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Showing NP-Card for 2,3-Dimethyl-3-hydroxyglutaric acid (NP0086844)

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Record Information
Version2.0
Created at2022-05-11 16:32:35 UTC
Updated at2022-05-11 16:32:35 UTC
NP-MRD IDNP0086844
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,3-Dimethyl-3-hydroxyglutaric acid
Description2,3-Dimethyl-3-hydroxyglutaric acid belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. 2,3-Dimethyl-3-hydroxyglutaric acid was first documented in 1983 (PMID: 6133567). 2,3-Dimethyl-3-hydroxyglutaric acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086844 (2,3-Dimethyl-3-hydroxyglutaric acid)

2-Keto-6-aminocaproic acid.mol
  Mrv0541 02231219192D          

 12 11  0  0  0  0            999 V2000
    1.1822    0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4678   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2467    0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6592   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4842   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1822    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8967   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8967   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8967    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9612    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1658    1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4678   -0.9355    0.0000 C   0  0  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  1  0  0  0  0
  4  5  1  0  0  0  0
  1  6  2  0  0  0  0
  1  7  1  0  0  0  0
  5  8  2  0  0  0  0
  5  9  1  0  0  0  0
  3 10  1  0  0  0  0
  3 11  1  0  0  0  0
  2 12  1  0  0  0  0
M  END
Download

3D MOL for NP0086844 (2,3-Dimethyl-3-hydroxyglutaric acid)

     RDKit          3D

 24 23  0  0  0  0  0  0  0  0999 V2000
   -2.0471   -1.2102   -0.1068 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0876   -0.2540    0.5614 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5752    1.1166    0.3178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8754    1.8726    1.2654 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7044    1.5760   -0.9768 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3301   -0.4719    0.1713 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5779   -0.3129   -1.3103 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7056   -1.7760    0.4931 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2055    0.4488    0.9828 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6309    0.2828    0.6437 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2739   -0.6873    1.1058 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2334    1.2011   -0.1786 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6113   -2.2248   -0.1306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0009   -1.1865    0.4862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2570   -0.8235   -1.1232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1583   -0.4723    1.6630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5310    2.1294   -1.2293 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6414   -0.6025   -1.4821 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3747    0.6986   -1.6848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0249   -1.0883   -1.8422 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0754   -2.1123    1.1725 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0079    0.2556    2.0718 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8826    1.4828    0.7817 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9339    2.1581   -0.2951 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  5  1  0
  3  4  2  0
  2  6  1  0
  6  7  1  0
  6  8  1  1
  6  9  1  0
  9 10  1  0
 10 12  1  0
 10 11  2  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  1
  5 17  1  0
  7 18  1  0
  7 19  1  0
  7 20  1  0
  8 21  1  0
  9 22  1  0
  9 23  1  0
 12 24  1  0
M  END
Download

3D SDF for NP0086844 (2,3-Dimethyl-3-hydroxyglutaric acid)

2-Keto-6-aminocaproic acid.mol
  Mrv0541 02231219192D          

 12 11  0  0  0  0            999 V2000
    1.1822    0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4678   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2467    0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6592   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4842   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1822    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8967   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8967   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8967    0.3020    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9612    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1658    1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4678   -0.9355    0.0000 C   0  0  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  1  0  0  0  0
  4  5  1  0  0  0  0
  1  6  2  0  0  0  0
  1  7  1  0  0  0  0
  5  8  2  0  0  0  0
  5  9  1  0  0  0  0
  3 10  1  0  0  0  0
  3 11  1  0  0  0  0
  2 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0086844

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H12O5/c1-4(6(10)11)7(2,12)3-5(8)9/h4,12H,3H2,1-2H3,(H,8,9)(H,10,11)

> <INCHI_KEY>
CCFYMOIEFAALDH-UHFFFAOYSA-N

> <FORMULA>
C7H12O5

> <MOLECULAR_WEIGHT>
176.1672

> <EXACT_MASS>
176.068473494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
16.45380498951939

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxy-2,3-dimethylpentanedioic acid

> <ALOGPS_LOGP>
-0.23

> <JCHEM_LOGP>
-0.20525496266666643

> <ALOGPS_LOGS>
0.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.533171477802076

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7862043774803276

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1203430193514716

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
38.712199999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.21e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-2,3-dimethylpentanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0086844 (2,3-Dimethyl-3-hydroxyglutaric acid)

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PDB for NP0086844 (2,3-Dimethyl-3-hydroxyglutaric acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 2-Keto-6-aminocaproic acid.mol                    
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       2.207   0.564   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.873  -0.206   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.461   0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.231  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.771  -0.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.207   2.104   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       3.541  -0.206   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -3.541  -2.104   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -3.541   0.564   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -1.794   1.334   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.309   1.897   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.873  -1.746   0.000  0.00  0.00           C+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3   12                                                  
CONECT    3    2    4   10   11                                             
CONECT    4    3    5                                                       
CONECT    5    4    8    9                                                  
CONECT    6    1                                                            
CONECT    7    1                                                            
CONECT    8    5                                                            
CONECT    9    5                                                            
CONECT   10    3                                                            
CONECT   11    3                                                            
CONECT   12    2                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

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3D PDB for NP0086844 (2,3-Dimethyl-3-hydroxyglutaric acid)
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SMILES for NP0086844 (2,3-Dimethyl-3-hydroxyglutaric acid)
CC(C(O)=O)C(C)(O)CC(O)=O
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INCHI for NP0086844 (2,3-Dimethyl-3-hydroxyglutaric acid)
InChI=1S/C7H12O5/c1-4(6(10)11)7(2,12)3-5(8)9/h4,12H,3H2,1-2H3,(H,8,9)(H,10,11)
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View in JSmol
Synonyms
ValueSource
2,3-Dimethyl-3-hydroxyglutarateGenerator
2,3-Dimethyl-3-hydroxy-glutarateHMDB
Chemical FormulaC7H12O5
Average Mass176.1672 Da
Monoisotopic Mass176.06847 Da
IUPAC Name3-hydroxy-2,3-dimethylpentanedioic acid
Traditional Name3-hydroxy-2,3-dimethylpentanedioic acid
CAS Registry NumberNot Available
SMILES
CC(C(O)=O)C(C)(O)CC(O)=O
InChI Identifier
InChI=1S/C7H12O5/c1-4(6(10)11)7(2,12)3-5(8)9/h4,12H,3H2,1-2H3,(H,8,9)(H,10,11)
InChI KeyCCFYMOIEFAALDH-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
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
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
  • Methyl-branched fatty acid
    • 

  • Short-chain hydroxy acid
    • 

  • Hydroxy fatty acid
    • 

  • Branched fatty acid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Tertiary alcohol
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.23ALOGPS
logP-0.21ChemAxon
logS0.1ALOGPS
pKa (Strongest Acidic)3.79ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity38.71 m³·mol⁻¹ChemAxon
Polarizability16.45 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002025  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022803  
KNApSAcK IDNot Available
Chemspider ID13628288  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6446  
PubChem Compound21252268  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Pollitt RJ: The occurrence of substituted 3-methyl-3-hydroxyglutaric acids in urine in propionic acidaemia and in beta-ketothiolase deficiency. Biomed Mass Spectrom. 1983 Apr;10(4):253-7. doi: 10.1002/bms.1200100403. [PubMed:6133567  ]