Showing metabocard for Glycylproline (MMDBc0000145)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:37:31 UTC
Update Date2024-04-30 19:31:12 UTC
Metabolite IDMMDBc0000145
Metabolite Identification
Common NameGlycylproline
DescriptionGlycylproline is a dipeptide composed of glycine and proline, and is an end product of collagen metabolism that is further cleaved by prolidase (EC 3.4.13.9). The resulting proline molecules are recycled into collagen or other proteins. Prolidase deficiency is a rare autosomal recessive disease characterized by chronic ulcerative dermatitis, mental retardation, frequent infections, and massive urinary excretion of iminodipeptides. Patients with this disease have reportedly decreased prolidase enzyme activity against glycylproline (Gly-Pro). The enzyme's activity against other substrates is not as affected. Some patients with prolidase deficiency have a marked urinary excretion of glycylproline. Patients with pressure sores contain significantly more urinary glycylproline than the control (PMID: 16009141 , 7629169 , 1536787 , 10582130 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9250d0c098>

      
  Mrv1652305271900142D          

 12 12  0  0  0  0            999 V2000
 2499.5974 2500.8461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2498.8823 2501.2578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2498.1613 2500.8583    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2500.3123 2501.2578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2501.1237 2500.0183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2501.8386 2499.6067    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2501.1237 2500.8440    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2499.5797 2500.0085    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2498.9124 2499.5234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2499.1673 2498.7389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2499.9923 2498.7389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2500.2471 2499.5234    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  2  0  0  0  0
  2  3  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  8  9  1  0  0  0  0
  8 12  1  0  0  0  0
 12  5  1  6  0  0  0
  1  8  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f9250d0c098>

HMDB0000721
     RDKit          3D
Glycylproline
 24 24  0  0  0  0  0  0  0  0999 V2000
    3.7128   -0.1500    0.4336 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3577    0.2697    0.2244 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3804   -0.7771    0.6310 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7744   -1.8726    1.0940 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0046   -0.5544    0.5023 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0812   -1.4380    0.8388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0801   -1.2644   -0.2748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8915    0.1810   -0.6558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6261    0.6548   -0.0137 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8357    1.6132    1.0857 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849    1.3182    2.2732 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4086    2.8476    0.8871 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7741   -1.1696    0.1628 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3827    0.3826   -0.1454 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1719    1.2075    0.7861 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2397    0.4810   -0.8772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7586   -2.4961    0.8367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5208   -1.2240    1.8367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7884   -1.8904   -1.1249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1055   -1.4598    0.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7644    0.2834   -1.7625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7574    0.8167   -0.3922 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0531    1.1602   -0.7521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7389    3.0805   -0.0339 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  9  5  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  2 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  6
 12 24  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f9250d0c098>

      
  Mrv1652305271900142D          

 12 12  0  0  0  0            999 V2000
 2499.5974 2500.8461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2498.8823 2501.2578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2498.1613 2500.8583    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2500.3123 2501.2578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2501.1237 2500.0183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2501.8386 2499.6067    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2501.1237 2500.8440    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2499.5797 2500.0085    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2498.9124 2499.5234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2499.1673 2498.7389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2499.9923 2498.7389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2500.2471 2499.5234    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  2  0  0  0  0
  2  3  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  8  9  1  0  0  0  0
  8 12  1  0  0  0  0
 12  5  1  6  0  0  0
  1  8  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000145

> <DATABASE_NAME>
MIME

> <SMILES>
NCC(=O)N1CCC[C@H]1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H12N2O3/c8-4-6(10)9-3-1-2-5(9)7(11)12/h5H,1-4,8H2,(H,11,12)/t5-/m0/s1

> <INCHI_KEY>
KZNQNBZMBZJQJO-YFKPBYRVSA-N

> <FORMULA>
C7H12N2O3

> <MOLECULAR_WEIGHT>
172.1818

> <EXACT_MASS>
172.08479226

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.750521460427823

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-1-(2-aminoacetyl)pyrrolidine-2-carboxylic acid

> <ALOGPS_LOGP>
-2.65

> <JCHEM_LOGP>
-3.676007803741153

> <ALOGPS_LOGS>
0.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6122621941395576

> <JCHEM_PKA_STRONGEST_BASIC>
8.132394754718373

> <JCHEM_POLAR_SURFACE_AREA>
83.63

> <JCHEM_REFRACTIVITY>
40.9899

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.79e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glycylproline

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f9250d0c098>

HMDB0000721
     RDKit          3D
Glycylproline
 24 24  0  0  0  0  0  0  0  0999 V2000
    3.7128   -0.1500    0.4336 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3577    0.2697    0.2244 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3804   -0.7771    0.6310 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7744   -1.8726    1.0940 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0046   -0.5544    0.5023 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0812   -1.4380    0.8388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0801   -1.2644   -0.2748 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8915    0.1810   -0.6558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6261    0.6548   -0.0137 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8357    1.6132    1.0857 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849    1.3182    2.2732 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4086    2.8476    0.8871 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7741   -1.1696    0.1628 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3827    0.3826   -0.1454 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1719    1.2075    0.7861 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2397    0.4810   -0.8772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7586   -2.4961    0.8367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5208   -1.2240    1.8367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7884   -1.8904   -1.1249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1055   -1.4598    0.0934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7644    0.2834   -1.7625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7574    0.8167   -0.3922 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0531    1.1602   -0.7521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7389    3.0805   -0.0339 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  9  5  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  2 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  6
 12 24  1  0
M  END
Download

