Showing metabocard for L-4-hydroxyglutamic semialdehyde (MMDBc0033098)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 04:34:42 UTC
Update Date2024-04-30 20:00:10 UTC
Metabolite IDMMDBc0033098
Metabolite Identification
Common NameL-4-hydroxyglutamic semialdehyde
DescriptionL-4-Hydroxyglutamate semialdehyde is an intermediate in arginine and proline metabolism. L-4-Hydroxyglutamate semialdehyde is the 4th to last step in the synthesis of glyoxylate and is converted from L-erythro-4-hydroxyglutamate via the enzyme 1-pyrroline-5-carboxylate dehydrogenase [EC 1.5.1.12]. It is then converted to L-1-pyrroline-3-hydroxy-5-carboxylate via enzymatic reaction.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645c6483070>


  Mrv0541 02231220432D          

 10  9  0  0  1  0            999 V2000
   11.0637  -10.7310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3493  -10.3185    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.6348  -10.7310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9203  -10.3185    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.2058  -10.7310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9203   -9.4935    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.3493   -9.4935    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0637  -11.5560    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4914  -10.3185    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2058  -11.5560    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  4  6  1  1  0  0  0
  2  7  1  1  0  0  0
  8  1  2  0  0  0  0
  9  5  1  0  0  0  0
 10  5  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00005645c6483070>

HMDB0006556
     RDKit          3D
L-4-Hydroxyglutamate semialdehyde
 19 18  0  0  0  0  0  0  0  0999 V2000
    0.8377    0.8087    1.2291 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8422   -0.3885    0.4839 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1713   -0.2975   -0.6578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5539   -0.0692   -0.0429 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5739    1.0960    0.6878 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5593   -0.0088   -1.1317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2467    0.9879   -1.2586 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1633   -0.6668   -0.1194 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3690   -1.6825   -0.8177 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1904    0.2216    0.0982 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5940    1.4679    1.0861 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3689    0.8025    2.1382 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5240   -1.2305    1.1620 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1125    0.5439   -1.3122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1761   -1.2150   -1.2765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7792   -0.9417    0.6103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2201    1.0379    1.4400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6804   -0.8441   -1.8077 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9588    0.3782   -0.5112 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
  4  6  1  0
  6  7  2  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  1
  3 14  1  0
  3 15  1  0
  4 16  1  1
  5 17  1  0
  6 18  1  0
 10 19  1  0
M  END
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3D SDF for #<Metabolite:0x00005645c6483070>


  Mrv0541 02231220432D          

 10  9  0  0  1  0            999 V2000
   11.0637  -10.7310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3493  -10.3185    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.6348  -10.7310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9203  -10.3185    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.2058  -10.7310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9203   -9.4935    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.3493   -9.4935    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0637  -11.5560    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4914  -10.3185    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2058  -11.5560    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  4  6  1  1  0  0  0
  2  7  1  1  0  0  0
  8  1  2  0  0  0  0
  9  5  1  0  0  0  0
 10  5  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033098

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO4/c6-4(5(9)10)1-3(8)2-7/h2-4,8H,1,6H2,(H,9,10)/t3-,4+/m1/s1

> <INCHI_KEY>
XCXUZPXOFFRGGP-DMTCNVIQSA-N

> <FORMULA>
C5H9NO4

> <MOLECULAR_WEIGHT>
147.1293

> <EXACT_MASS>
147.053157781

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
13.130810279312207

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4R)-2-amino-4-hydroxy-5-oxopentanoic acid

> <ALOGPS_LOGP>
-2.99

> <JCHEM_LOGP>
-4.296244297936337

> <ALOGPS_LOGS>
-0.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.549436865682306

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8790602397153457

> <JCHEM_PKA_STRONGEST_BASIC>
8.737168455350945

> <JCHEM_POLAR_SURFACE_AREA>
100.62

> <JCHEM_REFRACTIVITY>
31.810900000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.28e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4R)-2-amino-4-hydroxy-5-oxopentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00005645c6483070>

