Showing metabocard for 4-amino-5-phosphonooxymethyl-2-methylpyrimidine (MMDBc0031750)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-18 01:47:43 UTC
Update Date2024-04-30 19:51:53 UTC
Metabolite IDMMDBc0031750
Metabolite Identification
Common Name4-amino-5-phosphonooxymethyl-2-methylpyrimidine
DescriptionAn aminopyrimidine that is pyrimidine in which the hydrogens at positions 2, 4, and 5 are replaced by methyl, amino, and hydroxymethyl substituents, respectively
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f92522a71f0>

Structure #1
  Mrv0541 02241206592D          

 14 14  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
    1.4289    0.0000    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
    0.7145    1.2375    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
    0.0000    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
    1.4289    0.8250    0.0000 N   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
    0.0000   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  8  1  0  0  0  0
  3  5  1  0  0  0  0
  3 13  1  0  0  0  0
  4  8  2  0  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  9  1  0  0  0  0
 10 14  1  0  0  0  0
 11 14  1  0  0  0  0
 12 14  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f92522a71f0>

HMDB0243613
     RDKit          3D
(4-Amino-2-methylpyrimidin-5-YL)methyl dihydrogen phosphate
 24 24  0  0  0  0  0  0  0  0999 V2000
    4.2986    0.1545    0.9893 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8192    0.0389    0.7469 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9692   -0.3569    1.6877 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6482   -0.4452    1.4224 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1758   -0.1219    0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2606   -0.1960   -0.1969 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0453   -0.6211    0.8676 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6514   -0.6736    0.3650 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.1723   -2.0880    0.2922 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6097    0.1581    1.4777 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8210    0.0744   -1.1296 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0546    0.2889   -0.8145 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6348    0.5945   -1.9929 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3562    0.3498   -0.4673 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5950   -0.2792    1.9484 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6005    1.2382    0.9440 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7835   -0.3278    0.1134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0714   -0.7670    2.1753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3532   -0.8840   -1.0722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5777    0.8072   -0.5513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0297    0.8257    1.9325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9864    1.0421   -1.0601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3837    0.5232   -2.1872 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0268    0.6652   -1.2199 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
 10 21  1  0
 11 22  1  0
 13 23  1  0
 14 24  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f92522a71f0>

Structure #1
  Mrv0541 02241206592D          

 14 14  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
    1.4289    0.0000    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
    0.7145    1.2375    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
    0.0000    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
    1.4289    0.8250    0.0000 N   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
    0.0000   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  8  1  0  0  0  0
  3  5  1  0  0  0  0
  3 13  1  0  0  0  0
  4  8  2  0  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  9  1  0  0  0  0
 10 14  1  0  0  0  0
 11 14  1  0  0  0  0
 12 14  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031750

> <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)

> <INCHI_KEY>
PKYFHKIYHBRTPI-UHFFFAOYSA-N

> <FORMULA>
C6H10N3O4P

> <MOLECULAR_WEIGHT>
219.1351

> <EXACT_MASS>
219.040892335

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
18.825297834219008

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methoxy]phosphonic acid

> <ALOGPS_LOGP>
-1.06

> <JCHEM_LOGP>
-1.8085892731666544

> <ALOGPS_LOGS>
-2.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.613949242433612

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6236681682608518

> <JCHEM_PKA_STRONGEST_BASIC>
7.588072702550217

> <JCHEM_POLAR_SURFACE_AREA>
115.00000000000001

> <JCHEM_REFRACTIVITY>
58.8264

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.57e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f92522a71f0>

HMDB0243613
     RDKit          3D
(4-Amino-2-methylpyrimidin-5-YL)methyl dihydrogen phosphate
 24 24  0  0  0  0  0  0  0  0999 V2000
    4.2986    0.1545    0.9893 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8192    0.0389    0.7469 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9692   -0.3569    1.6877 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6482   -0.4452    1.4224 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1758   -0.1219    0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2606   -0.1960   -0.1969 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0453   -0.6211    0.8676 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6514   -0.6736    0.3650 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.1723   -2.0880    0.2922 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6097    0.1581    1.4777 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8210    0.0744   -1.1296 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0546    0.2889   -0.8145 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6348    0.5945   -1.9929 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3562    0.3498   -0.4673 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5950   -0.2792    1.9484 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6005    1.2382    0.9440 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7835   -0.3278    0.1134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0714   -0.7670    2.1753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3532   -0.8840   -1.0722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5777    0.8072   -0.5513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0297    0.8257    1.9325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9864    1.0421   -1.0601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3837    0.5232   -2.1872 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0268    0.6652   -1.2199 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
 10 21  1  0
 11 22  1  0
 13 23  1  0
 14 24  1  0
M  END
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PDB for #<Metabolite:0x00007f92522a71f0>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       1.334   3.850   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  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       0.000  -6.160   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -1.540  -4.620   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.540  -4.620   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       0.000  -4.620   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:0x00007f92522a71f0>

