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Showing metabocard for Allysine (HMDB0001263)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:34 UTC
HMDB IDHMDB0001263
Secondary Accession Numbers
  • HMDB0059595
  • HMDB01263
  • HMDB59595
Metabolite Identification
Common NameAllysine
DescriptionAllysine (CAS: 1962-83-0), also known as 2-amino-6-oxohexanoic acid or 6-oxonorleucine, belongs to the class of organic compounds known as alpha-amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Outside of the human body, allysine has been detected, but not quantified in, several different foods, such as winged beans, wasabi, common verbena, arrowhead, and oats. This could make allysine a potential biomarker for the consumption of these foods. Allysine is a derivative of lysine used in the production of elastin and collagen. It is produced by the actions of the enzyme lysyl oxidase in the extracellular matrix and is essential in the crosslink formation that stabilizes collagen and elastin.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001263 (Allysine)

  Mrv1652306222023452D          

 11 10  0  0  1  0            999 V2000
    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
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   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
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   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
    4.6184    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  5  7  1  1  0  0  0
  8  4  2  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
  5 11  1  1  0  0  0
M  END
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3D MOL for HMDB0001263 (Allysine)

HMDB0001263
     RDKit          3D
Allysine
 21 20  0  0  0  0  0  0  0  0999 V2000
    1.0379   -1.2244   -1.0501 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8705    0.0339   -0.3542 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2721   -0.2858    0.9977 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0522   -0.9700    0.7965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0520   -0.1528    0.0476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3876    1.1228    0.7014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9017    1.4714    1.7416 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1629    0.7077   -0.2759 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1752    0.1630   -0.7772 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3253    1.9416    0.3368 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3889   -1.9217   -0.3376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7764   -1.0906   -1.7986 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1533    0.7053   -0.8705 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2495    0.5637    1.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9431   -1.0537    1.4835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4841   -1.3420    1.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8445   -1.8816    0.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9918   -0.7772    0.0002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7605    0.0200   -1.0011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1067    1.7662    0.2112 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2259    2.2042    0.7471 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  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  6
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  6 20  1  0
 10 21  1  0
M  END
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3D SDF for HMDB0001263 (Allysine)

  Mrv1652306222023452D          

 11 10  0  0  1  0            999 V2000
    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
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   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
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   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
    4.6184    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  5  7  1  1  0  0  0
  8  4  2  0  0  0  0
  9  6  2  0  0  0  0
 10  6  1  0  0  0  0
  5 11  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0001263

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO3/c7-5(6(9)10)3-1-2-4-8/h4-5H,1-3,7H2,(H,9,10)/t5-/m0/s1

> <INCHI_KEY>
GFXYTQPNNXGICT-YFKPBYRVSA-N

> <FORMULA>
C6H11NO3

> <MOLECULAR_WEIGHT>
145.1564

> <EXACT_MASS>
145.073893223

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.583357065587663

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-6-oxohexanoic acid

> <ALOGPS_LOGP>
-2.20

> <JCHEM_LOGP>
-2.9081307009163337

> <ALOGPS_LOGS>
-0.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.588756721963396

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.249930329891744

> <JCHEM_PKA_STRONGEST_BASIC>
9.326170574223008

> <JCHEM_POLAR_SURFACE_AREA>
80.39000000000001

> <JCHEM_REFRACTIVITY>
34.963300000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.94e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-amino-6-oxo-hexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0001263 (Allysine)

HMDB0001263
     RDKit          3D
Allysine
 21 20  0  0  0  0  0  0  0  0999 V2000
    1.0379   -1.2244   -1.0501 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8705    0.0339   -0.3542 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2721   -0.2858    0.9977 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0522   -0.9700    0.7965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0520   -0.1528    0.0476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3876    1.1228    0.7014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9017    1.4714    1.7416 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1629    0.7077   -0.2759 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1752    0.1630   -0.7772 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3253    1.9416    0.3368 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3889   -1.9217   -0.3376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7764   -1.0906   -1.7986 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1533    0.7053   -0.8705 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2495    0.5637    1.6795 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9431   -1.0537    1.4835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4841   -1.3420    1.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8445   -1.8816    0.1757 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9918   -0.7772    0.0002 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7605    0.0200   -1.0011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1067    1.7662    0.2112 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2259    2.2042    0.7471 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  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  6
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  6 20  1  0
 10 21  1  0
M  END
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PDB for HMDB0001263 (Allysine)

