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Showing NP-Card for 6-phosphogluconolactone (NP0267133)

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Record Information
Version2.0
Created at2022-09-08 11:49:01 UTC
Updated at2022-09-08 11:49:02 UTC
NP-MRD IDNP0267133
Secondary Accession NumbersNone
Natural Product Identification
Common Name6-phosphogluconolactone
Description[(3,4,5-Trihydroxy-6-oxooxan-2-yl)methoxy]phosphonic acid belongs to the class of organic compounds known as hexose phosphates. These are carbohydrate derivatives containing a hexose substituted by one or more phosphate groups. [(3,4,5-Trihydroxy-6-oxooxan-2-yl)methoxy]phosphonic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0267133 (6-phosphogluconolactone)


  Mrv1652305171801442D          

 16 16  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -2.4750    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13  1  1  0  0  0  0
 15  9  1  0  0  0  0
 16  9  1  0  0  0  0
M  END
Download

3D MOL for NP0267133 (6-phosphogluconolactone)

     RDKit          3D

 27 27  0  0  0  0  0  0  0  0999 V2000
   -2.9752   -1.9892    1.5242 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2474   -1.1812    0.8652 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8998   -1.0384    1.0403 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1202   -0.7144   -0.0803 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3242   -0.4477    0.3497 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1122   -0.1260   -0.7389 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6807    0.1611   -0.2533 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.4637    0.7251   -1.4244 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4757   -1.2476    0.2455 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7093    1.2872    0.9999 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6357    0.4316   -0.8799 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2748    0.2110   -2.2238 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0936    0.7011   -0.7550 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3201    1.9002   -0.0382 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9185   -0.3556   -0.1463 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0723    0.1824    0.4702 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0843   -1.6334   -0.7187 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3250    0.4238    1.0363 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7554   -1.3517    0.8304 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8004   -1.9322    0.4938 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4267    2.1804    0.6672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0843    1.3474   -0.5767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1604   -0.7712   -2.3930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4887    0.9152   -1.7819 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5289    2.4877   -0.0522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3286   -1.0655   -0.9230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8405    0.9001    1.1094 H   0  0  0  0  0  0  0  0  0  0  0  0
 14 13  1  0
 13 11  1  0
 11 12  1  0
 11  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  9  1  0
  7 10  1  0
  7  8  2  0
  4  3  1  0
  3  2  1  0
  2  1  2  0
  2 15  1  0
 15 16  1  0
 15 13  1  0
 14 25  1  0
 13 24  1  6
 11 22  1  1
 12 23  1  0
  4 17  1  6
  5 18  1  0
  5 19  1  0
  9 20  1  0
 10 21  1  0
 15 26  1  6
 16 27  1  0
M  END
Download

3D SDF for NP0267133 (6-phosphogluconolactone)


  Mrv1652305171801442D          

 16 16  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -2.4750    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13  1  1  0  0  0  0
 15  9  1  0  0  0  0
 16  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0267133

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1C(O)C(COP(O)(O)=O)OC(=O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H11O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-5,7-9H,1H2,(H2,11,12,13)

> <INCHI_KEY>
IJOJIVNDFQSGAB-UHFFFAOYSA-N

> <FORMULA>
C6H11O9P

> <MOLECULAR_WEIGHT>
258.119

> <EXACT_MASS>
258.014068932

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
20.210601402315405

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(3,4,5-trihydroxy-6-oxooxan-2-yl)methoxy]phosphonic acid

> <ALOGPS_LOGP>
-1.99

> <JCHEM_LOGP>
-2.8688392173333335

> <ALOGPS_LOGS>
-0.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.329575480706394

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3037364832915905

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6629249867193456

> <JCHEM_POLAR_SURFACE_AREA>
153.75

> <JCHEM_REFRACTIVITY>
45.6517

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.26e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-phosphogluconolactone

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0267133 (6-phosphogluconolactone)

Download
PDB for NP0267133 (6-phosphogluconolactone)
HEADER    PROTEIN                                 17-MAY-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAY-18         0                                  
HETATM    1  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0      -0.000  -4.620   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0      -0.000  -6.160   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -1.540  -4.620   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.540  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2    3   13                                                  
CONECT    2    1                                                            
CONECT    3    1    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   15   16                                             
CONECT   10    9                                                            
CONECT   11    6   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14    1                                                  
CONECT   14   13                                                            
CONECT   15    9                                                            
CONECT   16    9                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

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3D PDB for NP0267133 (6-phosphogluconolactone)
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SMILES for NP0267133 (6-phosphogluconolactone)
OC1C(O)C(COP(O)(O)=O)OC(=O)C1O
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INCHI for NP0267133 (6-phosphogluconolactone)
InChI=1S/C6H11O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-5,7-9H,1H2,(H2,11,12,13)
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View in JSmol
Synonyms
ValueSource
[(3,4,5-Trihydroxy-6-oxooxan-2-yl)methoxy]phosphonateGenerator
6-O-Phosphonato-D-glucono-1,5-lactone dianionHMDB
6-PGDLHMDB
6-Phospho-D-glucono-1,5-lactoneHMDB
6-Phosphonoglucono-delta-lactoneHMDB
[(2R,3S,4S,5R)-3,4,5-Trihydroxy-6-oxotetrahydro-2H-pyran-2-yl]methyl phosphateHMDB
[(2R,3S,4S,5R)-3,4,5-Trihydroxy-6-oxotetrahydro-2H-pyran-2-yl]methyl phosphoric acidHMDB
Chemical FormulaC6H11O9P
Average Mass258.1190 Da
Monoisotopic Mass258.01407 Da
IUPAC Name[(3,4,5-trihydroxy-6-oxooxan-2-yl)methoxy]phosphonic acid
Traditional Name6-phosphogluconolactone
CAS Registry NumberNot Available
SMILES
OC1C(O)C(COP(O)(O)=O)OC(=O)C1O
InChI Identifier
InChI=1S/C6H11O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-5,7-9H,1H2,(H2,11,12,13)
InChI KeyIJOJIVNDFQSGAB-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hexose phosphates. These are carbohydrate derivatives containing a hexose substituted by one or more phosphate groups.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentHexose phosphates  
Alternative Parents
Substituents
  • Hexose phosphate
    • 

  • Gluconolactone
    • 

  • Monosaccharide phosphate
    • 

  • Delta valerolactone
    • 

  • Delta_valerolactone
    • 

  • Monoalkyl phosphate
    • 

  • Alkyl phosphate
    • 

  • Organic phosphoric acid derivative
    • 

  • Phosphoric acid ester
    • 

  • Oxane
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid ester
    • 

  • Lactone
    • 

  • Organoheterocyclic compound
    • 

  • Carboxylic acid derivative
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Oxacycle
    • 

  • Polyol
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
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-2ALOGPS
logP-2.9ChemAxon
logS-0.9ALOGPS
pKa (Strongest Acidic)1.3ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area153.75 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity45.65 m³·mol⁻¹ChemAxon
Polarizability20.21 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0062628  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound600  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]