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Showing metabocard for (2R,3S)-2,3-dimethylmalate (HMDB0303969)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 06:04:37 UTC
Update Date2021-09-24 06:04:37 UTC
HMDB IDHMDB0303969
Secondary Accession NumbersNone
Metabolite Identification
Common Name(2R,3S)-2,3-dimethylmalate
Description (2r,3s)-2,3-dimethylmalate is soluble (in water) and a weakly acidic compound (based on its pKa). (2r,3s)-2,3-dimethylmalate can be found in a number of food items such as pepper (c. frutescens), oregon yampah, green bean, and red raspberry, which makes (2r,3s)-2,3-dimethylmalate a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303969 ((2R,3S)-2,3-dimethylmalate)


  Mrv1533005141521352D          

 11 10  0  0  0  0            999 V2000
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.1434    0.0000 O   0  5  0  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
    1.9520    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  5  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
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
M  CHG  2   5  -1  11  -1
M  END
Download

3D MOL for HMDB0303969 ((2R,3S)-2,3-dimethylmalate)

HMDB0303969
     RDKit          3D
(2R,3S)-2,3-dimethylmalate
 19 18  0  0  0  0  0  0  0  0999 V2000
    1.5597    0.2890   -0.8337 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7730    0.2484    0.4490 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3029   -0.8071    1.3071 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4148   -0.6841    1.8564 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5866   -1.9604    1.5281 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.7127    0.1613    0.2111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1185   -1.0656   -0.5610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3203    0.0858    1.4569 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1246    1.4031   -0.4673 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7037    1.6903   -1.6072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9902    2.2714    0.1582 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.5416   -0.2123   -0.6948 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0590   -0.2606   -1.6668 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7707    1.3520   -1.1426 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9237    1.2540    0.9446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7698   -1.7450    0.0259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2515   -1.6444   -0.9378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6915   -0.7737   -1.4710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2491    0.3980    1.4450 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  6  7  1  0
  6  8  1  0
  6  9  1  0
  9 10  2  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  7 16  1  0
  7 17  1  0
  7 18  1  0
  8 19  1  0
M  CHG  2   5  -1  11  -1
M  END
Download

3D SDF for HMDB0303969 ((2R,3S)-2,3-dimethylmalate)


  Mrv1533005141521352D          

 11 10  0  0  0  0            999 V2000
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.1434    0.0000 O   0  5  0  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
    1.9520    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  5  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
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
M  CHG  2   5  -1  11  -1
M  END
> <DATABASE_ID>
HMDB0303969

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C([O-])=O)C(C)(O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O5/c1-3(4(7)8)6(2,11)5(9)10/h3,11H,1-2H3,(H,7,8)(H,9,10)/p-2

> <INCHI_KEY>
WTIIULQJLZEHGZ-UHFFFAOYSA-L

> <FORMULA>
C6H8O5

> <MOLECULAR_WEIGHT>
160.126

> <EXACT_MASS>
160.038270517

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
13.64170415113749

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-2,3-dimethylbutanedioate

> <ALOGPS_LOGP>
-0.08

> <JCHEM_LOGP>
-0.1378892636666666

> <ALOGPS_LOGS>
-0.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.402319009058225

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5013361723320924

> <JCHEM_PKA_STRONGEST_BASIC>
-4.053853431713915

> <JCHEM_POLAR_SURFACE_AREA>
100.49000000000001

> <JCHEM_REFRACTIVITY>
55.8372

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.71e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dimethylmalate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0303969 ((2R,3S)-2,3-dimethylmalate)

HMDB0303969
     RDKit          3D
(2R,3S)-2,3-dimethylmalate
 19 18  0  0  0  0  0  0  0  0999 V2000
    1.5597    0.2890   -0.8337 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7730    0.2484    0.4490 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3029   -0.8071    1.3071 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4148   -0.6841    1.8564 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5866   -1.9604    1.5281 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.7127    0.1613    0.2111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1185   -1.0656   -0.5610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3203    0.0858    1.4569 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1246    1.4031   -0.4673 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7037    1.6903   -1.6072 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9902    2.2714    0.1582 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.5416   -0.2123   -0.6948 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0590   -0.2606   -1.6668 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7707    1.3520   -1.1426 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9237    1.2540    0.9446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7698   -1.7450    0.0259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2515   -1.6444   -0.9378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6915   -0.7737   -1.4710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2491    0.3980    1.4450 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  6  7  1  0
  6  8  1  0
  6  9  1  0
  9 10  2  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  7 16  1  0
  7 17  1  0
  7 18  1  0
  8 19  1  0
M  CHG  2   5  -1  11  -1
M  END
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PDB for HMDB0303969 ((2R,3S)-2,3-dimethylmalate)

