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Showing metabocard for 3-Methyladipic acid (HMDB0000555)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-05-30 20:55:51 UTC
HMDB IDHMDB0000555
Secondary Accession Numbers
  • HMDB00555
Metabolite Identification
Common Name3-Methyladipic acid
Description3-Methyladipic acid is a metabolite of the catabolism of phytanic acid. Patients with adult Refsums disease (ARD) are unable to detoxify phytanic acid by alpha-oxidation, and so the w-oxidation pathway is the only metabolic pathway available for phytanic acid degradation. This pathway produces 3-methyladipic acid as the final metabolite, which is excreted in the urine (Wanders et al. 2001). Activity of the w-oxidation pathway is approximately doubled in ARD patients compared with normal individuals (PMID: 11948235 ).
Structure
Data?1676999696
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000555 (3-Methyladipic acid)

  Mrv1652305261923572D          

 11 10  0  0  1  0            999 V2000
   27.7039  -11.9668    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.9894  -13.2044    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.7024  -12.3794    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.4169  -11.1418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.5604  -12.3794    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   24.8459  -11.9668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.2748  -11.9668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5604  -13.2044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.1315  -12.3794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.9894  -12.3794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.4169  -11.9668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2 10  2  0  0  0  0
  3 11  1  0  0  0  0
  4 11  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  1  0  0  0
  6  9  1  0  0  0  0
  7 10  1  0  0  0  0
  9 11  1  0  0  0  0
M  END
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3D MOL for HMDB0000555 (3-Methyladipic acid)

HMDB0000555
     RDKit          3D
3-Methyladipic acid
 23 22  0  0  0  0  0  0  0  0999 V2000
   -0.7067   -0.7098   -1.1337 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3107   -0.5258    0.2927 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5272    0.6323    0.6007 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8611    0.7422   -0.0564 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8030   -0.3626    0.2321 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4634   -1.5837    0.1362 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1299   -0.1000    0.6316 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5504   -0.5636    1.1536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5612    0.4513    0.8525 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2987    1.7050    0.9704 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8513    0.1647    0.4211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0877   -1.7499   -1.2550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5160    0.0380   -1.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0918   -0.5544   -1.8651 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2754   -1.4500    0.6173 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7408    0.5909    1.7131 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0600    1.5902    0.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3190    1.6932    0.2761 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8066    0.7861   -1.1694 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4507    0.8506    0.5246 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0519   -1.5706    1.0588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2807   -0.5241    2.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1935    0.4498   -0.4909 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  2  0
  5  7  1  0
  2  8  1  0
  8  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  1
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
 11 23  1  0
M  END
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3D SDF for HMDB0000555 (3-Methyladipic acid)

  Mrv1652305261923572D          

 11 10  0  0  1  0            999 V2000
   27.7039  -11.9668    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.9894  -13.2044    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.7024  -12.3794    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.4169  -11.1418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.5604  -12.3794    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   24.8459  -11.9668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.2748  -11.9668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5604  -13.2044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.1315  -12.3794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.9894  -12.3794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.4169  -11.9668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2 10  2  0  0  0  0
  3 11  1  0  0  0  0
  4 11  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  1  0  0  0
  6  9  1  0  0  0  0
  7 10  1  0  0  0  0
  9 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000555

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H12O4/c1-5(4-7(10)11)2-3-6(8)9/h5H,2-4H2,1H3,(H,8,9)(H,10,11)/t5-/m0/s1

> <INCHI_KEY>
SYEOWUNSTUDKGM-YFKPBYRVSA-N

> <FORMULA>
C7H12O4

> <MOLECULAR_WEIGHT>
160.1678

> <EXACT_MASS>
160.073558872

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.897393534015553

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S)-3-methylhexanedioic acid

> <ALOGPS_LOGP>
0.65

> <JCHEM_LOGP>
0.777673459

> <ALOGPS_LOGS>
-0.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.808214919925216

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.043116214614612

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
37.287600000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.68e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S)-3-methylhexanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000555 (3-Methyladipic acid)

