535    0.0730 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3708    0.4182    1.5570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1087   -1.3411    1.1353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4459   -0.1825   -0.1899 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0046    2.1035    0.8901 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7571   -0.0828   -1.2290 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1378   -0.6853    0.3952 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1222   -2.1217   -0.8574 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3064   -2.0355   -0.1493 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
  7  8  1  0
  8  9  2  0
  8 10  1  0
  8 11  1  0
  5 12  1  0
 12 13  2  3
 12 14  1  0
 14  2  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  4 18  1  0
  6 19  1  0
  6 20  1  0
 13 21  1  0
 14 22  1  0
M  CHG  2  10  -1  11  -1
M  END
Download

3D SDF for #<Metabolite:0x0000564abd861b78>


  Mrv0541 01211515292D          

 14 14  0  0  0  0            999 V2000
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    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
    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 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.1250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.2539    3.3000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.6039    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  2  0  0  0  0
  8  2  1  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
  9  6  1  0  0  0  0
 13  3  1  0  0  0  0
 14 10  1  0  0  0  0
 14 11  1  0  0  0  0
 14 12  2  0  0  0  0
 14 13  1  0  0  0  0
M  CHG  2  10  -1  11  -1
M  END
> <DATABASE_ID>
MMDBc0030012

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=NC=C(COP([O-])([O-])=O)C(=N)N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H10N3O4P/c1-4-8-2-5(6(7)9-4)3-13-14(10,11)12/h2H,3H2,1H3,(H2,7,8,9)(H2,10,11,12)/p-2

> <INCHI_KEY>
PKYFHKIYHBRTPI-UHFFFAOYSA-L

> <FORMULA>
C6H8N3O4P

> <MOLECULAR_WEIGHT>
217.122

> <EXACT_MASS>
217.026339907

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
18.247583731001384

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl phosphate

> <ALOGPS_LOGP>
-0.59

> <JCHEM_LOGP>
-1.9571476964641903

> <ALOGPS_LOGS>
-1.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.3172349614948295

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.621124514300404

> <JCHEM_PKA_STRONGEST_BASIC>
12.199121172419524

> <JCHEM_POLAR_SURFACE_AREA>
120.66000000000001

> <JCHEM_REFRACTIVITY>
56.583000000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.32e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x0000564abd861b78>

HMDB0304169
     RDKit          3D
4-amino-2-methyl-5-phosphomethylpyrimidine
 22 22  0  0  0  0  0  0  0  0999 V2000
   -3.9596   -0.2883    0.8085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5062   -0.1051    0.5877 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8449    1.0304    0.8675 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5246    1.1766    0.6596 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1926    0.1347    0.1415 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6428    0.1607   -0.1354 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2388    1.3583    0.1797 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8816    1.2565   -0.1815 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.1621    2.1443   -1.3643 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3060   -0.3310   -0.6418 O   0  0  0  0  0  1  0  0  0  0  0  0
    4.8190    1.6545    1.1570 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.4852   -1.0371   -0.1481 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1059   -2.0740   -0.6395 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8182   -1.1535    0.0730 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3708    0.4182    1.5570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1087   -1.3411    1.1353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4459   -0.1825   -0.1899 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0046    2.1035    0.8901 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7571   -0.0828   -1.2290 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1378   -0.6853    0.3952 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1222   -2.1217   -0.8574 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3064   -2.0355   -0.1493 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
  7  8  1  0
  8  9  2  0
  8 10  1  0
  8 11  1  0
  5 12  1  0
 12 13  2  3
 12 14  1  0
 14  2  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  4 18  1  0
  6 19  1  0
  6 20  1  0
 13 21  1  0
 14 22  1  0
M  CHG  2  10  -1  11  -1
M  END
Download

