Hmdb loader

Showing metabocard for 3-Dehydro-L-gulonate (HMDB0006334)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Show more...Show more...Show more...
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2007-05-23 00:55:05 UTC
Update Date2023-02-21 17:17:17 UTC
HMDB IDHMDB0006334
Secondary Accession Numbers
  • HMDB06334
Metabolite Identification
Common Name3-Dehydro-L-gulonate
Description3-Dehydro-L-gulonate belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group. A derivative of L-gulonic acid having a keto group at the 3-position. 3-Dehydro-L-gulonate is an extremely weak basic (essentially neutral) compound (based on its pKa). 3-Dehydro-L-gulonate exists in all living organisms, ranging from bacteria to humans.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0006334 (3-Dehydro-L-gulonate)

  Mrv0541 02231220382D          

 13 12  0  0  1  0            999 V2000
   17.1753   -5.2526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4608   -3.1900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0318   -4.0151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6043   -5.2526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8898   -3.1900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0332   -4.4276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3188   -3.1900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1753   -4.4276    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.4608   -4.0151    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.8898   -4.0151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7464   -4.4276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6043   -4.4276    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.3188   -4.0151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  6  0  0  0
  9  2  1  6  0  0  0
  3 11  1  0  0  0  0
 12  4  1  1  0  0  0
  5 10  2  0  0  0  0
  6 13  1  0  0  0  0
  7 13  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
Download

3D MOL for HMDB0006334 (3-Dehydro-L-gulonate)

HMDB0006334
     RDKit          3D
3-Dehydro-L-gulonate
 23 22  0  0  0  0  0  0  0  0999 V2000
    3.5727   -0.6625    1.6324 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8696    0.2206    1.0928 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9096    1.5226    1.5479 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9977   -0.1587   -0.0392 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1186   -1.4918   -0.3175 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6057    0.2508    0.2947 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4585    1.4298    0.5484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5396   -0.6577    0.3300 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1336   -1.9866    0.0903 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5250   -0.2423   -0.7717 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5775   -1.1842   -0.6442 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0932    1.1220   -0.5645 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6525    1.3039    0.6836 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2919    2.2995    1.0426 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2998    0.4888   -0.9120 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0939   -1.7156   -0.2902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1066   -0.5959    1.2786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7148   -2.3815   -0.6256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0505   -0.3655   -1.7601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3771   -0.8852   -1.1651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9181    1.2322   -1.3373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3501    1.9203   -0.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1793    0.5368    1.0047 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
  4  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  3 14  1  0
  4 15  1  6
  5 16  1  0
  8 17  1  1
  9 18  1  0
 10 19  1  6
 11 20  1  0
 12 21  1  0
 12 22  1  0
 13 23  1  0
M  END
Download

3D SDF for HMDB0006334 (3-Dehydro-L-gulonate)

  Mrv0541 02231220382D          

 13 12  0  0  1  0            999 V2000
   17.1753   -5.2526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4608   -3.1900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0318   -4.0151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6043   -5.2526    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8898   -3.1900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0332   -4.4276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3188   -3.1900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1753   -4.4276    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.4608   -4.0151    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.8898   -4.0151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7464   -4.4276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6043   -4.4276    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.3188   -4.0151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  6  0  0  0
  9  2  1  6  0  0  0
  3 11  1  0  0  0  0
 12  4  1  1  0  0  0
  5 10  2  0  0  0  0
  6 13  1  0  0  0  0
  7 13  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0006334

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-3,5,7-9,11H,1H2,(H,12,13)/t2-,3+,5-/m0/s1

> <INCHI_KEY>
WTAHRPBPWHCMHW-LWKDLAHASA-N

> <FORMULA>
C6H10O7

> <MOLECULAR_WEIGHT>
194.1394

> <EXACT_MASS>
194.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
16.2999332828514

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4R,5S)-2,4,5,6-tetrahydroxy-3-oxohexanoic acid

> <ALOGPS_LOGP>
-2.56

> <JCHEM_LOGP>
-2.642378918666667

> <ALOGPS_LOGS>
-0.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.43781434344056

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.161083010088812

> <JCHEM_PKA_STRONGEST_BASIC>
-2.979764264053207

> <JCHEM_POLAR_SURFACE_AREA>
135.29000000000002

> <JCHEM_REFRACTIVITY>
37.5794

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.05e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-dehydro-L-gulonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0006334 (3-Dehydro-L-gulonate)

HMDB0006334
     RDKit          3D
3-Dehydro-L-gulonate
 23 22  0  0  0  0  0  0  0  0999 V2000
    3.5727   -0.6625    1.6324 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8696    0.2206    1.0928 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9096    1.5226    1.5479 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9977   -0.1587   -0.0392 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1186   -1.4918   -0.3175 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6057    0.2508    0.2947 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4585    1.4298    0.5484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5396   -0.6577    0.3300 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1336   -1.9866    0.0903 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5250   -0.2423   -0.7717 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.5775   -1.1842   -0.6442 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0932    1.1220   -0.5645 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6525    1.3039    0.6836 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2919    2.2995    1.0426 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2998    0.4888   -0.9120 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0939   -1.7156   -0.2902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1066   -0.5959    1.2786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7148   -2.3815   -0.6256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0505   -0.3655   -1.7601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3771   -0.8852   -1.1651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9181    1.2322   -1.3373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3501    1.9203   -0.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1793    0.5368    1.0047 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
  4  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
  3 14  1  0
  4 15  1  6
  5 16  1  0
  8 17  1  1
  9 18  1  0
 10 19  1  6
 11 20  1  0
 12 21  1  0
 12 22  1  0
 13 23  1  0
M  END
Download