HEADER    PROTEIN                                 22-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JUN-20         0                                  
HETATM    1  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   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       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       8.621   4.977   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0       1.953   2.667   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
HETATM   11  H   UNK     0       8.621   1.897   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    8                                                       
CONECT    5    3    6    7   11                                             
CONECT    6    5    9   10                                                  
CONECT    7    5                                                            
CONECT    8    4                                                            
CONECT    9    6                                                            
CONECT   10    6                                                            
CONECT   11    5                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0001263 (Allysine)

COMPND    HMDB0001263
HETATM    1  N1  UNL     1       1.038  -1.224  -1.050  1.00  0.00           N  
HETATM    2  C1  UNL     1       0.870   0.034  -0.354  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.272  -0.286   0.998  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.052  -0.970   0.797  1.00  0.00           C  
HETATM    5  C4  UNL     1      -2.052  -0.153   0.048  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.388   1.123   0.701  1.00  0.00           C  
HETATM    7  O1  UNL     1      -1.902   1.471   1.742  1.00  0.00           O  
HETATM    8  C6  UNL     1       2.163   0.708  -0.276  1.00  0.00           C  
HETATM    9  O2  UNL     1       3.175   0.163  -0.777  1.00  0.00           O  
HETATM   10  O3  UNL     1       2.325   1.942   0.337  1.00  0.00           O  
HETATM   11  H1  UNL     1       1.389  -1.922  -0.338  1.00  0.00           H  
HETATM   12  H2  UNL     1       1.776  -1.091  -1.799  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.153   0.705  -0.871  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.249   0.564   1.680  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.943  -1.054   1.484  1.00  0.00           H  
HETATM   16  H6  UNL     1      -1.484  -1.342   1.745  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.844  -1.882   0.176  1.00  0.00           H  
HETATM   18  H8  UNL     1      -2.992  -0.777   0.000  1.00  0.00           H  
HETATM   19  H9  UNL     1      -1.761   0.020  -1.001  1.00  0.00           H  
HETATM   20  H10 UNL     1      -3.107   1.766   0.211  1.00  0.00           H  
HETATM   21  H11 UNL     1       3.226   2.204   0.747  1.00  0.00           H  
CONECT    1    2   11   12
CONECT    2    3    8   13
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6   18   19
CONECT    6    7    7   20
CONECT    8    9    9   10
CONECT   10   21
END
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SMILES for HMDB0001263 (Allysine)

[H][C@](N)(CCCC=O)C(O)=O
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INCHI for HMDB0001263 (Allysine)

