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Showing metabocard for 2,2-Dimethylbutyric acid (HMDB0245333)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:24:51 UTC
Update Date2021-09-26 22:53:45 UTC
HMDB IDHMDB0245333
Secondary Accession NumbersNone
Metabolite Identification
Common Name2,2-Dimethylbutyric acid
Description2,2-dimethylbutyric acid, also known as DMB or a,a-dimethylbutanoate, belongs to the class of organic compounds known as methyl-branched fatty acids. These are fatty acids with an acyl chain that has a methyl branch. Usually, they are saturated and contain only one or more methyl group. However, branches other than methyl may be present. Based on a literature review a small amount of articles have been published on 2,2-dimethylbutyric acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2,2-dimethylbutyric acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2,2-Dimethylbutyric acid is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0245333 (2,2-Dimethylbutyric acid)


  Mrv1572004221603532D          

  8  7  0  0  0  0            999 V2000
    1.2375    2.1434    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 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
    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 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  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  6  2  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  5  2  0  0  0  0
  8  5  1  0  0  0  0
M  END
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3D MOL for HMDB0245333 (2,2-Dimethylbutyric acid)

HMDB0245333
     RDKit          3D
2,2-Dimethylbutyric acid
 20 19  0  0  0  0  0  0  0  0999 V2000
    1.9788   -0.5999   -0.4081 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0638    0.0787    0.5883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3856    0.0179    0.1361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8558   -1.4036   -0.0153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5522    0.6656   -1.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1775    0.6938    1.1739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0701    0.0917    1.7914 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9309    2.0104    1.4692 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9371   -0.0047   -1.3512 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0008   -0.5736    0.0414 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6068   -1.6288   -0.5367 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1488   -0.4782    1.5325 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3799    1.1065    0.7745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9530   -1.3528   -0.2337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3884   -1.8920   -0.8741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7034   -1.9243    0.9470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3775   -0.0934   -2.0219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6285    0.9651   -1.2925 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0740    1.5569   -1.3578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1673    2.7648    0.8701 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
  3  5  1  0
  3  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  4 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  5 19  1  0
  8 20  1  0
M  END
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3D SDF for HMDB0245333 (2,2-Dimethylbutyric acid)


  Mrv1572004221603532D          

  8  7  0  0  0  0            999 V2000
    1.2375    2.1434    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 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
    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 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  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  6  2  1  0  0  0  0
  6  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  5  2  0  0  0  0
  8  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245333

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC(C)(C)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O2/c1-4-6(2,3)5(7)8/h4H2,1-3H3,(H,7,8)

> <INCHI_KEY>
VUAXHMVRKOTJKP-UHFFFAOYSA-N

> <FORMULA>
C6H12O2

> <MOLECULAR_WEIGHT>
116.16

> <EXACT_MASS>
116.083729626

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
12.835410477468546

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,2-dimethylbutanoic acid

> <ALOGPS_LOGP>
1.84

> <JCHEM_LOGP>
2.020759378

> <ALOGPS_LOGS>
-0.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.0009040584471665

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
30.947100000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.94e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,2-dimethyl butyric acid

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0245333 (2,2-Dimethylbutyric acid)

HMDB0245333
     RDKit          3D
2,2-Dimethylbutyric acid
 20 19  0  0  0  0  0  0  0  0999 V2000
    1.9788   -0.5999   -0.4081 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0638    0.0787    0.5883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3856    0.0179    0.1361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8558   -1.4036   -0.0153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5522    0.6656   -1.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1775    0.6938    1.1739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0701    0.0917    1.7914 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9309    2.0104    1.4692 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9371   -0.0047   -1.3512 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0008   -0.5736    0.0414 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6068   -1.6288   -0.5367 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1488   -0.4782    1.5325 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3799    1.1065    0.7745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9530   -1.3528   -0.2337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3884   -1.8920   -0.8741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7034   -1.9243    0.9470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3775   -0.0934   -2.0219 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6285    0.9651   -1.2925 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0740    1.5569   -1.3578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1673    2.7648    0.8701 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
  3  5  1  0
  3  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  4 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  5 19  1  0
  8 20  1  0
M  END
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PDB for HMDB0245333 (2,2-Dimethylbutyric acid)

HEADER    PROTEIN                                 22-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-APR-16         0                                  
HETATM    1  C   UNK     0       2.310   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.644   0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.080   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    4                                                            
CONECT    2    6                                                            
CONECT    3    6                                                            
CONECT    4    1    6                                                       
CONECT    5    6    7    8                                                  
CONECT    6    2    3    4    5                                             
CONECT    7    5                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0245333 (2,2-Dimethylbutyric acid)