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.080   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   4.001   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.080   5.335   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       0.770   4.001   0.000  0.00  0.00           O-1
HETATM    6  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.644   0.564   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    2    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0303969 ((2R,3S)-2,3-dimethylmalate)

COMPND    HMDB0303969
HETATM    1  C1  UNL     1       1.560   0.289  -0.834  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.773   0.248   0.449  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.303  -0.807   1.307  1.00  0.00           C  
HETATM    4  O1  UNL     1       2.415  -0.684   1.856  1.00  0.00           O  
HETATM    5  O2  UNL     1       0.587  -1.960   1.528  1.00  0.00           O1-
HETATM    6  C4  UNL     1      -0.713   0.161   0.211  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.118  -1.066  -0.561  1.00  0.00           C  
HETATM    8  O3  UNL     1      -1.320   0.086   1.457  1.00  0.00           O  
HETATM    9  C6  UNL     1      -1.125   1.403  -0.467  1.00  0.00           C  
HETATM   10  O4  UNL     1      -0.704   1.690  -1.607  1.00  0.00           O  
HETATM   11  O5  UNL     1      -1.990   2.271   0.158  1.00  0.00           O1-
HETATM   12  H1  UNL     1       2.542  -0.212  -0.695  1.00  0.00           H  
HETATM   13  H2  UNL     1       1.059  -0.261  -1.667  1.00  0.00           H  
HETATM   14  H3  UNL     1       1.771   1.352  -1.143  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.924   1.254   0.945  1.00  0.00           H  
HETATM   16  H5  UNL     1      -1.770  -1.745   0.026  1.00  0.00           H  
HETATM   17  H6  UNL     1      -0.252  -1.644  -0.938  1.00  0.00           H  
HETATM   18  H7  UNL     1      -1.692  -0.774  -1.471  1.00  0.00           H  
HETATM   19  H8  UNL     1      -2.249   0.398   1.445  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    6   15
CONECT    3    4    4    5
CONECT    6    7    8    9
CONECT    7   16   17   18
CONECT    8   19
CONECT    9   10   10   11
END
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SMILES for HMDB0303969 ((2R,3S)-2,3-dimethylmalate)

CC(C([O-])=O)C(C)(O)C([O-])=O
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INCHI for HMDB0303969 ((2R,3S)-2,3-dimethylmalate)

InChI=1S/C6H10O5/c1-3(4(7)8)6(2,11)5(9)10/h3,11H,1-2H3,(H,7,8)(H,9,10)/p-2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Hydroxy-2,3-dimethylbutanedioic acidGenerator
(2R,3S)-2,3-Dimethylmalic acidGenerator
Chemical FormulaC6H8O5
Average Molecular Weight160.126
Monoisotopic Molecular Weight160.038270517
IUPAC Name2-hydroxy-2,3-dimethylbutanedioate
Traditional Name2,3-dimethylmalate
CAS Registry NumberNot Available
SMILES
CC(C([O-])=O)C(C)(O)C([O-])=O
InChI Identifier
InChI=1S/C6H10O5/c1-3(4(7)8)6(2,11)5(9)10/h3,11H,1-2H3,(H,7,8)(H,9,10)/p-2
InChI KeyWTIIULQJLZEHGZ-UHFFFAOYSA-L
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Branched fatty acid
  • Methyl-branched fatty acid
  • Short-chain hydroxy acid
  • Hydroxy fatty acid
  • Dicarboxylic acid or derivatives
  • Tertiary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Alcohol
  • Organic oxygen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Carbonyl group
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot 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-0.08ALOGPS
logP-0.14ChemAxon
logS-0.41ALOGPS
pKa (Strongest Acidic)3.5ChemAxon
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area100.49 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity55.84 m³·mol⁻¹ChemAxon
Polarizability13.64 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+135.32132859911
AllCCS[M+H-H2O]+131.37432859911
AllCCS[M+Na]+140.05532859911
AllCCS[M+NH4]+138.99632859911
AllCCS[M-H]-125.23532859911
AllCCS[M+Na-2H]-127.01332859911
AllCCS[M+HCOO]-129.01532859911
DeepCCS[M+H]+124.52730932474
DeepCCS[M-H]-120.80930932474
DeepCCS[M-2H]-157.36830932474
DeepCCS[M+Na]+133.08930932474

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030111
KNApSAcK IDNot Available
Chemspider ID11200799
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound22169130
PDB IDNot Available
ChEBI IDNot Available
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