InChI=1S/C6H11NO3/c7-5(6(9)10)3-1-2-4-8/h4-5H,1-3,7H2,(H,9,10)/t5-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H11NO3
Average Molecular Weight145.1564
Monoisotopic Molecular Weight145.073893223
IUPAC Name(2S)-2-amino-6-oxohexanoic acid
Traditional Name2-amino-6-oxo-hexanoic acid
CAS Registry Number6665-12-9
SMILES
[H][C@](N)(CCCC=O)C(O)=O
InChI Identifier
InChI=1S/C6H11NO3/c7-5(6(9)10)3-1-2-4-8/h4-5H,1-3,7H2,(H,9,10)/t5-/m0/s1
InChI KeyGFXYTQPNNXGICT-YFKPBYRVSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Medium-chain fatty acid
  • Amino fatty acid
  • Fatty acyl
  • Fatty acid
  • Alpha-hydrogen aldehyde
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Aldehyde
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Primary aliphatic amine
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Amine
  • Organic nitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Industrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified<0.2 uMInfant (0-1 year old)Not SpecifiedNormal details
UrineDetected and Quantified<1 umol/mmol creatinineInfant (0-1 year old)Not SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified1.6-28 umol/mmol creatinineInfant (0-1 year old)Not SpecifiedPyridoxine dependency with seizures (PDE) details
Associated Disorders and Diseases
Disease References
Pyridoxine-dependent epilepsy
  1. Plecko B, Paul K, Paschke E, Stoeckler-Ipsiroglu S, Struys E, Jakobs C, Hartmann H, Luecke T, di Capua M, Korenke C, Hikel C, Reutershahn E, Freilinger M, Baumeister F, Bosch F, Erwa W: Biochemical and molecular characterization of 18 patients with pyridoxine-dependent epilepsy and mutations of the antiquitin (ALDH7A1) gene. Hum Mutat. 2007 Jan;28(1):19-26. [PubMed:17068770 ]
Associated OMIM IDs
  • 266100 (Pyridoxine-dependent epilepsy)
DrugBank IDDB02571
Phenol Explorer Compound IDNot Available
FooDB IDFDB010644
KNApSAcK IDNot Available
Chemspider ID141126
KEGG Compound IDC04076
BioCyc IDALLYSINE
BiGG IDNot Available
Wikipedia LinkAllysine
METLIN IDNot Available
PubChem Compound160603
PDB IDNot Available
ChEBI ID17917
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Carbonyl reductase [NADPH] 1
General function:
Involved in oxidoreductase activity
Specific function:
NADPH-dependent reductase with broad substrate specificity. Catalyzes the reduction of a wide variety of carbonyl compounds including quinones, prostaglandins, menadione, plus various xenobiotics. Catalyzes the reduction of the antitumor anthracyclines doxorubicin and daunorubicin to the cardiotoxic compounds doxorubicinol and daunorubicinol. Can convert prostaglandin E2 to prostaglandin F2-alpha. Can bind glutathione, which explains its higher affinity for glutathione-conjugated substrates. Catalyzes the reduction of S-nitrosoglutathione.
Gene Name:
CBR1
Uniprot ID:
P16152
Molecular weight:
30374.73
Reactions
Allysine → 2-amino-6-hydroxyhexanoic aciddetails
Enzyme Details
2. Aldehyde oxidase
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
AOX1
Uniprot ID:
Q06278
Molecular weight:
147916.735
Reactions
Allysine → Aminoadipic aciddetails
Enzyme Details
3. Alpha-aminoadipic semialdehyde dehydrogenase
General function:
Involved in oxidoreductase activity
Specific function:
Multifunctional enzyme mediating important protective effects. Metabolizes betaine aldehyde to betaine, an important cellular osmolyte and methyl donor. Protects cells from oxidative stress by metabolizing a number of lipid peroxidation-derived aldehydes. Involved in lysine catabolism.
Gene Name:
ALDH7A1
Uniprot ID:
P49419
Molecular weight:
58486.74
Reactions
Allysine + NAD(P)(+) + Water → Aminoadipic acid + NAD(P)Hdetails
Allysine + NAD + Water → Aminoadipic acid + NADH + Hydrogen Iondetails
Allysine + NADP + Water → Aminoadipic acid + NADPH + Hydrogen Iondetails
alpha-Aminoadipoyl-S-acyl enzyme + NADPH + Hydrogen Ion → Allysine + Holo-Lys2 + NADPdetails
Enzyme Details
4. Alpha-aminoadipic semialdehyde synthase, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Bifunctional enzyme that catalyzes the first two steps in lysine degradation. The N-terminal and the C-terminal contain lysine-ketoglutarate reductase and saccharopine dehydrogenase activity, respectively.
Gene Name:
AASS
Uniprot ID:
Q9UDR5
Molecular weight:
102130.895
Reactions
N(6)-(L-1,3-dicarboxypropyl)-L-lysine + NAD + Water → Glutamic acid + Allysine + NADHdetails
Saccharopine + NAD + Water → Glutamic acid + Allysine + NADH + Hydrogen Iondetails
Enzyme Details
5. Acyl-CoA synthetase family member 4
General function:
Involved in acyl carrier activity
Specific function:
Acyl-CoA synthases catalyze the initial reaction in fatty acid metabolism, by forming a thioester with CoA
Gene Name:
AASDH
Uniprot ID:
Q4L235
Molecular weight:
122596.1
Enzyme Details
6. 5-phosphohydroxy-L-lysine phospho-lyase
General function:
Involved in transaminase activity
Specific function:
Catalyzes the pyridoxal-phosphate-dependent breakdown of 5-phosphohydroxy-L-lysine, converting it to ammonia, inorganic phosphate and 2-aminoadipate semialdehyde.
Gene Name:
AGXT2L2
Uniprot ID:
Q8IUZ5
Molecular weight:
49710.245
Reactions
5-phosphonooxy-L-lysine + Water → Allysine + Ammonia + Phosphatedetails