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Showing metabocard for 6-hydroxymethyl-7,8-dihydropterin (HMDB0304227)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 08:10:47 UTC
Update Date2021-09-24 08:10:47 UTC
HMDB IDHMDB0304227
Secondary Accession NumbersNone
Metabolite Identification
Common Name6-hydroxymethyl-7,8-dihydropterin
Description2-amino-6-(hydroxymethyl)-7,8-dihydropteridin-4-ol, also known as hmdp cpd, belongs to pterins and derivatives class of compounds. Those are polycyclic aromatic compounds containing a pterin moiety, which consist of a pteridine ring bearing a ketone and an amine group to form 2-aminopteridin-4(3H)-one. 2-amino-6-(hydroxymethyl)-7,8-dihydropteridin-4-ol is slightly soluble (in water) and a very weakly acidic compound (based on its pKa). 2-amino-6-(hydroxymethyl)-7,8-dihydropteridin-4-ol can be found in a number of food items such as cardoon, sunburst squash (pattypan squash), climbing bean, and fenugreek, which makes 2-amino-6-(hydroxymethyl)-7,8-dihydropteridin-4-ol a potential biomarker for the consumption of these food products. 2-amino-6-(hydroxymethyl)-7,8-dihydropteridin-4-ol exists in E.coli (prokaryote) and yeast (eukaryote).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304227 (6-hydroxymethyl-7,8-dihydropterin)

  Mrv1652303082008122D          

 14 15  0  0  0  0            999 V2000
   -1.4289   -1.6500    0.0000 N   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   -1.6500    0.0000 N   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
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    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
    2.8579    0.8250    0.0000 O   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   -1.6500    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 O   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  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  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
  5 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
  2 14  1  0  0  0  0
M  END
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3D MOL for HMDB0304227 (6-hydroxymethyl-7,8-dihydropterin)

HMDB0304227
     RDKit          3D
6-hydroxymethyl-7,8-dihydropterin
 23 24  0  0  0  0  0  0  0  0999 V2000
   -4.0941    0.7719    1.0873 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8339    0.4073    0.5216 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6684    0.6575    1.1560 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4780    0.3030    0.6018 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5003   -0.3185   -0.6257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6887   -0.5820   -1.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6587   -1.1523   -2.4091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8265   -0.2027   -0.6795 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7623   -0.6666   -1.1586 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8779   -0.4465   -0.5897 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1733   -0.8755   -1.2779 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9880    0.2057   -1.5068 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9943    0.2045    0.7074 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7328    0.5685    1.2716 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8343    1.2140    0.4973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3368    0.6212    2.0903 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7576   -0.3792   -1.1401 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9455   -1.3855   -2.2132 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6704   -1.5236   -0.5284 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7086    1.0423   -1.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4726   -0.5719    1.3954 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7179    1.0610    0.6976 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6337    1.0475    2.2031 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  2  0
  6  8  1  0
  5  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
  8  2  1  0
 14  4  1  0
  1 15  1  0
  1 16  1  0
  8 17  1  0
 11 18  1  0
 11 19  1  0
 12 20  1  0
 13 21  1  0
 13 22  1  0
 14 23  1  0
M  END
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3D SDF for HMDB0304227 (6-hydroxymethyl-7,8-dihydropterin)

  Mrv1652303082008122D          

 14 15  0  0  0  0            999 V2000
   -1.4289   -1.6500    0.0000 N   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   -1.6500    0.0000 N   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
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    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
    2.8579    0.8250    0.0000 O   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   -1.6500    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 O   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  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  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
  5 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
  2 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304227

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC2=C(N=C(CO)CN2)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C7H9N5O2/c8-7-11-5-4(6(14)12-7)10-3(2-13)1-9-5/h13H,1-2H2,(H4,8,9,11,12,14)

> <INCHI_KEY>
CQQNNQTXUGLUEV-UHFFFAOYSA-N

> <FORMULA>
C7H9N5O2

> <MOLECULAR_WEIGHT>
195.1787

> <EXACT_MASS>
195.075624557

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
18.400015811514606

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-6-(hydroxymethyl)-3,4,7,8-tetrahydropteridin-4-one

> <ALOGPS_LOGP>
-1.69

> <JCHEM_LOGP>
-1.8859297996666662

> <ALOGPS_LOGS>
-1.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.259137167948449

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.624953086632588

> <JCHEM_PKA_STRONGEST_BASIC>
0.7635096882825214

> <JCHEM_POLAR_SURFACE_AREA>
112.1

> <JCHEM_REFRACTIVITY>
57.856899999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.47e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-amino-6-(hydroxymethyl)-7,8-dihydro-3H-pteridin-4-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0304227 (6-hydroxymethyl-7,8-dihydropterin)

HMDB0304227
     RDKit          3D
6-hydroxymethyl-7,8-dihydropterin
 23 24  0  0  0  0  0  0  0  0999 V2000
   -4.0941    0.7719    1.0873 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8339    0.4073    0.5216 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6684    0.6575    1.1560 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4780    0.3030    0.6018 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5003   -0.3185   -0.6257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6887   -0.5820   -1.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6587   -1.1523   -2.4091 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8265   -0.2027   -0.6795 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7623   -0.6666   -1.1586 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8779   -0.4465   -0.5897 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1733   -0.8755   -1.2779 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9880    0.2057   -1.5068 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9943    0.2045    0.7074 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7328    0.5685    1.2716 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8343    1.2140    0.4973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3368    0.6212    2.0903 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7576   -0.3792   -1.1401 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9455   -1.3855   -2.2132 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6704   -1.5236   -0.5284 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7086    1.0423   -1.0952 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4726   -0.5719    1.3954 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7179    1.0610    0.6976 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6337    1.0475    2.2031 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  2  0
  6  8  1  0
  5  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
 13 14  1  0
  8  2  1  0
 14  4  1  0
  1 15  1  0
  1 16  1  0
  8 17  1  0
 11 18  1  0
 11 19  1  0
 12 20  1  0
 13 21  1  0
 13 22  1  0
 14 23  1  0
M  END
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PDB for HMDB0304227 (6-hydroxymethyl-7,8-dihydropterin)