COMPND    HMDB0243613
HETATM    1  C1  UNL     1       4.299   0.155   0.989  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.819   0.039   0.747  1.00  0.00           C  
HETATM    3  N1  UNL     1       1.969  -0.357   1.688  1.00  0.00           N  
HETATM    4  C3  UNL     1       0.648  -0.445   1.422  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.176  -0.122   0.163  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.261  -0.196  -0.197  1.00  0.00           C  
HETATM    7  O1  UNL     1      -2.045  -0.621   0.868  1.00  0.00           O  
HETATM    8  P1  UNL     1      -3.651  -0.674   0.365  1.00  0.00           P  
HETATM    9  O2  UNL     1      -4.172  -2.088   0.292  1.00  0.00           O  
HETATM   10  O3  UNL     1      -4.610   0.158   1.478  1.00  0.00           O  
HETATM   11  O4  UNL     1      -3.821   0.074  -1.130  1.00  0.00           O  
HETATM   12  C6  UNL     1       1.055   0.289  -0.814  1.00  0.00           C  
HETATM   13  N2  UNL     1       0.635   0.594  -1.993  1.00  0.00           N  
HETATM   14  N3  UNL     1       2.356   0.350  -0.467  1.00  0.00           N  
HETATM   15  H1  UNL     1       4.595  -0.279   1.948  1.00  0.00           H  
HETATM   16  H2  UNL     1       4.601   1.238   0.944  1.00  0.00           H  
HETATM   17  H3  UNL     1       4.784  -0.328   0.113  1.00  0.00           H  
HETATM   18  H4  UNL     1      -0.071  -0.767   2.175  1.00  0.00           H  
HETATM   19  H5  UNL     1      -1.353  -0.884  -1.072  1.00  0.00           H  
HETATM   20  H6  UNL     1      -1.578   0.807  -0.551  1.00  0.00           H  
HETATM   21  H7  UNL     1      -4.030   0.826   1.932  1.00  0.00           H  
HETATM   22  H8  UNL     1      -3.986   1.042  -1.060  1.00  0.00           H  
HETATM   23  H9  UNL     1      -0.384   0.523  -2.187  1.00  0.00           H  
HETATM   24  H10 UNL     1       3.027   0.665  -1.220  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   10   21
CONECT   11   22
CONECT   12   13   13   14
CONECT   13   23
CONECT   14   24
END
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SMILES for #<Metabolite:0x00007f92522a71f0>

CC1=NC=C(COP(O)(O)=O)C(=N)N1
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INCHI for #<Metabolite:0x00007f92522a71f0>

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)
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Synonyms
ValueSource
4-Amino-2-methyl-5-hydroxymethylpyrimidine phosphateChEBI
4-Amino-2-methyl-5-phosphonooxymethylpyrimidineChEBI
4-Amino-5-phosphomethyl-2-methylpyrimidineChEBI
HMP-pChEBI
(4-Amino-2-methylpyrimidin-5-yl)methyl phosphateKegg
4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphateKegg
4-Amino-2-methyl-5-hydroxymethylpyrimidine phosphoric acidGenerator
(4-Amino-2-methylpyrimidin-5-yl)methyl phosphoric acidGenerator
4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphoric acidGenerator
4-Amino-2-methyl-5-phosphomethylpyrimidineChEBI
Molecular FormulaC6H10N3O4P
Average Mass219.1351
Monoisotopic Mass219.040892335
IUPAC Name[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methoxy]phosphonic acid
Traditional Name(4-imino-2-methyl-3H-pyrimidin-5-yl)methoxyphosphonic acid
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)
InChI KeyPKYFHKIYHBRTPI-UHFFFAOYSA-N