HMDB0006556
     RDKit          3D
L-4-Hydroxyglutamate semialdehyde
 19 18  0  0  0  0  0  0  0  0999 V2000
    0.8377    0.8087    1.2291 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8422   -0.3885    0.4839 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1713   -0.2975   -0.6578 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5539   -0.0692   -0.0429 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5739    1.0960    0.6878 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5593   -0.0088   -1.1317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2467    0.9879   -1.2586 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1633   -0.6668   -0.1194 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3690   -1.6825   -0.8177 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1904    0.2216    0.0982 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5940    1.4679    1.0861 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3689    0.8025    2.1382 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5240   -1.2305    1.1620 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1125    0.5439   -1.3122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1761   -1.2150   -1.2765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7792   -0.9417    0.6103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2201    1.0379    1.4400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6804   -0.8441   -1.8077 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9588    0.3782   -0.5112 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
  4  6  1  0
  6  7  2  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  1
  3 14  1  0
  3 15  1  0
  4 16  1  1
  5 17  1  0
  6 18  1  0
 10 19  1  0
M  END
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PDB for #<Metabolite:0x00005645c6483070>

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      20.652 -20.031   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      19.319 -19.261   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      17.985 -20.031   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.651 -19.261   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      15.317 -20.031   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      16.651 -17.721   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      19.319 -17.721   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      20.652 -21.571   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      13.984 -19.261   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      15.317 -21.571   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4    9   10                                                  
CONECT    6    4                                                            
CONECT    7    2                                                            
CONECT    8    1                                                            
CONECT    9    5                                                            
CONECT   10    5                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for #<Metabolite:0x00005645c6483070>

COMPND    HMDB0006556
HETATM    1  N1  UNL     1       0.838   0.809   1.229  1.00  0.00           N  
HETATM    2  C1  UNL     1       0.842  -0.388   0.484  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.171  -0.297  -0.658  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.554  -0.069  -0.043  1.00  0.00           C  
HETATM    5  O1  UNL     1      -1.574   1.096   0.688  1.00  0.00           O  
HETATM    6  C4  UNL     1      -2.559  -0.009  -1.132  1.00  0.00           C  
HETATM    7  O2  UNL     1      -3.247   0.988  -1.259  1.00  0.00           O  
HETATM    8  C5  UNL     1       2.163  -0.667  -0.119  1.00  0.00           C  
HETATM    9  O3  UNL     1       2.369  -1.682  -0.818  1.00  0.00           O  
HETATM   10  O4  UNL     1       3.190   0.222   0.098  1.00  0.00           O  
HETATM   11  H1  UNL     1       1.594   1.468   1.086  1.00  0.00           H  
HETATM   12  H2  UNL     1       0.369   0.803   2.138  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.524  -1.231   1.162  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.113   0.544  -1.312  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.176  -1.215  -1.276  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.779  -0.942   0.610  1.00  0.00           H  
HETATM   17  H7  UNL     1      -2.220   1.038   1.440  1.00  0.00           H  
HETATM   18  H8  UNL     1      -2.680  -0.844  -1.808  1.00  0.00           H  
HETATM   19  H9  UNL     1       3.959   0.378  -0.511  1.00  0.00           H  
CONECT    1    2   11   12
CONECT    2    3    8   13
CONECT    3    4   14   15
CONECT    4    5    6   16
CONECT    5   17
CONECT    6    7    7   18
CONECT    8    9    9   10
CONECT   10   19
END
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SMILES for #<Metabolite:0x00005645c6483070>

N[C@@H](C[C@@H](O)C=O)C(O)=O
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INCHI for #<Metabolite:0x00005645c6483070>

InChI=1S/C5H9NO4/c6-4(5(9)10)1-3(8)2-7/h2-4,8H,1,6H2,(H,9,10)/t3-,4+/m1/s1
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Synonyms
ValueSource
(4R)-4-Hydroxy-5-oxo-L-norvalineChEBI
4-Amino-3,4-dideoxy-D-erythro-penturonic acidChEBI
4-Amino-3,4-dideoxy-D-erythro-penturonateGenerator
L-4-Hydroxyglutamic acid semialdehydeGenerator
Molecular FormulaC5H9NO4
Average Mass147.1293
Monoisotopic Mass147.053157781
IUPAC Name(2S,4R)-2-amino-4-hydroxy-5-oxopentanoic acid
Traditional Name(2S,4R)-2-amino-4-hydroxy-5-oxopentanoic acid
CAS Registry NumberNot Available
SMILES
N[C@@H](C[C@@H](O)C=O)C(O)=O
InChI Identifier
InChI=1S/C5H9NO4/c6-4(5(9)10)1-3(8)2-7/h2-4,8H,1,6H2,(H,9,10)/t3-,4+/m1/s1
InChI KeyXCXUZPXOFFRGGP-DMTCNVIQSA-N