Showing metabocard for Prolylglycine (MMDBc0000259)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:47:51 UTC
Update Date2024-04-30 19:31:42 UTC
Metabolite IDMMDBc0000259
Metabolite Identification
Common NameProlylglycine
DescriptionProlylglycine is a dipeptide composed of proline and glycine. It is an incomplete breakdown product of protein digestion or protein catabolism. Some dipeptides are known to have physiological or cell-signaling effects although most are simply short-lived intermediates on their way to specific amino acid degradation pathways following further proteolysis. It is found in urine (PMID: 3782411 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9202a3b3d0>


  Mrv1652305161920092D          

 12 12  0  0  0  0            999 V2000
 2499.5954 2500.2059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2500.3102 2499.7940    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2501.0251 2500.2059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2501.7421 2499.7940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2502.4571 2500.2059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2501.7421 2498.9686    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2499.5954 2501.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2498.2094 2500.2882    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2497.5420 2499.8032    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2497.7969 2499.0186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2498.6219 2499.0186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2498.8768 2499.8032    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  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  1  1  6  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f9202a3b3d0>

HMDB0011178
     RDKit          3D
Prolylglycine
 24 24  0  0  0  0  0  0  0  0999 V2000
    3.5786   -0.9759   -2.0213 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7483    0.0205   -1.2820 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9799    0.6668   -1.3041 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7166    0.5649   -0.3755 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4826   -0.1641   -0.4200 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4066    0.2410    0.3926 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5182    1.2513    1.1691 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9095   -0.4722    0.3976 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5836   -0.2448   -0.9469 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0524   -0.0600   -0.6459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1103   -0.3504    0.8364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8331    0.1353    1.3076 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2692    1.3342   -0.5946 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5052    1.6329   -0.6531 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1190    0.5365    0.6648 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3814   -0.9769   -1.0398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7539   -1.5331    0.6152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1845    0.7095   -1.3752 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4055   -1.0708   -1.6428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3768    0.9929   -0.8702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6308   -0.7667   -1.2479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1800   -1.4652    0.9352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9720    0.1412    1.3321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7134   -0.1470    2.2952 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12  8  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  8 17  1  1
  9 18  1  0
  9 19  1  0
 10 20  1  0
 10 21  1  0
 11 22  1  0
 11 23  1  0
 12 24  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f9202a3b3d0>


  Mrv1652305161920092D          

 12 12  0  0  0  0            999 V2000
 2499.5954 2500.2059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2500.3102 2499.7940    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2501.0251 2500.2059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2501.7421 2499.7940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2502.4571 2500.2059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2501.7421 2498.9686    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2499.5954 2501.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2498.2094 2500.2882    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2497.5420 2499.8032    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2497.7969 2499.0186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2498.6219 2499.0186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2498.8768 2499.8032    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  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  1  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000259

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)CNC(=O)[C@@H]1CCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C7H12N2O3/c10-6(11)4-9-7(12)5-2-1-3-8-5/h5,8H,1-4H2,(H,9,12)(H,10,11)/t5-/m0/s1

> <INCHI_KEY>
RNKSNIBMTUYWSH-YFKPBYRVSA-N

> <FORMULA>
C7H12N2O3

> <MOLECULAR_WEIGHT>
172.1818

> <EXACT_MASS>
172.08479226

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.794332963867234

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[(2S)-pyrrolidin-2-yl]formamido}acetic acid

> <ALOGPS_LOGP>
-2.89

> <JCHEM_LOGP>
-3.674605415139806

> <ALOGPS_LOGS>
-1.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.294567708692291

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6649261286438968

> <JCHEM_PKA_STRONGEST_BASIC>
9.806650942736733

> <JCHEM_POLAR_SURFACE_AREA>
78.43

> <JCHEM_REFRACTIVITY>
40.86780000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.91e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
Pro-Gly

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f9202a3b3d0>

HMDB0011178
     RDKit          3D
Prolylglycine
 24 24  0  0  0  0  0  0  0  0999 V2000
    3.5786   -0.9759   -2.0213 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7483    0.0205   -1.2820 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9799    0.6668   -1.3041 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7166    0.5649   -0.3755 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4826   -0.1641   -0.4200 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4066    0.2410    0.3926 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5182    1.2513    1.1691 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9095   -0.4722    0.3976 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5836   -0.2448   -0.9469 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0524   -0.0600   -0.6459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1103   -0.3504    0.8364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8331    0.1353    1.3076 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2692    1.3342   -0.5946 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5052    1.6329   -0.6531 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1190    0.5365    0.6648 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3814   -0.9769   -1.0398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7539   -1.5331    0.6152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1845    0.7095   -1.3752 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4055   -1.0708   -1.6428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3768    0.9929   -0.8702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6308   -0.7667   -1.2479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1800   -1.4652    0.9352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9720    0.1412    1.3321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7134   -0.1470    2.2952 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12  8  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  8 17  1  1
  9 18  1  0
  9 19  1  0
 10 20  1  0
 10 21  1  0
 11 22  1  0
 11 23  1  0
 12 24  1  0
M  END
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PDB for #<Metabolite:0x00007f9202a3b3d0>