PDB for #<Metabolite:0x00007f9250d0c098>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0    4665.9154668.246   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    4664.5804669.015   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0    4663.2344668.269   0.000  0.00  0.00           N+0
HETATM    4  O   UNK     0    4667.2504669.015   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    4668.7644666.701   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    4670.0994665.933   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    4668.7644668.242   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0    4665.8824666.683   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0    4664.6364665.777   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    4665.1124664.313   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    4666.6524664.313   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    4667.1284665.777   0.000  0.00  0.00           C+0
CONECT    1    2    4    8                                                  
CONECT    2    1    3                                                       
CONECT    3    2                                                            
CONECT    4    1                                                            
CONECT    5    6    7   12                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    9   12    1                                                  
CONECT    9   10    8                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    8    5                                                  
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for #<Metabolite:0x00007f9250d0c098>

COMPND    HMDB0000721
HETATM    1  N1  UNL     1       3.713  -0.150   0.434  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.358   0.270   0.224  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.380  -0.777   0.631  1.00  0.00           C  
HETATM    4  O1  UNL     1       1.774  -1.873   1.094  1.00  0.00           O  
HETATM    5  N2  UNL     1      -0.005  -0.554   0.502  1.00  0.00           N  
HETATM    6  C3  UNL     1      -1.081  -1.438   0.839  1.00  0.00           C  
HETATM    7  C4  UNL     1      -2.080  -1.264  -0.275  1.00  0.00           C  
HETATM    8  C5  UNL     1      -1.891   0.181  -0.656  1.00  0.00           C  
HETATM    9  C6  UNL     1      -0.626   0.655  -0.014  1.00  0.00           C  
HETATM   10  C7  UNL     1      -0.836   1.613   1.086  1.00  0.00           C  
HETATM   11  O2  UNL     1      -0.485   1.318   2.273  1.00  0.00           O  
HETATM   12  O3  UNL     1      -1.409   2.848   0.887  1.00  0.00           O  
HETATM   13  H1  UNL     1       3.774  -1.170   0.163  1.00  0.00           H  
HETATM   14  H2  UNL     1       4.383   0.383  -0.145  1.00  0.00           H  
HETATM   15  H3  UNL     1       2.172   1.207   0.786  1.00  0.00           H  
HETATM   16  H4  UNL     1       2.240   0.481  -0.877  1.00  0.00           H  
HETATM   17  H5  UNL     1      -0.759  -2.496   0.837  1.00  0.00           H  
HETATM   18  H6  UNL     1      -1.521  -1.224   1.837  1.00  0.00           H  
HETATM   19  H7  UNL     1      -1.788  -1.890  -1.125  1.00  0.00           H  
HETATM   20  H8  UNL     1      -3.105  -1.460   0.093  1.00  0.00           H  
HETATM   21  H9  UNL     1      -1.764   0.283  -1.762  1.00  0.00           H  
HETATM   22  H10 UNL     1      -2.757   0.817  -0.392  1.00  0.00           H  
HETATM   23  H11 UNL     1       0.053   1.160  -0.752  1.00  0.00           H  
HETATM   24  H12 UNL     1      -1.739   3.080  -0.034  1.00  0.00           H  
CONECT    1    2   13   14
CONECT    2    3   15   16
CONECT    3    4    4    5
CONECT    5    6    9
CONECT    6    7   17   18
CONECT    7    8   19   20
CONECT    8    9   21   22
CONECT    9   10   23
CONECT   10   11   11   12
CONECT   12   24
END
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SMILES for #<Metabolite:0x00007f9250d0c098>

NCC(=O)N1CCC[C@H]1C(O)=O
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INCHI for #<Metabolite:0x00007f9250d0c098>

InChI=1S/C7H12N2O3/c8-4-6(10)9-3-1-2-5(9)7(11)12/h5H,1-4,8H2,(H,11,12)/t5-/m0/s1
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Synonyms
ValueSource
1-(Aminoacetyl)prolineChEBI
1-GlycylprolineChEBI
Gly-L-proChEBI
GPChEBI
N-Glycyl-L-prolineChEBI
N-GlycylprolineChEBI
Glycyl-L-prolineHMDB
(S)-1-(2-Aminoacetyl)pyrrolidine-2-carboxylic acidHMDB
1-Glycyl-L-prolineHMDB
g-p DipeptideHMDB
GP DipeptideHMDB
Gly-proHMDB
Glycine proline dipeptideHMDB
Glycine-proline dipeptideHMDB
Glycyl-prolineHMDB
NSC 97929HMDB
GlycylprolineChEBI
Molecular FormulaC7H12N2O3
Average Mass172.1818
Monoisotopic Mass172.08479226
IUPAC Name(2S)-1-(2-aminoacetyl)pyrrolidine-2-carboxylic acid
Traditional Nameglycylproline
CAS Registry Number704-15-4
SMILES
NCC(=O)N1CCC[C@H]1C(O)=O
InChI Identifier
InChI=1S/C7H12N2O3/c8-4-6(10)9-3-1-2-5(9)7(11)12/h5H,1-4,8H2,(H,11,12)/t5-/m0/s1
InChI KeyKZNQNBZMBZJQJO-YFKPBYRVSA-N