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Showing metabocard for Succinylserine (HMDB0341441)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 21:12:56 UTC
Update Date2022-09-22 18:35:16 UTC
HMDB IDHMDB0341441
Secondary Accession NumbersNone
Metabolite Identification
Common NameSuccinylserine
DescriptionSuccinylserine, also known as ser(suc)OH, 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. Based on a literature review a small amount of articles have been published on Succinylserine.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341441 (Succinylserine)


  Mrv1652309092223512D          

 14 13  0  0  1  0            999 V2000
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2836    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  7 11  1  6  0  0  0
  1 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
M  END
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3D MOL for HMDB0341441 (Succinylserine)

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3D SDF for HMDB0341441 (Succinylserine)

  Mrv1652309092223512D          

 14 13  0  0  1  0            999 V2000
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2836    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  7 11  1  6  0  0  0
  1 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0341441

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H11NO6/c8-4(7(12)13)3-14-6(11)2-1-5(9)10/h4H,1-3,8H2,(H,9,10)(H,12,13)/t4-/m0/s1

> <INCHI_KEY>
ZAHSBRLHJRVFAU-BYPYZUCNSA-N

> <FORMULA>
C7H11NO6

> <MOLECULAR_WEIGHT>
205.166

> <EXACT_MASS>
205.058637078

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
18.46678200140598

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-[(2S)-2-amino-2-carboxyethoxy]-4-oxobutanoic acid

> <JCHEM_LOGP>
-3.675699988274044

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.007762124033174

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6349274092133426

> <JCHEM_PKA_STRONGEST_BASIC>
8.603146122997607

> <JCHEM_POLAR_SURFACE_AREA>
126.92

> <JCHEM_REFRACTIVITY>
42.085800000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
4-[(2S)-2-amino-2-carboxyethoxy]-4-oxobutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341441 (Succinylserine)
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PDB for HMDB0341441 (Succinylserine)
HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      10.931   6.311   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       9.597   4.001   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.596   4.771   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.263   4.001   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       5.596   6.311   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0       6.930   2.461   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      14.932   2.461   0.000  0.00  0.00           O+0
CONECT    1    2   12                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   11                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    7                                                            
CONECT   12    1   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

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3D PDB for HMDB0341441 (Succinylserine)
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SMILES for HMDB0341441 (Succinylserine)
N[C@@H](COC(=O)CCC(O)=O)C(O)=O
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INCHI for HMDB0341441 (Succinylserine)
InChI=1S/C7H11NO6/c8-4(7(12)13)3-14-6(11)2-1-5(9)10/h4H,1-3,8H2,(H,9,10)(H,12,13)/t4-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
O-SuccinylserineChEBI
Ser(suc)OHChEBI
Chemical FormulaC7H11NO6
Average Molecular Weight205.166
Monoisotopic Molecular Weight205.058637078
IUPAC Name4-[(2S)-2-amino-2-carboxyethoxy]-4-oxobutanoic acid
Traditional Name4-[(2S)-2-amino-2-carboxyethoxy]-4-oxobutanoic acid
CAS Registry NumberNot Available
SMILES
N[C@@H](COC(=O)CCC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C7H11NO6/c8-4(7(12)13)3-14-6(11)2-1-5(9)10/h4H,1-3,8H2,(H,9,10)(H,12,13)/t4-/m0/s1
InChI KeyZAHSBRLHJRVFAU-BYPYZUCNSA-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
    • 

  • Tricarboxylic acid or derivatives
    • 

  • Fatty acid ester
    • 

  • Fatty acyl
    • 

  • Carboxylic acid ester
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Amine
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
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
PropertyValueSource
logP-3.7ChemAxon
pKa (Strongest Acidic)1.63ChemAxon
pKa (Strongest Basic)8.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area126.92 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity42.09 m³·mol⁻¹ChemAxon
Polarizability18.47 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Kovats Retention Indices
Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma  details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma  details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID64808712  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12086047  
PDB IDNot Available
ChEBI ID134286  
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 References
  1. Meister I, Zhang P, Sinha A, Skold CM, Wheelock AM, Izumi T, Chaleckis R, Wheelock CE: High-Precision Automated Workflow for Urinary Untargeted Metabolomic Epidemiology. Anal Chem. 2021 Mar 30;93(12):5248-5258. doi: 10.1021/acs.analchem.1c00203. Epub  2021 Mar 19. [PubMed:33739820  ]