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Showing NP-Card for 3-Hydroxyglutaric acid (NP0001470)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:23:46 UTC
NP-MRD IDNP0001470
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Hydroxyglutaric acid
Description3-Hydroxyglutaric acid is a member of the class of compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups. 3-Hydroxyglutaric acid is soluble (in water) and a weakly acidic compound (based on its pKa). When present in sufficiently high levels, 3-hydroxyglutaric acid can act as act as an acidogen and a metabotoxin. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Chronically high levels of 3-hydroxyglutaric acid are associated with glutaric aciduria type I (glutaric acidemia type I, glutaryl-CoA dehydrogenase deficiency, GA1, or GAT1). GA1 is an inherited disorder in which the body is unable to completely break down the amino acids lysine, hydroxylysine and tryptophan. Excessive levels of their intermediate breakdown products (e.G. Glutaric acid, glutaryl-CoA, 3-hydroxyglutaric acid, glutaconic acid) can accumulate and cause damage to the brain (and also other organs). Babies with glutaric acidemia type I are often born with unusually large heads (macrocephaly). Macrocephaly is amongst the earliest signs of GA1. GA1 also causes secondary carnitine deficiency because 3-hydroxyglutaric acid, like other organic acids, is detoxified by carnitine. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. In infants with acidosis, the initial symptoms include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart, liver, and kidney abnormalities, seizures, coma, and possibly death. These are also the characteristic symptoms of untreated glutaric aciduria or glutaric acidemia. Many affected children with organic acidemias experience intellectual disability or delayed development. In adults, acidosis or acidemia is characterized by headaches, confusion, feeling tired, tremors, sleepiness, and seizures. It is believed that the excretion of 3-hydroxyglutaric acid is increased during ketosis, which occurs during glutaryl-CoA dehydrogenase deficiency.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001470 (3-Hydroxyglutaric acid)


  Mrv1652305261923572D          

 10  9  0  0  0  0            999 V2000
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   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
  4  6  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
M  END
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3D MOL for NP0001470 (3-Hydroxyglutaric acid)

HMDB0000428
     RDKit          3D
3-Hydroxyglutaric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.8710   -0.7692    1.7389 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1833   -0.1698    0.8502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7585    0.8075    0.0463 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7517   -0.5455    0.6985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1554    0.3057   -0.4054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8998    0.0145   -1.5661 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2697   -0.1211   -0.7151 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1693   -0.0072    0.4385 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1512   -0.9046    1.3180 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0523    1.0423    0.6245 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1011    0.4712   -0.8662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1813   -0.3599    1.6325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7115   -1.6158    0.3979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2025    1.3637   -0.1334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5003   -0.7825   -1.9934 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2097   -1.2019   -0.9812 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6444    0.4698   -1.5725 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8197    2.0029    0.4878 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
  7 17  1  0
 10 18  1  0
M  END
Download

3D SDF for NP0001470 (3-Hydroxyglutaric acid)


  Mrv1652305261923572D          

 10  9  0  0  0  0            999 V2000
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   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
  4  6  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0001470

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O5/c6-3(1-4(7)8)2-5(9)10/h3,6H,1-2H2,(H,7,8)(H,9,10)

> <INCHI_KEY>
ZQHYXNSQOIDNTL-UHFFFAOYSA-N

> <FORMULA>
C5H8O5

> <MOLECULAR_WEIGHT>
148.114

> <EXACT_MASS>
148.037173366

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.809688049870932

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxypentanedioic acid

> <ALOGPS_LOGP>
-1.17

> <JCHEM_LOGP>
-1.0288179093333332

> <ALOGPS_LOGS>
0.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.294116866528298

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5233997663487395

> <JCHEM_PKA_STRONGEST_BASIC>
-2.913303860550256

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
29.4995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.72e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxyglutaric acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001470 (3-Hydroxyglutaric acid)

HMDB0000428
     RDKit          3D
3-Hydroxyglutaric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.8710   -0.7692    1.7389 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1833   -0.1698    0.8502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7585    0.8075    0.0463 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7517   -0.5455    0.6985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1554    0.3057   -0.4054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8998    0.0145   -1.5661 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2697   -0.1211   -0.7151 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1693   -0.0072    0.4385 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1512   -0.9046    1.3180 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0523    1.0423    0.6245 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1011    0.4712   -0.8662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1813   -0.3599    1.6325 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7115   -1.6158    0.3979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2025    1.3637   -0.1334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5003   -0.7825   -1.9934 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2097   -1.2019   -0.9812 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6444    0.4698   -1.5725 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8197    2.0029    0.4878 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  7 16  1  0
  7 17  1  0
 10 18  1  0
M  END
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PDB for NP0001470 (3-Hydroxyglutaric 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       7.287   1.127   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    2    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for NP0001470 (3-Hydroxyglutaric acid)

