Showing metabocard for L-Proline (MMDBc0000050)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:28:34 UTC
Update Date2024-09-28 01:48:25 UTC
Metabolite IDMMDBc0000050
Metabolite Identification
Common NameL-Proline
DescriptionL-proline is one of the twenty amino acids used in living organisms as the building blocks of proteins. Proline is sometimes called an imino acid, although the IUPAC definition of an imine requires a carbon-nitrogen double bond. Proline is a non-essential amino acid that is synthesized from glutamic acid. It is an essential component of collagen and is important for proper functioning of joints and tendons. Proline is derived from the amino acid L-glutamate in which glutamate-5-semialdehyde is first formed by glutamate 5-kinase and glutamate-5-semialdehyde dehydrogenase (which requires NADH or NADPH). This semialdehyde can then either spontaneously cyclize to form 1-pyrroline-5-carboxylic acid, which is reduced to proline by pyrroline-5-carboxylate reductase, or turned into ornithine by ornithine aminotransferase, followed by cyclization by ornithine cyclodeaminase to form proline. L-Proline has been found to act as a weak agonist of the glycine receptor and of both NMDA and non-NMDA ionotropic glutamate receptors. It has been proposed to be a potential endogenous excitotoxin/neurotoxin. Studies in rats have shown that when injected into the brain, proline non-selectively destroys pyramidal and granule cells (PMID: 3409032 ). Therefore, under certain conditions proline 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 proline 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. People with hyperprolinemia type I often do not show any symptoms even though they have proline levels in their blood between 3 and 10 times the normal level. Some individuals with hyperprolinemia type I exhibit seizures, intellectual disability, or other neurological or psychiatric problems. Hyperprolinemia type II results in proline levels in the blood between 10 and 15 times higher than normal, and high levels of a related compound called pyrroline-5-carboxylate. Hyperprolinemia type II has signs and symptoms that vary in severity, and is more likely than type I to involve seizures or intellectual disability.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f92527771d0>


  Mrv1652309272007462D          

  8  8  0  0  1  0            999 V2000
   -1.1385    0.8581    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8060    0.3731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5510   -0.4116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7259   -0.4116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2434    0.7856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4710    0.3731    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2434    1.6107    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9580    0.3731    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  6  5  1  6  0  0  0
  5  7  2  0  0  0  0
  5  8  1  0  0  0  0
  4  6  1  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f92527771d0>

HMDB0000162
     RDKit          3D
L-Proline
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.4994    1.2834    0.1628 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9665    0.1455    0.1637 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7840   -0.9463   -0.0948 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5479   -0.1007    0.4183 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1821   -0.6805   -0.7714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6276   -0.4626   -0.3655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5629    0.8583    0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1909    1.1205    0.6733 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4977   -1.1733    0.6106 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4193   -0.7802    1.2626 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0489   -0.1574   -1.7185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0100   -1.7668   -0.8141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3008   -0.4010   -1.2429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9210   -1.2812    0.3301 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9872    1.6721   -0.2757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1667    0.8082    1.2945 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1855    1.8619    0.0181 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  1  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
  7 16  1  0
  8 17  1  0
M  END
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3D SDF for #<Metabolite:0x00007f92527771d0>


  Mrv1652309272007462D          

  8  8  0  0  1  0            999 V2000
   -1.1385    0.8581    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8060    0.3731    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5510   -0.4116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7259   -0.4116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2434    0.7856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4710    0.3731    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2434    1.6107    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9580    0.3731    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  6  5  1  6  0  0  0
  5  7  2  0  0  0  0
  5  8  1  0  0  0  0
  4  6  1  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000050

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1

> <INCHI_KEY>
ONIBWKKTOPOVIA-BYPYZUCNSA-N

> <FORMULA>
C5H9NO2

> <MOLECULAR_WEIGHT>
115.1305

> <EXACT_MASS>
115.063328537

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.50403298353395

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.71

> <JCHEM_LOGP>
-2.568638276039985

> <ALOGPS_LOGS>
0.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.9406707712827913

> <JCHEM_PKA_STRONGEST_BASIC>
11.332026115136207

> <JCHEM_POLAR_SURFACE_AREA>
49.33

> <JCHEM_REFRACTIVITY>
28.064299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.65e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-proline

