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Showing NP-Card for ribulose (NP0328987)

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Record Information
Version2.0
Created at2022-09-12 12:56:05 UTC
Updated at2022-09-12 12:56:06 UTC
NP-MRD IDNP0328987
Secondary Accession NumbersNone
Natural Product Identification
Common Nameribulose
DescriptionD-Ribulose, also known as D-arabinoketose or D-rul, 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). D-Ribulose exists in all living organisms, ranging from bacteria to humans. In humans, D-ribulose is involved in pentose phosphate pathway. ribulose is found in Daphnia pulex, Homo sapiens, Streptomyces albidoflavus and Streptomyces coelicolor. ribulose was first documented in 1971 (PMID: 4928018). The D-stereoisomer of ribulose (PMID: 22344653) (PMID: 24391356).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0328987 (ribulose)


  Mrv1652305221917262D          

 10  9  0  0  0  0            999 V2000
 9998.9477 9999.1697    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.2331 9998.7576    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9997.5183 9999.1697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.8035 9998.7576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2331 9997.9323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6622 9998.7576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.3797 9999.1697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.0932 9998.7576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6622 9997.9323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9477 9999.9944    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  1 10  1  1  0  0  0
  2  3  1  0  0  0  0
  2  5  1  6  0  0  0
  3  4  1  0  0  0  0
  6  7  1  0  0  0  0
  6  9  2  0  0  0  0
  7  8  1  0  0  0  0
M  END
Download

3D MOL for NP0328987 (ribulose)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
   -0.3726   -2.1351    0.9719 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7983   -1.0643    0.5736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9448   -1.1205   -0.3624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3220    0.1484   -0.7305 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2434    0.2366    0.9674 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8895    1.3090    0.3888 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2298    0.3586    0.7484 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7040    1.5260    1.3144 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5942    0.3275   -0.7197 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1385   -0.8291   -1.3355 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7788   -1.6999    0.1020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6917   -1.6743   -1.2991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1489    0.4184   -0.2593 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4088    0.3331    2.0788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2311    1.9755    0.0604 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7486   -0.4912    1.2693 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7131    2.2969    0.6945 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6832    0.3733   -0.8772 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1506    1.1985   -1.2251 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8677   -1.4872   -1.4235 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  1
  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 NP0328987 (ribulose)


  Mrv1652305221917262D          

 10  9  0  0  0  0            999 V2000
 9998.9477 9999.1697    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.2331 9998.7576    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9997.5183 9999.1697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.8035 9998.7576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2331 9997.9323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6622 9998.7576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.3797 9999.1697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.0932 9998.7576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6622 9997.9323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9477 9999.9944    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  1 10  1  1  0  0  0
  2  3  1  0  0  0  0
  2  5  1  6  0  0  0
  3  4  1  0  0  0  0
  6  7  1  0  0  0  0
  6  9  2  0  0  0  0
  7  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0328987

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H](O)[C@@H](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/t3-,5-/m1/s1

> <INCHI_KEY>
ZAQJHHRNXZUBTE-NQXXGFSBSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.47344240400903

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4R)-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>
97.99000000000001

> <JCHEM_REFRACTIVITY>
31.5993

> <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 NP0328987 (ribulose)

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PDB for NP0328987 (ribulose)
HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0    8664.7028665.117   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8663.3688664.348   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8662.0348665.117   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8660.7008664.348   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8663.3688662.807   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0    8666.0368664.348   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8667.3768665.117   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0    8668.7078664.348   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8666.0368662.807   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8664.7028666.656   0.000  0.00  0.00           O+0
CONECT    1    2    6   10                                                  
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2                                                            
CONECT    6    1    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    6                                                            
CONECT   10    1                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0328987 (ribulose)
Download
SMILES for NP0328987 (ribulose)
OC[C@@H](O)[C@@H](O)C(=O)CO
Download
INCHI for NP0328987 (ribulose)
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3,5-8,10H,1-2H2/t3-,5-/m1/s1
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View in JSmol
Synonyms
ValueSource
D-ArabinoketoseChEBI
D-ArabinuloseChEBI
D-Erythro-2-pentuloseChEBI
D-Erythro-pent-2-uloseChEBI
D-RiboketoseChEBI
D-RulChEBI
D(-)-RibuloseHMDB
D-AdonoseHMDB
D-AraboketoseHMDB
D-erythro-2-KeptopentoseHMDB
D-erythro-PentuloseHMDB
D-ErythropentuloseHMDB
D-RibosoneHMDB
Ribulose, (erythro-L)-isomerMeSH, HMDB
DL-erythro-PentuloseMeSH, HMDB
RibuloseMeSH, HMDB
Ribulose, (erythro-D)-isomerMeSH, HMDB
Chemical FormulaC5H10O5
Average Mass150.1299 Da
Monoisotopic Mass150.05282 Da
IUPAC Name(3R,4R)-1,3,4,5-tetrahydroxypentan-2-one
Traditional NameD-ribulose
CAS Registry NumberNot Available
SMILES
OC[C@@H](O)[C@@H](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/t3-,5-/m1/s1
InChI KeyZAQJHHRNXZUBTE-NQXXGFSBSA-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 Origin
Species NameSourceReference
Daphnia pulexLOTUS Database
Homo sapiensLOTUS Database
Streptomyces albidoflavusLOTUS Database
Streptomyces coelicolorLOTUS Database
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
Polarizability13.47 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0160638  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00001131  
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDD-RIBULOSE  
BiGG IDNot Available
Wikipedia LinkRibulose  
METLIN IDNot Available
PubChem Compound151261  
PDB IDNot Available
ChEBI ID17173  
Good Scents IDNot Available
References
General References
  1. Moon HJ, Tiwari MK, Singh R, Kang YC, Lee JK: Molecular determinants of the cofactor specificity of ribitol dehydrogenase, a short-chain dehydrogenase/reductase. Appl Environ Microbiol. 2012 May;78(9):3079-86. doi: 10.1128/AEM.07751-11. Epub 2012 Feb 17. [PubMed:22344653  ] 
  2. Sarwar MW, Saleem IB, Ali A, Abbas F: insilico Characterization and Homology Modeling of Arabitol Dehydrogenase (ArDH) from Candida albican. Bioinformation. 2013 Dec 6;9(19):952-7. doi: 10.6026/97320630009952. eCollection  2013. [PubMed:24391356  ] 
  3. LeBlanc DJ, Mortlock RP: Metabolism of D-arabinose: a new pathway in Escherichia coli. J Bacteriol. 1971 Apr;106(1):90-6. doi: 10.1128/jb.106.1.90-96.1971. [PubMed:4928018  ] 
  4. LOTUS database [Link]