HEADER    PROTEIN                                 16-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-19         0                                  
HETATM    1  C   UNK     0    4665.9114667.051   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0    4667.2464666.282   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0    4668.5804667.051   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    4669.9194666.282   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    4671.2534667.051   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    4669.9194664.741   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    4665.9114668.592   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0    4663.3244667.205   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0    4662.0784666.299   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    4662.5544664.835   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    4664.0944664.835   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    4664.5704666.299   0.000  0.00  0.00           C+0
CONECT    1    2    7   12                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    1                                                            
CONECT    8    9   12                                                       
CONECT    9   10    8                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    8    1                                                  
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for #<Metabolite:0x00007f9202a3b3d0>

COMPND    HMDB0011178
HETATM    1  O1  UNL     1       3.579  -0.976  -2.021  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.748   0.021  -1.282  1.00  0.00           C  
HETATM    3  O2  UNL     1       4.980   0.667  -1.304  1.00  0.00           O  
HETATM    4  C2  UNL     1       2.717   0.565  -0.375  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.483  -0.164  -0.420  1.00  0.00           N  
HETATM    6  C3  UNL     1       0.407   0.241   0.393  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.518   1.251   1.169  1.00  0.00           O  
HETATM    8  C4  UNL     1      -0.909  -0.472   0.398  1.00  0.00           C  
HETATM    9  C5  UNL     1      -1.584  -0.245  -0.947  1.00  0.00           C  
HETATM   10  C6  UNL     1      -3.052  -0.060  -0.646  1.00  0.00           C  
HETATM   11  C7  UNL     1      -3.110  -0.350   0.836  1.00  0.00           C  
HETATM   12  N2  UNL     1      -1.833   0.135   1.308  1.00  0.00           N  
HETATM   13  H1  UNL     1       5.269   1.334  -0.595  1.00  0.00           H  
HETATM   14  H2  UNL     1       2.505   1.633  -0.653  1.00  0.00           H  
HETATM   15  H3  UNL     1       3.119   0.537   0.665  1.00  0.00           H  
HETATM   16  H4  UNL     1       1.381  -0.977  -1.040  1.00  0.00           H  
HETATM   17  H5  UNL     1      -0.754  -1.533   0.615  1.00  0.00           H  
HETATM   18  H6  UNL     1      -1.184   0.709  -1.375  1.00  0.00           H  
HETATM   19  H7  UNL     1      -1.405  -1.071  -1.643  1.00  0.00           H  
HETATM   20  H8  UNL     1      -3.377   0.993  -0.870  1.00  0.00           H  
HETATM   21  H9  UNL     1      -3.631  -0.767  -1.248  1.00  0.00           H  
HETATM   22  H10 UNL     1      -3.180  -1.465   0.935  1.00  0.00           H  
HETATM   23  H11 UNL     1      -3.972   0.141   1.332  1.00  0.00           H  
HETATM   24  H12 UNL     1      -1.713  -0.147   2.295  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   13
CONECT    4    5   14   15
CONECT    5    6   16
CONECT    6    7    7    8
CONECT    8    9   12   17
CONECT    9   10   18   19
CONECT   10   11   20   21
CONECT   11   12   22   23
CONECT   12   24
END
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SMILES for #<Metabolite:0x00007f9202a3b3d0>

OC(=O)CNC(=O)[C@@H]1CCCN1
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INCHI for #<Metabolite:0x00007f9202a3b3d0>

InChI=1S/C7H12N2O3/c10-6(11)4-9-7(12)5-2-1-3-8-5/h5,8H,1-4H2,(H,9,12)(H,10,11)/t5-/m0/s1
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Synonyms
ValueSource
L-Pro-glyChEBI
L-ProlinylglycineChEBI
P-GChEBI
PGChEBI
Pro-glyChEBI
L-ProlylglycineHMDB
N-L-ProlylglycineHMDB
N-ProlylglycineHMDB
NSC 89175HMDB
p-g DipeptideHMDB
PG DipeptideHMDB
Proline glycine dipeptideHMDB
Proline-glycine dipeptideHMDB
Prolyl-glycineHMDB
ProlylglycineChEBI
Molecular FormulaC7H12N2O3
Average Mass172.1818
Monoisotopic Mass172.08479226
IUPAC Name2-{[(2S)-pyrrolidin-2-yl]formamido}acetic acid
Traditional NamePro-Gly
CAS Registry Number2578-57-6
SMILES
OC(=O)CNC(=O)[C@@H]1CCCN1
InChI Identifier
InChI=1S/C7H12N2O3/c10-6(11)4-9-7(12)5-2-1-3-8-5/h5,8H,1-4H2,(H,9,12)(H,10,11)/t5-/m0/s1
InChI KeyRNKSNIBMTUYWSH-YFKPBYRVSA-N