Showing metabocard for 1-Pyrroline-5-carboxylic acid (MMDBc0000386)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:36:38 UTC
Update Date2022-08-31 06:02:59 UTC
Metabolite IDMMDBc0000386
Metabolite Identification
Common Name1-Pyrroline-5-carboxylic acid
Description1-Pyrroline-5-carboxylic acid (CAS: 2906-39-0) is an enamine or an imino acid that forms upon the spontaneous dehydration of L-glutamate gamma-semialdehyde in aqueous solutions. The stereoisomer (S)-1-pyrroline-5-carboxylate is an intermediate in glutamate metabolism, arginine degradation, and proline biosynthesis and degradation. It can also be converted into or be formed from three amino acids: L-glutamate, L-ornithine, and L-proline. In particular, it is synthesized via the oxidation of proline by pyrroline-5-carboxylate reductase 1 (PYCR1) (EC 1.5.1.2) or by proline dehydrogenase (PRODH) (EC 1.5.99.8). It is hydrolyzed into L-glutamate by delta-1-pyrroline-5-carboxylate dehydrogenase (ALDH4A1) (EC 1.5.1.12). It is also one of the few metabolites that can act as a precursor to other metabolites of both the urea cycle and the tricarboxylic acid (TCA) cycle. Under certain conditions, pyrroline-5-carboxylate can act as a neurotoxin and a metabotoxin. A neurotoxin causes damage to nerve cells and nerve tissues. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Chronically high levels of pyrroline-5-carboxylate are associated with at least five inborn errors of metabolism, including hyperprolinemia type I, hyperprolinemia type II, iminoglycinuria, prolinemia type II, and pyruvate carboxylase deficiency. Hyperprolinemia type II results in high levels of pyrroline-5-carboxylate. People with hyperprolinemia type II have signs and symptoms that vary in severity, but they are more likely than type I to have seizures or intellectual disability. Pyrroline-5-carboxylate is highly reactive and excess quantities have been shown to cause cell death and apoptosis (PMID: 15548746 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x000055c798a816b8>


  Mrv1652309142020202D          

  8  8  0  0  0  0            999 V2000
    0.6685    0.1811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3836   -0.2303    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6685    1.0054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7162    0.2642    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3836   -0.2207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1287   -1.0053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3037   -1.0053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0488   -0.2207    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  5  2  0  0  0  0
  4  8  1  0  0  0  0
  8  1  1  6  0  0  0
M  END
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3D MOL for #<Metabolite:0x000055c798a816b8>

HMDB0001301
     RDKit          3D
1-Pyrroline-5-carboxylic acid
 15 15  0  0  0  0  0  0  0  0999 V2000
    1.6190    1.4570    1.3885 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6296    0.3445    0.8034 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8678   -0.1099    0.3681 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3718   -0.3699    0.6288 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0319   -0.5351   -0.8186 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5340   -0.6820   -0.6723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7820    0.2155    0.4969 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7091    0.3588    1.1833 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1878   -0.0714   -0.5821 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4516   -1.4052    1.0476 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3550   -1.4759   -1.2600 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1929    0.3317   -1.4409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0870   -0.3509   -1.5642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8072   -1.7096   -0.3511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7243    0.7053    0.7727 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  1  0
  7  8  2  0
  8  4  1  0
  3  9  1  0
  4 10  1  1
  5 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
M  END
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3D SDF for #<Metabolite:0x000055c798a816b8>


  Mrv1652309142020202D          

  8  8  0  0  0  0            999 V2000
    0.6685    0.1811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3836   -0.2303    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6685    1.0054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7162    0.2642    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3836   -0.2207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1287   -1.0053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3037   -1.0053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0488   -0.2207    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  5  2  0  0  0  0
  4  8  1  0  0  0  0
  8  1  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000386

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)[C@@H]1CCC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H7NO2/c7-5(8)4-2-1-3-6-4/h3-4H,1-2H2,(H,7,8)/t4-/m0/s1

> <INCHI_KEY>
DWAKNKKXGALPNW-BYPYZUCNSA-N

> <FORMULA>
C5H7NO2

> <MOLECULAR_WEIGHT>
113.1146

> <EXACT_MASS>
113.047678473

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.721633827168107

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-3,4-dihydro-2H-pyrrole-2-carboxylic acid

> <ALOGPS_LOGP>
-0.01

> <JCHEM_LOGP>
-2.279439073313947

> <ALOGPS_LOGS>
-0.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8219556318598356

> <JCHEM_PKA_STRONGEST_BASIC>
6.073045352102196

> <JCHEM_POLAR_SURFACE_AREA>
49.66

> <JCHEM_REFRACTIVITY>
27.397299999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.31e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-1-pyrroline-5-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x000055c798a816b8>