COMPND    HMDB0000428
HETATM    1  O1  UNL     1      -2.871  -0.769   1.739  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.183  -0.170   0.850  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.758   0.808   0.046  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.752  -0.546   0.699  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.155   0.306  -0.405  1.00  0.00           C  
HETATM    6  O3  UNL     1      -0.900   0.014  -1.566  1.00  0.00           O  
HETATM    7  C4  UNL     1       1.270  -0.121  -0.715  1.00  0.00           C  
HETATM    8  C5  UNL     1       2.169  -0.007   0.439  1.00  0.00           C  
HETATM    9  O4  UNL     1       2.151  -0.905   1.318  1.00  0.00           O  
HETATM   10  O5  UNL     1       3.052   1.042   0.624  1.00  0.00           O  
HETATM   11  H1  UNL     1      -3.101   0.471  -0.866  1.00  0.00           H  
HETATM   12  H2  UNL     1      -0.181  -0.360   1.632  1.00  0.00           H  
HETATM   13  H3  UNL     1      -0.712  -1.616   0.398  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.202   1.364  -0.133  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.500  -0.783  -1.993  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.210  -1.202  -0.981  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.644   0.470  -1.573  1.00  0.00           H  
HETATM   18  H8  UNL     1       2.820   2.003   0.488  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   11
CONECT    4    5   12   13
CONECT    5    6    7   14
CONECT    6   15
CONECT    7    8   16   17
CONECT    8    9    9   10
CONECT   10   18
END
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SMILES for NP0001470 (3-Hydroxyglutaric acid)

OC(CC(O)=O)CC(O)=O
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INCHI for NP0001470 (3-Hydroxyglutaric acid)

InChI=1S/C5H8O5/c6-3(1-4(7)8)2-5(9)10/h3,6H,1-2H2,(H,7,8)(H,9,10)
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View in JSmol
Synonyms
ValueSource
3-Hydroxy-glutaric acidChEBI
beta-Hydroxyglutaric acidChEBI
3-Hydroxy-glutarateGenerator
b-HydroxyglutarateGenerator
b-Hydroxyglutaric acidGenerator
beta-HydroxyglutarateGenerator
Β-hydroxyglutarateGenerator
Β-hydroxyglutaric acidGenerator
3-HydroxyglutarateGenerator
3-Hydroxypentanedioic acidHMDB
2,4-Dideoxypentaric acidHMDB
3-HydroxypentanedioateHMDB
3-Hydroxyglutaric acidMeSH
Chemical FormulaC5H8O5
Average Mass148.1140 Da
Monoisotopic Mass148.03717 Da
IUPAC Name3-hydroxypentanedioic acid
Traditional Name3-hydroxyglutaric acid
CAS Registry Number638-18-6
SMILES
OC(CC(O)=O)CC(O)=O
InChI Identifier
InChI=1S/C5H8O5/c6-3(1-4(7)8)2-5(9)10/h3,6H,1-2H2,(H,7,8)(H,9,10)
InChI KeyZQHYXNSQOIDNTL-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)Varshavi.d262021-08-31View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)v.dorna83@yahoo.comNot AvailableNot Available2021-08-13View Spectrum
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 beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassBeta hydroxy acids and derivatives
Direct ParentBeta hydroxy acids and derivatives
Alternative Parents
Substituents
  • Short-chain hydroxy acid
  • Beta-hydroxy acid
  • Fatty acid
  • Dicarboxylic acid or derivatives
  • Secondary 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 DescriptorsNot Available
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility172 g/LALOGPS
logP-1.2ALOGPS
logP-1ChemAxon
logS0.06ALOGPS
pKa (Strongest Acidic)3.52ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity29.5 m³·mol⁻¹ChemAxon
Polarizability12.81 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000428
DrugBank IDDB04594
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022040
KNApSAcK IDNot Available
Chemspider ID158277
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkAlpha-Hydroxyglutaric acid
METLIN ID5417
PubChem Compound181976
PDB IDNot Available
ChEBI ID39980
Good Scents IDNot Available
References
General References
  1. Baric I, Wagner L, Feyh P, Liesert M, Buckel W, Hoffmann GF: Sensitivity and specificity of free and total glutaric acid and 3-hydroxyglutaric acid measurements by stable-isotope dilution assays for the diagnosis of glutaric aciduria type I. J Inherit Metab Dis. 1999 Dec;22(8):867-81. [PubMed:10604139 ]
  2. Kolker S, Hoffmann GF, Schor DS, Feyh P, Wagner L, Jeffrey I, Pourfarzam M, Okun JG, Zschocke J, Baric I, Bain MD, Jakobs C, Chalmers RA: Glutaryl-CoA dehydrogenase deficiency: region-specific analysis of organic acids and acylcarnitines in post mortem brain predicts vulnerability of the putamen. Neuropediatrics. 2003 Jun;34(5):253-60. [PubMed:14598231 ]
  3. Wajner M, Kolker S, Souza DO, Hoffmann GF, de Mello CF: Modulation of glutamatergic and GABAergic neurotransmission in glutaryl-CoA dehydrogenase deficiency. J Inherit Metab Dis. 2004;27(6):825-8. [PubMed:15505388 ]
  4. Nyhan WL, Zschocke J, Hoffmann G, Stein DE, Bao L, Goodman S: Glutaryl-CoA dehydrogenase deficiency presenting as 3-hydroxyglutaric aciduria. Mol Genet Metab. 1999 Mar;66(3):199-204. [PubMed:10066389 ]
  5. Molven A, Matre GE, Duran M, Wanders RJ, Rishaug U, Njolstad PR, Jellum E, Sovik O: Familial hyperinsulinemic hypoglycemia caused by a defect in the SCHAD enzyme of mitochondrial fatty acid oxidation. Diabetes. 2004 Jan;53(1):221-7. [PubMed:14693719 ]
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