Showing metabocard for L-Homoserine (MMDBc0000144)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:37:28 UTC
Update Date2024-10-13 08:06:03 UTC
Metabolite IDMMDBc0000144
Metabolite Identification
Common NameL-Homoserine
DescriptionHomoserine is a more reactive variant of the amino acid serine. In this variant, the hydroxyl side chain contains an additional CH2 group which brings the hydroxyl group closer to its own carboxyl group, allowing it to chemically react to form a five-membered ring. This occurs at the point that amino acids normally join to their neighbours in a peptide bond. Homoserine is therefore unsuitable for forming proteins and has been eliminated from the repertoire of amino acids used by living things. Homoserine is the final product on the C-terminal end of the N-terminal fragment following a cyanogen bromide cleavage. (wikipedia). Homoserine is also a microbial metabolite.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9258055b30>


  Mrv1652309042000062D          

  8  7  0  0  1  0            999 V2000
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f9258055b30>

HMDB0000719
     RDKit          3D
L-Homoserine
 17 16  0  0  0  0  0  0  0  0999 V2000
   -1.5027    1.3775   -0.2642 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6651    0.2448   -0.6080 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7316    0.4466   -0.1212 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6854   -0.6504   -0.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9530   -0.3506    0.0855 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3218   -0.9768   -0.1869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8478   -2.1255   -0.3475 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5541   -0.9328    0.4384 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3720    1.0996    0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9580    2.0130    0.3695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6055    0.2668   -1.7390 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1610    1.3917   -0.5153 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6859    0.5784    0.9847 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4135   -1.6355   -0.0287 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8315   -0.7809   -1.5264 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0045    0.6473    0.2037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6395   -0.6131    1.4103 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
  2  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  6
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  8 17  1  0
M  END
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3D SDF for #<Metabolite:0x00007f9258055b30>


  Mrv1652309042000062D          

  8  7  0  0  1  0            999 V2000
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000144

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H9NO3/c5-3(1-2-6)4(7)8/h3,6H,1-2,5H2,(H,7,8)/t3-/m0/s1

> <INCHI_KEY>
UKAUYVFTDYCKQA-VKHMYHEASA-N

> <FORMULA>
C4H9NO3

> <MOLECULAR_WEIGHT>
119.1192

> <EXACT_MASS>
119.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.439148714602187

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-4-hydroxybutanoic acid

> <ALOGPS_LOGP>
-3.31

> <JCHEM_LOGP>
-3.8277325124850385

> <ALOGPS_LOGS>
0.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.933083327320805

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.223319649729163

> <JCHEM_PKA_STRONGEST_BASIC>
9.159110100742131

> <JCHEM_POLAR_SURFACE_AREA>
83.55000000000001

> <JCHEM_REFRACTIVITY>
26.906399999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.23e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-homoserine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f9258055b30>

HMDB0000719
     RDKit          3D
L-Homoserine
 17 16  0  0  0  0  0  0  0  0999 V2000
   -1.5027    1.3775   -0.2642 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6651    0.2448   -0.6080 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7316    0.4466   -0.1212 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6854   -0.6504   -0.4150 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9530   -0.3506    0.0855 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3218   -0.9768   -0.1869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8478   -2.1255   -0.3475 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5541   -0.9328    0.4384 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3720    1.0996    0.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9580    2.0130    0.3695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6055    0.2668   -1.7390 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1610    1.3917   -0.5153 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6859    0.5784    0.9847 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4135   -1.6355   -0.0287 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8315   -0.7809   -1.5264 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0045    0.6473    0.2037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6395   -0.6131    1.4103 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
  2  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  6
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  8 17  1  0
M  END
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PDB for #<Metabolite:0x00007f9258055b30>

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       3.644   3.644   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.357   1.334   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    2    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for #<Metabolite:0x00007f9258055b30>

COMPND    HMDB0000719
HETATM    1  N1  UNL     1      -1.503   1.378  -0.264  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.665   0.245  -0.608  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.732   0.447  -0.121  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.685  -0.650  -0.415  1.00  0.00           C  
HETATM    5  O1  UNL     1       2.953  -0.351   0.086  1.00  0.00           O  
HETATM    6  C4  UNL     1      -1.322  -0.977  -0.187  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.848  -2.126  -0.347  1.00  0.00           O  
HETATM    8  O3  UNL     1      -2.554  -0.933   0.438  1.00  0.00           O  
HETATM    9  H1  UNL     1      -2.372   1.100   0.247  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.958   2.013   0.369  1.00  0.00           H  
HETATM   11  H3  UNL     1      -0.606   0.267  -1.739  1.00  0.00           H  
HETATM   12  H4  UNL     1       1.161   1.392  -0.515  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.686   0.578   0.985  1.00  0.00           H  
HETATM   14  H6  UNL     1       1.414  -1.635  -0.029  1.00  0.00           H  
HETATM   15  H7  UNL     1       1.831  -0.781  -1.526  1.00  0.00           H  
HETATM   16  H8  UNL     1       3.005   0.647   0.204  1.00  0.00           H  
HETATM   17  H9  UNL     1      -2.640  -0.613   1.410  1.00  0.00           H  
CONECT    1    2    9   10
CONECT    2    3    6   11
CONECT    3    4   12   13
CONECT    4    5   14   15
CONECT    5   16
CONECT    6    7    7    8
CONECT    8   17
END
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SMILES for #<Metabolite:0x00007f9258055b30>

N[C@@H](CCO)C(O)=O
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INCHI for #<Metabolite:0x00007f9258055b30>

InChI=1S/C4H9NO3/c5-3(1-2-6)4(7)8/h3,6H,1-2,5H2,(H,7,8)/t3-/m0/s1
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Synonyms
ValueSource
(2S)-2-Amino-4-hydroxybutanoic acidChEBI
2-Amino-4-hydroxybutanoic acidChEBI
2-Amino-4-hydroxybutyric acidChEBI
HomoserineChEBI
(2S)-2-Amino-4-hydroxybutanoateGenerator
2-Amino-4-hydroxybutanoateGenerator
2-Amino-4-hydroxybutyrateGenerator
(S)-2-Amino-4-hydroxy-butanoateHMDB
(S)-2-Amino-4-hydroxy-butanoic acidHMDB
(S)-2-Amino-4-hydroxybutanoateHMDB
(S)-2-Amino-4-hydroxybutanoic acidHMDB
(S)-HomoserineHMDB
2-Amino-4-hydroxy-butyrateHMDB
2-Amino-4-hydroxy-butyric acidHMDB
2-Amino-4-hydroxy-L-butyrateHMDB
2-Amino-4-hydroxy-L-butyric acidHMDB
Homoserine L-isomerHMDB
L Isomer OF homoserineHMDB
L-Isomer OF homoserineHMDB
Molecular FormulaC4H9NO3
Average Mass119.1192
Monoisotopic Mass119.058243159
IUPAC Name(2S)-2-amino-4-hydroxybutanoic acid
Traditional NameL-homoserine
CAS Registry Number672-15-1
SMILES
N[C@@H](CCO)C(O)=O
InChI Identifier
InChI=1S/C4H9NO3/c5-3(1-2-6)4(7)8/h3,6H,1-2,5H2,(H,7,8)/t3-/m0/s1
InChI KeyUKAUYVFTDYCKQA-VKHMYHEASA-N