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f92527771d0>

HMDB0000162
     RDKit          3D
L-Proline
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.4994    1.2834    0.1628 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9665    0.1455    0.1637 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7840   -0.9463   -0.0948 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5479   -0.1007    0.4183 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1821   -0.6805   -0.7714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6276   -0.4626   -0.3655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5629    0.8583    0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1909    1.1205    0.6733 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4977   -1.1733    0.6106 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4193   -0.7802    1.2626 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0489   -0.1574   -1.7185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0100   -1.7668   -0.8141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3008   -0.4010   -1.2429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9210   -1.2812    0.3301 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9872    1.6721   -0.2757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1667    0.8082    1.2945 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1855    1.8619    0.0181 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  1  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
  7 16  1  0
  8 17  1  0
M  END
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PDB for #<Metabolite:0x00007f92527771d0>

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  N   UNK     0      -2.125   1.602   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -3.371   0.696   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.895  -0.768   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.355  -0.768   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.454   1.466   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.879   0.696   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.454   3.007   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.788   0.696   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    3    1                                                       
CONECT    3    2    4                                                       
CONECT    4    3    6                                                       
CONECT    5    6    7    8                                                  
CONECT    6    5    4    1                                                  
CONECT    7    5                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for #<Metabolite:0x00007f92527771d0>

COMPND    HMDB0000162
HETATM    1  O1  UNL     1       2.499   1.283   0.163  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.967   0.146   0.164  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.784  -0.946  -0.095  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.548  -0.101   0.418  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.182  -0.680  -0.771  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.628  -0.463  -0.366  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.563   0.858   0.349  1.00  0.00           C  
HETATM    8  N1  UNL     1      -0.191   1.121   0.673  1.00  0.00           N  
HETATM    9  H1  UNL     1       3.498  -1.173   0.611  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.419  -0.780   1.263  1.00  0.00           H  
HETATM   11  H3  UNL     1       0.049  -0.157  -1.718  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.010  -1.767  -0.814  1.00  0.00           H  
HETATM   13  H5  UNL     1      -2.301  -0.401  -1.243  1.00  0.00           H  
HETATM   14  H6  UNL     1      -1.921  -1.281   0.330  1.00  0.00           H  
HETATM   15  H7  UNL     1      -1.987   1.672  -0.276  1.00  0.00           H  
HETATM   16  H8  UNL     1      -2.167   0.808   1.294  1.00  0.00           H  
HETATM   17  H9  UNL     1       0.186   1.862   0.018  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   15   16
CONECT    8   17
END
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SMILES for #<Metabolite:0x00007f92527771d0>

OC(=O)[C@@H]1CCCN1
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INCHI for #<Metabolite:0x00007f92527771d0>

InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1
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Synonyms
ValueSource
(-)-(S)-ProlineChEBI
(-)-2-Pyrrolidinecarboxylic acidChEBI
(-)-ProlineChEBI
(2S)-Pyrrolidine-2-carboxylic acidChEBI
(S)-2-CarboxypyrrolidineChEBI
(S)-2-Pyrrolidinecarboxylic acidChEBI
(S)-Pyrrolidine-2-carboxylic acidChEBI
2-Pyrrolidinecarboxylic acidChEBI
L-(-)-ProlineChEBI
L-alpha-Pyrrolidinecarboxylic acidChEBI
L-ProlinChEBI
L-Pyrrolidine-2-carboxylic acidChEBI
PChEBI
ProlinaChEBI
PROLINEChEBI
ProlinumChEBI
(-)-2-PyrrolidinecarboxylateGenerator
(2S)-Pyrrolidine-2-carboxylateGenerator
(S)-2-PyrrolidinecarboxylateGenerator
(S)-Pyrrolidine-2-carboxylateGenerator
2-PyrrolidinecarboxylateGenerator
L-a-PyrrolidinecarboxylateGenerator
L-a-Pyrrolidinecarboxylic acidGenerator
L-alpha-PyrrolidinecarboxylateGenerator
L-Α-pyrrolidinecarboxylateGenerator
L-Α-pyrrolidinecarboxylic acidGenerator
L-Pyrrolidine-2-carboxylateGenerator
(S)-(-)-ProlineHMDB
(S)-(-)-Pyrrolidine-2-carboxylateHMDB
(S)-(-)-Pyrrolidine-2-carboxylic acidHMDB
(S)-2-PyrralidinecarboxylateHMDB
(S)-2-Pyrralidinecarboxylic acidHMDB
(S)-ProlineHMDB
L ProlineHMDB
Molecular FormulaC5H9NO2
Average Mass115.1305
Monoisotopic Mass115.063328537
IUPAC Name(2S)-pyrrolidine-2-carboxylic acid
Traditional NameL-proline
CAS Registry Number147-85-3
SMILES
OC(=O)[C@@H]1CCCN1
InChI Identifier
InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1
InChI KeyONIBWKKTOPOVIA-BYPYZUCNSA-N