HMDB0001301
     RDKit          3D
1-Pyrroline-5-carboxylic acid
 15 15  0  0  0  0  0  0  0  0999 V2000
    1.6190    1.4570    1.3885 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6296    0.3445    0.8034 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8678   -0.1099    0.3681 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3718   -0.3699    0.6288 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0319   -0.5351   -0.8186 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5340   -0.6820   -0.6723 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7820    0.2155    0.4969 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7091    0.3588    1.1833 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1878   -0.0714   -0.5821 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4516   -1.4052    1.0476 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3550   -1.4759   -1.2600 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1929    0.3317   -1.4409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0870   -0.3509   -1.5642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8072   -1.7096   -0.3511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7243    0.7053    0.7727 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  1  0
  7  8  2  0
  8  4  1  0
  3  9  1  0
  4 10  1  1
  5 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
  7 15  1  0
M  END
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PDB for #<Metabolite:0x000055c798a816b8>

HEADER    PROTEIN                                 14-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-SEP-20         0                                  
HETATM    1  C   UNK     0       1.248   0.338   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.583  -0.430   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       1.248   1.877   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      -1.337   0.493   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -2.583  -0.412   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.107  -1.877   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.567  -1.877   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.091  -0.412   0.000  0.00  0.00           C+0
CONECT    1    2    3    8                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    5    8                                                       
CONECT    5    6    4                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    4    1                                                  
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for #<Metabolite:0x000055c798a816b8>

COMPND    HMDB0001301
HETATM    1  O1  UNL     1       1.619   1.457   1.388  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.630   0.344   0.803  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.868  -0.110   0.368  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.372  -0.370   0.629  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.032  -0.535  -0.819  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.534  -0.682  -0.672  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.782   0.216   0.497  1.00  0.00           C  
HETATM    8  N1  UNL     1      -0.709   0.359   1.183  1.00  0.00           N  
HETATM    9  H1  UNL     1       3.188  -0.071  -0.582  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.452  -1.405   1.048  1.00  0.00           H  
HETATM   11  H3  UNL     1       0.355  -1.476  -1.260  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.193   0.332  -1.441  1.00  0.00           H  
HETATM   13  H5  UNL     1      -2.087  -0.351  -1.564  1.00  0.00           H  
HETATM   14  H6  UNL     1      -1.807  -1.710  -0.351  1.00  0.00           H  
HETATM   15  H7  UNL     1      -2.724   0.705   0.773  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5    8   10
CONECT    5    6   11   12
CONECT    6    7   13   14
CONECT    7    8    8   15
END
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SMILES for #<Metabolite:0x000055c798a816b8>

OC(=O)[C@@H]1CCC=N1
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INCHI for #<Metabolite:0x000055c798a816b8>

InChI=1S/C5H7NO2/c7-5(8)4-2-1-3-6-4/h3-4H,1-2H2,(H,7,8)/t4-/m0/s1
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Synonyms
ValueSource
1-Pyrroline-5-carboxylateChEBI, KEGG
L-1-Pyrroline-5-carboxylateChEBI, KEGG
1-Pyrroline-5-carboxylic acidGenerator
(S)-1-Pyrroline-5-carboxylic acidGenerator
L-1-Pyrroline-5-carboxylic acidGenerator
delta-1-Pyrroline-5-carboxylateMeSH
delta-1-Pyrroline-5-carboxylate, (+-)-isomerMeSH
delta-1-Pyrroline-5-carboxylic acidMeSH
delta-1-Pyrroline-5-carboxylate, 14C-labeled, (+-)-isomerMeSH
delta(1)Pyrroline-5-carboxylateMeSH
Pyrroline-5-carboxylateMeSH
(2S)-3,4-Dihydro-2H-pyrrole-2-carboxylic acidHMDB
(S)-1-Pyrroline-5-carboxylateHMDB
3,4-Dihydro-2H-pyrrole-2-carboxylic acidHMDB
delta1-Pyrroline-5-carboxylic acidHMDB
Δ1-Pyrroline-5-carboxylic acidHMDB
Molecular FormulaC5H7NO2
Average Mass113.1146
Monoisotopic Mass113.047678473
IUPAC Name(2S)-3,4-dihydro-2H-pyrrole-2-carboxylic acid
Traditional NameL-1-pyrroline-5-carboxylate
CAS Registry NumberNot Available
SMILES
OC(=O)[C@@H]1CCC=N1
InChI Identifier
InChI=1S/C5H7NO2/c7-5(8)4-2-1-3-6-4/h3-4H,1-2H2,(H,7,8)/t4-/m0/s1
InChI KeyDWAKNKKXGALPNW-BYPYZUCNSA-N