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Showing NP-Card for D-Ribulose (NP0086512)

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Record Information
Version2.0
Created at2022-05-11 16:22:54 UTC
Updated at2022-05-11 16:22:54 UTC
NP-MRD IDNP0086512
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Ribulose
DescriptionD-Ribulose belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-Ribulose is an extremely weak basic (essentially neutral) compound (based on its pKa). For example, d-ribulose is an intermediate in the fungal pathway for d-arabitol production. Ribulose sugars are composed in the pentose phosphate pathway. They are important in the formation of many bioactive substances. In humans, D-ribulose is involved in pentose phosphate pathway. Outside of the human body, D-Ribulose has been detected, but not quantified in, red beetroots. This could make D-ribulose a potential biomarker for the consumption of these foods. D-Ribulose is the diastereomer of d-xylulose. Also, as the 1,5-bisphosphate, d-ribulose combines with carbon dioxide at the start of the photosynthesis process in green plants (carbon dioxide trap). It has chemical formula C5H10O5. Two enantiomers are possible, d-ribulose (d-erythro-pentulose) and l-ribulose (l-erythro-pentulose). D-Ribulose is found in Streptomyces albidoflavus. Ribulose is a ketopentose — a monosaccharide containing five carbon atoms, and including a ketone functional group.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086512 (D-Ribulose)


  Mrv1652310071715402D          

 10  9  0  0  0  0            999 V2000
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  2  0  0  0  0
 10  5  1  0  0  0  0
M  END
Download

3D MOL for NP0086512 (D-Ribulose)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
   -1.4680    1.8041   -0.3783 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3998    0.5919   -0.1035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5322   -0.2546   -0.5006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3320   -1.5591   -0.1415 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2100    0.0399    0.6000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4038   -1.3211    0.7734 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9861    0.3341   -0.2870 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0789    1.7201   -0.3864 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2574   -0.2596    0.2779 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2848    0.1032   -0.6194 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4950    0.1418   -0.0816 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6625   -0.2310   -1.6174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7226   -1.6912    0.7605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0599    0.5425    1.5971 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0811   -1.8179    0.0921 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7905   -0.1573   -1.2600 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9632    2.0639    0.5478 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1779   -1.3524    0.3665 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4815    0.2543    1.2336 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1845    1.0482   -0.8732 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9  7  1  0
  7  8  1  0
  7  5  1  0
  5  6  1  0
  5  2  1  0
  2  1  2  0
  2  3  1  0
  3  4  1  0
 10 20  1  0
  9 18  1  0
  9 19  1  0
  7 16  1  6
  8 17  1  0
  5 14  1  1
  6 15  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
M  END
Download

3D SDF for NP0086512 (D-Ribulose)


  Mrv1652310071715402D          

 10  9  0  0  0  0            999 V2000
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  2  0  0  0  0
 10  5  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0086512

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC(O)C(O)C(=O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3,5-8,10H,1-2H2

> <INCHI_KEY>
ZAQJHHRNXZUBTE-UHFFFAOYSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.497603156749445

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,3,4,5-tetrahydroxypentan-2-one

> <ALOGPS_LOGP>
-2.16

> <JCHEM_LOGP>
-2.63669695

> <ALOGPS_LOGS>
0.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.995534588386644

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.569923731220491

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9797457089641277

> <JCHEM_POLAR_SURFACE_AREA>
97.99

> <JCHEM_REFRACTIVITY>
31.599299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.78e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-ribulose

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0086512 (D-Ribulose)

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PDB for NP0086512 (D-Ribulose)
HEADER    PROTEIN                                 07-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-OCT-17         0                                  
HETATM    1  C   UNK     0      -2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.025   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.976   2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.691   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.357   1.334   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -3.644   2.104   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.358   2.104   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.976   3.644   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.691   3.644   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.357  -0.206   0.000  0.00  0.00           O+0
CONECT    1    3    6                                                       
CONECT    2    4    7                                                       
CONECT    3    1    5    8                                                  
CONECT    4    2    5    9                                                  
CONECT    5    3    4   10                                                  
CONECT    6    1                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0086512 (D-Ribulose)
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SMILES for NP0086512 (D-Ribulose)
OCC(O)C(O)C(=O)CO
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INCHI for NP0086512 (D-Ribulose)
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3,5-8,10H,1-2H2
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View in JSmol
Synonyms
ValueSource
RibuloseMeSH
Ribulose, (erythro-D)-isomerMeSH
DL-erythro-PentuloseMeSH
Ribulose, (erythro-L)-isomerMeSH
Chemical FormulaC5H10O5
Average Mass150.1299 Da
Monoisotopic Mass150.05282 Da
IUPAC Name1,3,4,5-tetrahydroxypentan-2-one
Traditional NameD-ribulose
CAS Registry NumberNot Available
SMILES
OCC(O)C(O)C(=O)CO
InChI Identifier
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3,5-8,10H,1-2H2
InChI KeyZAQJHHRNXZUBTE-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
Streptomyces albidoflavusLOTUS Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentPentoses  
Alternative Parents
Substituents
  • Pentose monosaccharide
    • 

  • Beta-hydroxy ketone
    • 

  • Acyloin
    • 

  • Alpha-hydroxy ketone
    • 

  • Secondary alcohol
    • 

  • Ketone
    • 

  • Polyol
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • 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-2.2ALOGPS
logP-2.6ChemAxon
logS0.65ALOGPS
pKa (Strongest Acidic)10.57ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.6 m³·mol⁻¹ChemAxon
Polarizability13.5 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB004270  
KNApSAcK IDC00001131  
Chemspider IDNot Available
KEGG Compound IDC05052  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkRibulose  
METLIN IDNot Available
PubChem Compound619  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available