HMDB0000555
     RDKit          3D
3-Methyladipic acid
 23 22  0  0  0  0  0  0  0  0999 V2000
   -0.7067   -0.7098   -1.1337 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3107   -0.5258    0.2927 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5272    0.6323    0.6007 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8611    0.7422   -0.0564 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8030   -0.3626    0.2321 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4634   -1.5837    0.1362 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1299   -0.1000    0.6316 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5504   -0.5636    1.1536 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5612    0.4513    0.8525 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2987    1.7050    0.9704 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8513    0.1647    0.4211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0877   -1.7499   -1.2550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5160    0.0380   -1.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0918   -0.5544   -1.8651 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2754   -1.4500    0.6173 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7408    0.5909    1.7131 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0600    1.5902    0.5109 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3190    1.6932    0.2761 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8066    0.7861   -1.1694 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4507    0.8506    0.5246 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0519   -1.5706    1.0588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2807   -0.5241    2.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1935    0.4498   -0.4909 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  2  0
  5  7  1  0
  2  8  1  0
  8  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  1
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
 11 23  1  0
M  END
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PDB for HMDB0000555 (3-Methyladipic acid)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  O   UNK     0      51.714 -22.338   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      50.380 -24.648   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      42.378 -23.108   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      43.712 -20.798   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      47.713 -23.108   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      46.379 -22.338   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      49.046 -22.338   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      47.713 -24.648   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      45.045 -23.108   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      50.380 -23.108   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      43.712 -22.338   0.000  0.00  0.00           C+0
CONECT    1   10                                                            
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4   11                                                            
CONECT    5    6    7    8                                                  
CONECT    6    5    9                                                       
CONECT    7    5   10                                                       
CONECT    8    5                                                            
CONECT    9    6   11                                                       
CONECT   10    1    2    7                                                  
CONECT   11    3    4    9                                                  
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0000555 (3-Methyladipic acid)

COMPND    HMDB0000555
HETATM    1  C1  UNL     1      -0.707  -0.710  -1.134  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.311  -0.526   0.293  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.527   0.632   0.601  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.861   0.742  -0.056  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.803  -0.363   0.232  1.00  0.00           C  
HETATM    6  O1  UNL     1       2.463  -1.584   0.136  1.00  0.00           O  
HETATM    7  O2  UNL     1       4.130  -0.100   0.632  1.00  0.00           O  
HETATM    8  C6  UNL     1      -1.550  -0.564   1.154  1.00  0.00           C  
HETATM    9  C7  UNL     1      -2.561   0.451   0.853  1.00  0.00           C  
HETATM   10  O3  UNL     1      -2.299   1.705   0.970  1.00  0.00           O  
HETATM   11  O4  UNL     1      -3.851   0.165   0.421  1.00  0.00           O  
HETATM   12  H1  UNL     1      -1.088  -1.750  -1.255  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.516   0.038  -1.392  1.00  0.00           H  
HETATM   14  H3  UNL     1       0.092  -0.554  -1.865  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.275  -1.450   0.617  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.741   0.591   1.713  1.00  0.00           H  
HETATM   17  H6  UNL     1      -0.060   1.590   0.511  1.00  0.00           H  
HETATM   18  H7  UNL     1       2.319   1.693   0.276  1.00  0.00           H  
HETATM   19  H8  UNL     1       1.807   0.786  -1.169  1.00  0.00           H  
HETATM   20  H9  UNL     1       4.451   0.851   0.525  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.052  -1.571   1.059  1.00  0.00           H  
HETATM   22  H11 UNL     1      -1.281  -0.524   2.247  1.00  0.00           H  
HETATM   23  H12 UNL     1      -4.194   0.450  -0.491  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    8   15
CONECT    3    4   16   17
CONECT    4    5   18   19
CONECT    5    6    6    7
CONECT    7   20
CONECT    8    9   21   22
CONECT    9   10   10   11
CONECT   11   23
END
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SMILES for HMDB0000555 (3-Methyladipic acid)

C[C@@H](CCC(O)=O)CC(O)=O
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INCHI for HMDB0000555 (3-Methyladipic acid)