PDB for #<Metabolite:0x0000564abd861b78>

HEADER    PROTEIN                                 21-JAN-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-JAN-15         0                                  
HETATM    1  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   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       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.334   2.310   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       2.667  -0.000   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       2.667   7.700   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       4.207   6.160   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0       1.127   6.160   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       2.667   6.160   0.000  0.00  0.00           P+0
CONECT    1    4                                                            
CONECT    2    5    8                                                       
CONECT    3    5   13                                                       
CONECT    4    1    8    9                                                  
CONECT    5    2    3    6                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6                                                            
CONECT    8    2    4                                                       
CONECT    9    4    6                                                       
CONECT   10   14                                                            
CONECT   11   14                                                            
CONECT   12   14                                                            
CONECT   13    3   14                                                       
CONECT   14   10   11   12   13                                             
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END
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3D PDB for #<Metabolite:0x0000564abd861b78>

COMPND    HMDB0304169
HETATM    1  C1  UNL     1      -3.960  -0.288   0.808  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.506  -0.105   0.588  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.845   1.030   0.867  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.525   1.177   0.660  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.193   0.135   0.141  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.643   0.161  -0.135  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.239   1.358   0.180  1.00  0.00           O  
HETATM    8  P1  UNL     1       3.882   1.257  -0.181  1.00  0.00           P  
HETATM    9  O2  UNL     1       4.162   2.144  -1.364  1.00  0.00           O  
HETATM   10  O3  UNL     1       4.306  -0.331  -0.642  1.00  0.00           O1-
HETATM   11  O4  UNL     1       4.819   1.655   1.157  1.00  0.00           O1-
HETATM   12  C6  UNL     1      -0.485  -1.037  -0.148  1.00  0.00           C  
HETATM   13  N2  UNL     1       0.106  -2.074  -0.640  1.00  0.00           N  
HETATM   14  N3  UNL     1      -1.818  -1.153   0.073  1.00  0.00           N  
HETATM   15  H1  UNL     1      -4.371   0.418   1.557  1.00  0.00           H  
HETATM   16  H2  UNL     1      -4.109  -1.341   1.135  1.00  0.00           H  
HETATM   17  H3  UNL     1      -4.446  -0.182  -0.190  1.00  0.00           H  
HETATM   18  H4  UNL     1       0.005   2.104   0.890  1.00  0.00           H  
HETATM   19  H5  UNL     1       1.757  -0.083  -1.229  1.00  0.00           H  
HETATM   20  H6  UNL     1       2.138  -0.685   0.395  1.00  0.00           H  
HETATM   21  H7  UNL     1       1.122  -2.122  -0.857  1.00  0.00           H  
HETATM   22  H8  UNL     1      -2.306  -2.036  -0.149  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3    3   14
CONECT    3    4
CONECT    4    5    5   18
CONECT    5    6   12
CONECT    6    7   19   20
CONECT    7    8
CONECT    8    9    9   10   11
CONECT   12   13   13   14
CONECT   13   21
CONECT   14   22
END
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SMILES for #<Metabolite:0x0000564abd861b78>

CC1=NC=C(COP([O-])([O-])=O)C(=N)N1
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INCHI for #<Metabolite:0x0000564abd861b78>

InChI=1S/C6H10N3O4P/c1-4-8-2-5(6(7)9-4)3-13-14(10,11)12/h2H,3H2,1H3,(H2,7,8,9)(H2,10,11,12)/p-2
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Synonyms
ValueSource
4-Amino-2-methyl-5-(phosphooxymethyl)pyrimidineChEBI
4-Amino-2-methyl-5-phosphonatooxymethylpyrimidineChEBI
4-Amino-2-methyl-5-phosphonatooxymethylpyrimidine dianionChEBI
4-amino-2-Methyl-5-(phosphonooxymethyl)pyrimidineChEBI
Chemical FormulaC6H8N3O4P
Average Molecular Weight217.122
Monoisotopic Molecular Weight217.026339907
IUPAC Name(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl phosphate
Traditional Name(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl phosphate
CAS Registry NumberNot Available
SMILES
CC1=NC=C(COP([O-])([O-])=O)C(=N)N1
InChI Identifier
InChI=1S/C6H10N3O4P/c1-4-8-2-5(6(7)9-4)3-13-14(10,11)12/h2H,3H2,1H3,(H2,7,8,9)(H2,10,11,12)/p-2
InChI KeyPKYFHKIYHBRTPI-UHFFFAOYSA-L