COMPND    HMDB0245333
HETATM    1  C1  UNL     1       1.979  -0.600  -0.408  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.064   0.079   0.588  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.386   0.018   0.136  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.856  -1.404  -0.015  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.552   0.666  -1.233  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.177   0.694   1.174  1.00  0.00           C  
HETATM    7  O1  UNL     1      -2.070   0.092   1.791  1.00  0.00           O  
HETATM    8  O2  UNL     1      -0.931   2.010   1.469  1.00  0.00           O  
HETATM    9  H1  UNL     1       1.937  -0.005  -1.351  1.00  0.00           H  
HETATM   10  H2  UNL     1       3.001  -0.574   0.041  1.00  0.00           H  
HETATM   11  H3  UNL     1       1.607  -1.629  -0.537  1.00  0.00           H  
HETATM   12  H4  UNL     1       1.149  -0.478   1.532  1.00  0.00           H  
HETATM   13  H5  UNL     1       1.380   1.107   0.774  1.00  0.00           H  
HETATM   14  H6  UNL     1      -1.953  -1.353  -0.234  1.00  0.00           H  
HETATM   15  H7  UNL     1      -0.388  -1.892  -0.874  1.00  0.00           H  
HETATM   16  H8  UNL     1      -0.703  -1.924   0.947  1.00  0.00           H  
HETATM   17  H9  UNL     1      -0.377  -0.093  -2.022  1.00  0.00           H  
HETATM   18  H10 UNL     1      -1.629   0.965  -1.293  1.00  0.00           H  
HETATM   19  H11 UNL     1       0.074   1.557  -1.358  1.00  0.00           H  
HETATM   20  H12 UNL     1      -1.167   2.765   0.870  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3   12   13
CONECT    3    4    5    6
CONECT    4   14   15   16
CONECT    5   17   18   19
CONECT    6    7    7    8
CONECT    8   20
END
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SMILES for HMDB0245333 (2,2-Dimethylbutyric acid)

CCC(C)(C)C(O)=O
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INCHI for HMDB0245333 (2,2-Dimethylbutyric acid)

InChI=1S/C6H12O2/c1-4-6(2,3)5(7)8/h4H2,1-3H3,(H,7,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
alpha,alpha-Dimethylbutanoic acidChEBI
alpha,alpha-Dimethylbutyric acidChEBI
DMBChEBI
a,a-DimethylbutanoateGenerator
a,a-Dimethylbutanoic acidGenerator
alpha,alpha-DimethylbutanoateGenerator
Α,α-dimethylbutanoateGenerator
Α,α-dimethylbutanoic acidGenerator
a,a-DimethylbutyrateGenerator
a,a-Dimethylbutyric acidGenerator
alpha,alpha-DimethylbutyrateGenerator
Α,α-dimethylbutyrateGenerator
Α,α-dimethylbutyric acidGenerator
2,2-DimethylbutyrateGenerator
2,2-DimethylbutanoateGenerator
Sodium 2,2-dimethylbutyrateMeSH
2,2-Dimethylbutyric acidMeSH
ST-20 CompoundMeSH
2,2-DMBMeSH
2,2-Dimethylbutanoic acidMeSH
SDMBMeSH
Chemical FormulaC6H12O2
Average Molecular Weight116.16
Monoisotopic Molecular Weight116.083729626
IUPAC Name2,2-dimethylbutanoic acid
Traditional Name2,2-dimethyl butyric acid
CAS Registry NumberNot Available
SMILES
CCC(C)(C)C(O)=O
InChI Identifier
InChI=1S/C6H12O2/c1-4-6(2,3)5(7)8/h4H2,1-3H3,(H,7,8)
InChI KeyVUAXHMVRKOTJKP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as methyl-branched fatty acids. These are fatty acids with an acyl chain that has a methyl branch. Usually, they are saturated and contain only one or more methyl group. However, branches other than methyl may be present.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMethyl-branched fatty acids
Alternative Parents
Substituents
  • Methyl-branched fatty acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
logP1.84ALOGPS
logP2.02ChemAxon
logS-0.78ALOGPS
pKa (Strongest Acidic)5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity30.95 m³·mol⁻¹ChemAxon
Polarizability12.84 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+129.97630932474
DeepCCS[M-H]-127.21430932474
DeepCCS[M-2H]-163.69730932474
DeepCCS[M+Na]+138.44930932474
AllCCS[M+H]+127.732859911
AllCCS[M+H-H2O]+123.632859911
AllCCS[M+NH4]+131.632859911
AllCCS[M+Na]+132.832859911
AllCCS[M-H]-127.232859911
AllCCS[M+Na-2H]-130.632859911
AllCCS[M+HCOO]-134.432859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202213.1122 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.15 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1689.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid437.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid151.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid278.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid127.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid478.1 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid582.2 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)138.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid933.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid384.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1202.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid338.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid347.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate471.2 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA408.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water45.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2,2-Dimethylbutyric acidCCC(C)(C)C(O)=O1592.5Standard polar33892256
2,2-Dimethylbutyric acidCCC(C)(C)C(O)=O866.4Standard non polar33892256
2,2-Dimethylbutyric acidCCC(C)(C)C(O)=O904.8Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID11193
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID38649
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]