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Showing NP-Card for 3-Dehydro-L-gulonate (NP0087496)

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Record Information
Version2.0
Created at2022-05-11 16:51:17 UTC
Updated at2022-05-11 16:51:17 UTC
NP-MRD IDNP0087496
Secondary Accession NumbersNone
Natural Product 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
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0087496 (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 NP0087496 (3-Dehydro-L-gulonate)

     RDKit          3D

 23 22  0  0  0  0  0  0  0  0999 V2000
   -2.7820   -1.7714    1.7871 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8874   -0.9119    0.8777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0187   -0.0810    0.9143 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8531   -0.7932   -0.1811 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2211    0.2329   -1.0515 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5024   -0.5614    0.3906 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0671   -1.3878    1.1661 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3357    0.6181    0.0657 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4069    1.4051   -0.8372 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6206    0.2724   -0.6175 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2759    1.4890   -0.9201 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5805   -0.4553    0.3223 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8103   -0.6716   -0.3199 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9367    0.9271    0.9164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8308   -1.7565   -0.7586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2141    0.2715   -1.1258 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5529    1.1847    0.9913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1236    1.2242   -1.7618 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5162   -0.2716   -1.5532 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0363    2.1298   -0.2123 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7587    0.1805    1.2029 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2006   -1.4383    0.6375 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1565    0.1648   -0.7195 H   0  0  0  0  0  0  0  0  0  0  0  0
 13 12  1  0
 12 10  1  0
 10 11  1  0
 10  8  1  0
  8  9  1  0
  8  6  1  0
  6  7  2  0
  6  4  1  0
  4  5  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
 13 23  1  0
 12 21  1  0
 12 22  1  0
 10 19  1  6
 11 20  1  0
  8 17  1  1
  9 18  1  0
  4 15  1  6
  5 16  1  0
  3 14  1  0
M  END
Download

3D SDF for NP0087496 (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>
NP0087496

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
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3D-SDF for NP0087496 (3-Dehydro-L-gulonate)

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PDB for NP0087496 (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

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3D PDB for NP0087496 (3-Dehydro-L-gulonate)
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SMILES for NP0087496 (3-Dehydro-L-gulonate)
OC[C@H](O)[C@@H](O)C(=O)[C@H](O)C(O)=O
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INCHI for NP0087496 (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
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View in JSmol
Synonyms
ValueSource
3-Dehydro-L-gulonic acidGenerator
L-Xylo-hex-3-ulosonic acidHMDB
Chemical FormulaC6H10O7
Average Mass194.1394 Da
Monoisotopic Mass194.04265 Da
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
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 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
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-2.6ALOGPS
logP-2.6ChemAxon
logS-0.27ALOGPS
pKa (Strongest Acidic)3.16ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area135.29 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity37.58 m³·mol⁻¹ChemAxon
Polarizability16.3 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0006334  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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  
Good Scents IDNot Available
References
General ReferencesNot Available