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Showing NP-Card for 3-Methyladipic acid (NP0000074)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:42:32 UTC
NP-MRD IDNP0000074
Secondary Accession NumbersNone
Natural Product 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000074 (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
Download

3D MOL for NP0000074 (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
Download

3D SDF for NP0000074 (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>
NP0000074

> <DATABASE_NAME>
NP-MRD

> <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 NP0000074 (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
Download

PDB for NP0000074 (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
Download

3D PDB for NP0000074 (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 NP0000074 (3-Methyladipic acid)

C[C@@H](CCC(O)=O)CC(O)=O
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INCHI for NP0000074 (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 JSmol
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 Mass160.1678 Da
Monoisotopic Mass160.07356 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)KNApSAcK Database
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point101 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility248 mg/mL at 26 °CYalkowsky, S. H., & Dannenfelser, R. M. (1992). Aquasol database of aqueous solubility. College of Pharmacy, University of Arizona, Tucson, AZ, 189.
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility16.8 g/LALOGPS
logP0.65ALOGPS
logP0.78ChemAxon
logS-0.98ALOGPS
pKa (Strongest Acidic)4.04ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity37.29 m³·mol⁻¹ChemAxon
Polarizability15.9 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000555
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDNot Available
References
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 ]
  2. Pesek JJ, Matyska MT: Ammonium fluoride as a mobile phase additive in aqueous normal phase chromatography. J Chromatogr A. 2015 Jul 3;1401:69-74. doi: 10.1016/j.chroma.2015.05.010. Epub 2015 May 14. [PubMed:26008598 ]
  3. Gangjee A, Zhao Y, Hamel E, Westbrook C, Mooberry SL: Synthesis and biological activities of (R)- and (S)-N-(4-Methoxyphenyl)-N,2,6-trimethyl-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-a minium chloride as potent cytotoxic antitubulin agents. J Med Chem. 2011 Sep 8;54(17):6151-5. doi: 10.1021/jm2007722. Epub 2011 Aug 5. [PubMed:21786793 ]
  4. Ha JM, Hillmyer MA, Ward MD: Thermotropic properties of organic nanocrystals embedded in ultrasmall crystallization chambers. J Phys Chem B. 2005 Feb 3;109(4):1392-9. doi: 10.1021/jp045488v. [PubMed:16851108 ]
  5. Barbera J, Puig L, Romero P, Serrano JL, Sierra T: Supramolecular helical mesomorphic polymers. Chiral induction through H-bonding. J Am Chem Soc. 2005 Jan 12;127(1):458-64. doi: 10.1021/ja046644e. [PubMed:15631497 ]