PDB for HMDB0006334 (3-Dehydro-L-gulonate)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      32.061  -9.805   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      30.727  -5.955   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      28.059  -7.495   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      34.728  -9.805   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      33.394  -5.955   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      37.395  -8.265   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      36.062  -5.955   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      32.061  -8.265   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      30.727  -7.495   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      33.394  -7.495   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      29.393  -8.265   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      34.728  -8.265   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      36.062  -7.495   0.000  0.00  0.00           C+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3   11                                                            
CONECT    4   12                                                            
CONECT    5   10                                                            
CONECT    6   13                                                            
CONECT    7   13                                                            
CONECT    8    1    9   10                                                  
CONECT    9    2    8   11                                                  
CONECT   10    5    8   12                                                  
CONECT   11    3    9                                                       
CONECT   12    4   10   13                                                  
CONECT   13    6    7   12                                                  
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
Download

3D PDB for HMDB0006334 (3-Dehydro-L-gulonate)

COMPND    HMDB0006334
HETATM    1  O1  UNL     1       3.573  -0.663   1.632  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.870   0.221   1.093  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.910   1.523   1.548  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.998  -0.159  -0.039  1.00  0.00           C  
HETATM    5  O3  UNL     1       2.119  -1.492  -0.318  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.606   0.251   0.295  1.00  0.00           C  
HETATM    7  O4  UNL     1       0.459   1.430   0.548  1.00  0.00           O  
HETATM    8  C4  UNL     1      -0.540  -0.658   0.330  1.00  0.00           C  
HETATM    9  O5  UNL     1      -0.134  -1.987   0.090  1.00  0.00           O  
HETATM   10  C5  UNL     1      -1.525  -0.242  -0.772  1.00  0.00           C  
HETATM   11  O6  UNL     1      -2.578  -1.184  -0.644  1.00  0.00           O  
HETATM   12  C6  UNL     1      -2.093   1.122  -0.565  1.00  0.00           C  
HETATM   13  O7  UNL     1      -2.653   1.304   0.684  1.00  0.00           O  
HETATM   14  H1  UNL     1       3.292   2.299   1.043  1.00  0.00           H  
HETATM   15  H2  UNL     1       2.300   0.489  -0.912  1.00  0.00           H  
HETATM   16  H3  UNL     1       3.094  -1.716  -0.290  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.107  -0.596   1.279  1.00  0.00           H  
HETATM   18  H5  UNL     1      -0.715  -2.382  -0.626  1.00  0.00           H  
HETATM   19  H6  UNL     1      -1.050  -0.365  -1.760  1.00  0.00           H  
HETATM   20  H7  UNL     1      -3.377  -0.885  -1.165  1.00  0.00           H  
HETATM   21  H8  UNL     1      -2.918   1.232  -1.337  1.00  0.00           H  
HETATM   22  H9  UNL     1      -1.350   1.920  -0.730  1.00  0.00           H  
HETATM   23  H10 UNL     1      -3.179   0.537   1.005  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5    6   15
CONECT    5   16
CONECT    6    7    7    8
CONECT    8    9   10   17
CONECT    9   18
CONECT   10   11   12   19
CONECT   11   20
CONECT   12   13   21   22
CONECT   13   23
END
Download

SMILES for HMDB0006334 (3-Dehydro-L-gulonate)

OC[C@H](O)[C@@H](O)C(=O)[C@H](O)C(O)=O
Download

INCHI for HMDB0006334 (3-Dehydro-L-gulonate)

InChI=1S/C6H10O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-3,5,7-9,11H,1H2,(H,12,13)/t2-,3+,5-/m0/s1
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-Dehydro-L-gulonic acidGenerator
L-Xylo-hex-3-ulosonic acidHMDB
Chemical FormulaC6H10O7
Average Molecular Weight194.1394
Monoisotopic Molecular Weight194.042652674
IUPAC Name(2S,4R,5S)-2,4,5,6-tetrahydroxy-3-oxohexanoic acid
Traditional Name3-dehydro-L-gulonic acid
CAS Registry NumberNot Available
SMILES
OC[C@H](O)[C@@H](O)C(=O)[C@H](O)C(O)=O
InChI Identifier
InChI=1S/C6H10O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-3,5,7-9,11H,1H2,(H,12,13)/t2-,3+,5-/m0/s1
InChI KeyWTAHRPBPWHCMHW-LWKDLAHASA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar acids and derivatives
Alternative Parents
Substituents
  • Hexose monosaccharide
  • Medium-chain keto acid
  • Beta-keto acid
  • Sugar acid
  • Acyloin
  • Alpha-hydroxy acid
  • Beta-hydroxy ketone
  • Hydroxy acid
  • Keto acid
  • 1,3-dicarbonyl compound
  • Monosaccharide
  • Alpha-hydroxy ketone
  • Ketone
  • Secondary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Monocarboxylic acid or derivatives
  • Polyol
  • Alcohol
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Primary alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023894
KNApSAcK IDNot Available
Chemspider ID388406
KEGG Compound IDC00618
BioCyc IDNot Available
BiGG ID35509
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound439273
PDB IDNot Available
ChEBI ID16142
Food Biomarker OntologyNot Available
VMH ID3DHGULN
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Lambda-crystallin homolog
General function:
Involved in 3-hydroxyacyl-CoA dehydrogenase activity
Specific function:
Not Available
Gene Name:
CRYL1
Uniprot ID:
Q9Y2S2
Molecular weight:
35418.91
Reactions
Gulonic acid + NAD → 3-Dehydro-L-gulonate + NADHdetails
Gulonic acid + NAD → 3-Dehydro-L-gulonate + NADH + Hydrogen Iondetails