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  N   UNK     0      -2.667  -3.080   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       0.000  -3.080   0.000  0.00  0.00           N+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  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       2.667  -3.080   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6   12                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8                                                            
CONECT   10    7   11                                                       
CONECT   11   10    4                                                       
CONECT   12    5   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    2                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END
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3D PDB for HMDB0304227 (6-hydroxymethyl-7,8-dihydropterin)

COMPND    HMDB0304227
HETATM    1  N1  UNL     1      -4.094   0.772   1.087  1.00  0.00           N  
HETATM    2  C1  UNL     1      -2.834   0.407   0.522  1.00  0.00           C  
HETATM    3  N2  UNL     1      -1.668   0.658   1.156  1.00  0.00           N  
HETATM    4  C2  UNL     1      -0.478   0.303   0.602  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.500  -0.318  -0.626  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.689  -0.582  -1.289  1.00  0.00           C  
HETATM    7  O1  UNL     1      -1.659  -1.152  -2.409  1.00  0.00           O  
HETATM    8  N3  UNL     1      -2.827  -0.203  -0.679  1.00  0.00           N  
HETATM    9  N4  UNL     1       0.762  -0.667  -1.159  1.00  0.00           N  
HETATM   10  C5  UNL     1       1.878  -0.447  -0.590  1.00  0.00           C  
HETATM   11  C6  UNL     1       3.173  -0.875  -1.278  1.00  0.00           C  
HETATM   12  O2  UNL     1       3.988   0.206  -1.507  1.00  0.00           O  
HETATM   13  C7  UNL     1       1.994   0.204   0.707  1.00  0.00           C  
HETATM   14  N5  UNL     1       0.733   0.569   1.272  1.00  0.00           N  
HETATM   15  H1  UNL     1      -4.834   1.214   0.497  1.00  0.00           H  
HETATM   16  H2  UNL     1      -4.337   0.621   2.090  1.00  0.00           H  
HETATM   17  H3  UNL     1      -3.758  -0.379  -1.140  1.00  0.00           H  
HETATM   18  H4  UNL     1       2.945  -1.386  -2.213  1.00  0.00           H  
HETATM   19  H5  UNL     1       3.670  -1.524  -0.528  1.00  0.00           H  
HETATM   20  H6  UNL     1       3.709   1.042  -1.095  1.00  0.00           H  
HETATM   21  H7  UNL     1       2.473  -0.572   1.395  1.00  0.00           H  
HETATM   22  H8  UNL     1       2.718   1.061   0.698  1.00  0.00           H  
HETATM   23  H9  UNL     1       0.634   1.047   2.203  1.00  0.00           H  
CONECT    1    2   15   16
CONECT    2    3    3    8
CONECT    3    4
CONECT    4    5    5   14
CONECT    5    6    9
CONECT    6    7    7    8
CONECT    8   17
CONECT    9   10   10
CONECT   10   11   13
CONECT   11   12   18   19
CONECT   12   20
CONECT   13   14   21   22
CONECT   14   23
END
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SMILES for HMDB0304227 (6-hydroxymethyl-7,8-dihydropterin)

NC1=NC2=C(N=C(CO)CN2)C(=O)N1
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INCHI for HMDB0304227 (6-hydroxymethyl-7,8-dihydropterin)

InChI=1S/C7H9N5O2/c8-7-11-5-4(6(14)12-7)10-3(2-13)1-9-5/h13H,1-2H2,(H4,8,9,11,12,14)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridineChEBI
HMDP CPDMeSH
Chemical FormulaC7H9N5O2
Average Molecular Weight195.1787
Monoisotopic Molecular Weight195.075624557
IUPAC Name2-amino-6-(hydroxymethyl)-3,4,7,8-tetrahydropteridin-4-one
Traditional Name2-amino-6-(hydroxymethyl)-7,8-dihydro-3H-pteridin-4-one
CAS Registry NumberNot Available
SMILES
NC1=NC2=C(N=C(CO)CN2)C(=O)N1
InChI Identifier
InChI=1S/C7H9N5O2/c8-7-11-5-4(6(14)12-7)10-3(2-13)1-9-5/h13H,1-2H2,(H4,8,9,11,12,14)
InChI KeyCQQNNQTXUGLUEV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pterins and derivatives. These are polycyclic aromatic compounds containing a pterin moiety, which consist of a pteridine ring bearing a ketone and an amine group to form 2-aminopteridin-4(3H)-one.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPteridines and derivatives
Sub ClassPterins and derivatives
Direct ParentPterins and derivatives
Alternative Parents
Substituents
  • Pterin
  • Secondary aliphatic/aromatic amine
  • Hydroxypyrimidine
  • Pyrimidine
  • Heteroaromatic compound
  • Ketimine
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Secondary amine
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Imine
  • Amine
  • Hydrocarbon derivative
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
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 LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB02119
Phenol Explorer Compound IDNot Available
FooDB IDFDB030597
KNApSAcK IDC00007501
Chemspider ID213
KEGG Compound IDC01300
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID17083
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 ReferencesNot Available