Showing metabocard for 3-Methyladipic acid (MMDBc0000527)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:39:47 UTC
Update Date2024-04-30 19:32:48 UTC
Metabolite IDMMDBc0000527
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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fb7e03f3e60>

  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 #<Metabolite:0x00007fb7e03f3e60>

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
Download

3D SDF for #<Metabolite:0x00007fb7e03f3e60>

  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>
MMDBc0000527

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007fb7e03f3e60>

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 #<Metabolite:0x00007fb7e03f3e60>

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 #<Metabolite:0x00007fb7e03f3e60>

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 #<Metabolite:0x00007fb7e03f3e60>

C[C@@H](CCC(O)=O)CC(O)=O
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INCHI for #<Metabolite:0x00007fb7e03f3e60>

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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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
Molecular FormulaC7H12O4
Average Mass160.1678
Monoisotopic Mass160.073558872
IUPAC Name(3S)-3-methylhexanedioic acid
Traditional Name(3S)-3-methylhexanedioic acid
CAS Registry NumberNot Available
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