InChI=1S/C7H12O4/c1-5(4-7(10)11)2-3-6(8)9/h5H,2-4H2,1H3,(H,8,9)(H,10,11)/t5-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-MethyladipateGenerator
(+/-)-3-methyladipic acidHMDB
3-Methyl-hexanedioateHMDB
3-Methyl-hexanedioic acidHMDB
3-MethylhexanedioateHMDB
3-Methylhexanedioic acidHMDB
b-Methyl-adipic acidHMDB
b-MethyladipateHMDB
b-Methyladipic acidHMDB
beta-Methyl-adipic acidHMDB
beta-MethyladipateHMDB
beta-Methyladipic acidHMDB
(3S)-3-MethylhexanedioateHMDB
3-Methyladipic acidMeSH
Chemical FormulaC7H12O4
Average Molecular Weight160.1678
Monoisotopic Molecular Weight160.073558872
IUPAC Name(3S)-3-methylhexanedioic acid
Traditional Name(3S)-3-methylhexanedioic acid
CAS Registry Number3058-01-3
SMILES
C[C@@H](CCC(O)=O)CC(O)=O
InChI Identifier
InChI=1S/C7H12O4/c1-5(4-7(10)11)2-3-6(8)9/h5H,2-4H2,1H3,(H,8,9)(H,10,11)/t5-/m0/s1
InChI KeySYEOWUNSTUDKGM-YFKPBYRVSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMedium-chain fatty acids
Alternative Parents
Substituents
  • Medium-chain fatty acid
  • Methyl-branched fatty acid
  • Branched fatty acid
  • Dicarboxylic 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 DescriptorsNot Available
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point101 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility248 mg/mL at 26 °CYALKOWSKY,SH & DANNENFELSER,RM (1992)
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg129.00730932474
[M-H]-Not Available129.007http://allccs.zhulab.cn/database/detail?ID=AllCCS00000200
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Crohn's disease
  1. Azario I, Pievani A, Del Priore F, Antolini L, Santi L, Corsi A, Cardinale L, Sawamoto K, Kubaski F, Gentner B, Bernardo ME, Valsecchi MG, Riminucci M, Tomatsu S, Aiuti A, Biondi A, Serafini M: Neonatal umbilical cord blood transplantation halts skeletal disease progression in the murine model of MPS-I. Sci Rep. 2017 Aug 25;7(1):9473. doi: 10.1038/s41598-017-09958-9. [PubMed:28842642 ]
Ulcerative colitis
  1. Azario I, Pievani A, Del Priore F, Antolini L, Santi L, Corsi A, Cardinale L, Sawamoto K, Kubaski F, Gentner B, Bernardo ME, Valsecchi MG, Riminucci M, Tomatsu S, Aiuti A, Biondi A, Serafini M: Neonatal umbilical cord blood transplantation halts skeletal disease progression in the murine model of MPS-I. Sci Rep. 2017 Aug 25;7(1):9473. doi: 10.1038/s41598-017-09958-9. [PubMed:28842642 ]
Colorectal cancer
  1. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Refsum's disease
  1. Greter J, Lindstedt S, Steen G: 2,6-Dimethyloctanedioic acid--a metabolite of phytanic acid in Refsum's disease. Clin Chem. 1983 Mar;29(3):434-7. [PubMed:6186413 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022115
KNApSAcK IDC00052149
Chemspider ID5367267
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID3797
PubChem Compound6999745
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000186
Good Scents IDNot Available
References
Synthesis ReferenceVogel, Arthur I. Syntheses of cyclic compounds. VIII. Conversion of b-methyladipic acid into 3-methylcyclopentanone and the preparation of 3-methylcyclopentane-1,1-diacetic acid. Journal of the Chemical Society (1931), 907-14.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Wierzbicki AS, Lloyd MD, Schofield CJ, Feher MD, Gibberd FB: Refsum's disease: a peroxisomal disorder affecting phytanic acid alpha-oxidation. J Neurochem. 2002 Mar;80(5):727-35. [PubMed:11948235 ]