Showing metabocard for L-Glutamic-gamma-semialdehyde (MMDBc0029612)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:34:33 UTC
Update Date2022-08-31 13:59:39 UTC
Metabolite IDMMDBc0029612
Metabolite Identification
Common NameL-Glutamic-gamma-semialdehyde
DescriptionGlutamic gamma-semialdehyde is the metabolic precursor for proline biosynthesis. The conversion from L-Glutamate, an ATP- and NADPH-dependent reaction, is catalyzed by the enzyme Delta-1-pyrroline-5-carboxylate synthetase (P5CS) (OMIM 138250 ). L-Glutamic-gamma-semialdehyde can also be converted to or be formed from the amino acids L-ornithine (EC 2.6.1.13) and L-proline (EC 1.5.99.8 and EC 1.5.1.2). It is also one of the few metabolites that can be a precursor to other metabolites of both the urea cycle and the citric acid cycle (BioCyc)
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fe2a2148660>


  Mrv1652309042000262D          

  9  8  0  0  1  0            999 V2000
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fe2a2148660>

HMDB0002104
     RDKit          3D
L-Glutamic gamma-semialdehyde
 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.2454   -0.8836   -0.8421 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8141   -0.3319    0.4155 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5137    0.3561    0.3531 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6377   -0.5528   -0.0827 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8804    0.2799   -0.0858 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4911    0.5434    0.9429 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8103    0.6622    0.8907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5792    1.2423    1.9844 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9274    0.9116    0.1370 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3606   -0.1157   -1.5483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1265   -1.4098   -0.7823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7205   -1.1851    1.1344 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4420    1.1651   -0.4187 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7388    0.7812    1.3346 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7439   -1.4219    0.6011 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4695   -0.8827   -1.1229 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2696    0.6714   -1.0154 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6027    0.1705   -0.1070 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  2  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  1
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  9 18  1  0
M  END
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3D SDF for #<Metabolite:0x00007fe2a2148660>


  Mrv1652309042000262D          

  9  8  0  0  1  0            999 V2000
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029612

> <DATABASE_NAME>
MIME

> <SMILES>
N[C@@H](CCC=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO3/c6-4(5(8)9)2-1-3-7/h3-4H,1-2,6H2,(H,8,9)/t4-/m0/s1

> <INCHI_KEY>
KABXUUFDPUOJMW-BYPYZUCNSA-N

> <FORMULA>
C5H9NO3

> <MOLECULAR_WEIGHT>
131.1299

> <EXACT_MASS>
131.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.564831407259124

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-5-oxopentanoic acid

> <ALOGPS_LOGP>
-2.57

> <JCHEM_LOGP>
-3.3526724661068794

> <ALOGPS_LOGS>
0.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.41410334872977

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.121741402538836

> <JCHEM_PKA_STRONGEST_BASIC>
9.113974095724268

> <JCHEM_POLAR_SURFACE_AREA>
80.39000000000001

> <JCHEM_REFRACTIVITY>
30.3623

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.44e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-carboxy-4-aminobutanal

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fe2a2148660>

HMDB0002104
     RDKit          3D
L-Glutamic gamma-semialdehyde
 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.2454   -0.8836   -0.8421 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8141   -0.3319    0.4155 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5137    0.3561    0.3531 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6377   -0.5528   -0.0827 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8804    0.2799   -0.0858 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4911    0.5434    0.9429 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8103    0.6622    0.8907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5792    1.2423    1.9844 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9274    0.9116    0.1370 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3606   -0.1157   -1.5483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1265   -1.4098   -0.7823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7205   -1.1851    1.1344 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4420    1.1651   -0.4187 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7388    0.7812    1.3346 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7439   -1.4219    0.6011 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4695   -0.8827   -1.1229 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2696    0.6714   -1.0154 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6027    0.1705   -0.1070 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  2  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  1
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  9 18  1  0
M  END
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PDB for #<Metabolite:0x00007fe2a2148660>

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0       8.621   4.977   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    2    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for #<Metabolite:0x00007fe2a2148660>

COMPND    HMDB0002104
HETATM    1  N1  UNL     1      -1.245  -0.884  -0.842  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.814  -0.332   0.415  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.514   0.356   0.353  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.638  -0.553  -0.083  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.880   0.280  -0.086  1.00  0.00           C  
HETATM    6  O1  UNL     1       3.491   0.543   0.943  1.00  0.00           O  
HETATM    7  C5  UNL     1      -1.810   0.662   0.891  1.00  0.00           C  
HETATM    8  O2  UNL     1      -1.579   1.242   1.984  1.00  0.00           O  
HETATM    9  O3  UNL     1      -2.927   0.912   0.137  1.00  0.00           O  
HETATM   10  H1  UNL     1      -1.361  -0.116  -1.548  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.127  -1.410  -0.782  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.721  -1.185   1.134  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.442   1.165  -0.419  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.739   0.781   1.335  1.00  0.00           H  
HETATM   15  H6  UNL     1       1.744  -1.422   0.601  1.00  0.00           H  
HETATM   16  H7  UNL     1       1.469  -0.883  -1.123  1.00  0.00           H  
HETATM   17  H8  UNL     1       3.270   0.671  -1.015  1.00  0.00           H  
HETATM   18  H9  UNL     1      -3.603   0.170  -0.107  1.00  0.00           H  
CONECT    1    2   10   11
CONECT    2    3    7   12
CONECT    3    4   13   14
CONECT    4    5   15   16
CONECT    5    6    6   17
CONECT    7    8    8    9
CONECT    9   18
END
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SMILES for #<Metabolite:0x00007fe2a2148660>

N[C@@H](CCC=O)C(O)=O
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INCHI for #<Metabolite:0x00007fe2a2148660>

InChI=1S/C5H9NO3/c6-4(5(8)9)2-1-3-7/h3-4H,1-2,6H2,(H,8,9)/t4-/m0/s1
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Synonyms
ValueSource
5-oxo-L-NorvalineChEBI
L-Glutamate 5-semialdehydeChEBI
L-Glutamate gamma-semialdehydeChEBI
L-Glutamic acid 5-semialdehydeGenerator
L-Glutamate g-semialdehydeGenerator
L-Glutamate γ-semialdehydeGenerator
L-Glutamic acid g-semialdehydeGenerator
L-Glutamic acid gamma-semialdehydeGenerator
L-Glutamic acid γ-semialdehydeGenerator
L-Glutamic g-semialdehydeGenerator
L-Glutamic γ-semialdehydeGenerator
Glutamate-semialdehydeHMDB
Glutamic gamma-semialdehydeHMDB
L-Glutamate-5-semialdehydeHMDB
L-Glutamate-gamma-semialdehydeHMDB
L-Glutamic-gamma-semialdehydeHMDB
gamma-Glutamyl semialdehydeHMDB
Glutamate gamma-semialdehydeHMDB
Glutamic acid gamma-semialdehydeHMDB
Glutamic acid gamma-semialdehyde, (L)-isomerHMDB
Molecular FormulaC5H9NO3
Average Mass131.1299
Monoisotopic Mass131.058243159
IUPAC Name(2S)-2-amino-5-oxopentanoic acid
Traditional Name4-carboxy-4-aminobutanal
CAS Registry Number496-92-4
SMILES
N[C@@H](CCC=O)C(O)=O
InChI Identifier
InChI=1S/C5H9NO3/c6-4(5(8)9)2-1-3-7/h3-4H,1-2,6H2,(H,8,9)/t4-/m0/s1
InChI KeyKABXUUFDPUOJMW-BYPYZUCNSA-N