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Showing NP-Card for D-Ribose (NP0001055)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:39:29 UTC
NP-MRD IDNP0001055
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Ribose
DescriptionD-Ribose, commonly referred to as simply ribose, is a five-carbon sugar found in all living cells. Ribose is not an essential nutrient because it can be synthesized by almost every tissue in the body from other substances, such as glucose. It is vital for life as a component of DNA, RNA, ATP, ADP, and AMP. In nature, small amounts of ribose can be found in ripe fruits and vegetables. Brewer's yeast, which has a high concentration of RNA, is another rich source of ribose. D-ribose is also a component of many so-called energy drinks and anti-ageing products available on the market today. Ribose is a structural component of ATP, which is the primary energy source for exercising muscle. The adenosine component is an adenine base attached to the five-carbon sugar ribose. ATP provides energy to working muscles by releasing a phosphate group, hence becoming ADP, which in turn may release a phosphate group, then becoming AMP. During intense muscular activity, the total amount of ATP available is quickly depleted. In an effort to correct this imbalance, AMP is broken down in the muscle and secreted from the cell. Once the breakdown products of AMP are released from the cell, the energy potential (TAN pool) of the muscle is reduced and ATP must then be reformed using ribose. Ribose helps restore the level of adenine nucleotides by bypassing the rate-limiting step in the de novo (oxidative pentose phosphate) pathway, which regenerates phosphoribosyl pyrophosphate (PRPP), the essential precursor for ATP. If ribose is not readily available to a cell, glucose may be converted to ribose. Ribose supplementation has been shown to increase the rate of ATP resynthesis following intense exercise. The use of ribose in men with severe coronary artery disease resulted in improved exercise tolerance. Hence, there is interest in the potential of ribose supplements to boost muscular performance in athletic activities (PMID: 17618002 , Curr Sports Med Rep. 2007 Jul;6(4):254-7.).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001055 (D-Ribose)


  Mrv1652305271900072D          

 10 10  0  0  1  0            999 V2000
   12.9398   -2.8516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0424   -4.7885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8374   -4.7885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3163   -2.2746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5274   -4.1211    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.2725   -3.3365    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.3524   -4.1211    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.6075   -3.3365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4878   -3.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3920   -3.0816    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  1  8  1  0  0  0  0
  5  2  1  6  0  0  0
  7  3  1  6  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  9  1  1  0  0  0
  7  8  1  0  0  0  0
  8 10  1  0  0  0  0
M  END
Download

3D MOL for NP0001055 (D-Ribose)

HMDB0000283
     RDKit          3D
D-Ribose
 20 20  0  0  0  0  0  0  0  0999 V2000
    2.5759   -1.6543   -0.0424 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8696   -0.5817    0.4914 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7707   -0.1109   -0.4628 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1386   -1.1041   -0.7295 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4117   -0.5249   -0.6620 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4202   -1.4315   -0.6017 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2545    0.2758    0.6333 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3100    1.1436    0.8199 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0327    0.9985    0.2672 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3235    1.9954   -0.6558 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2839   -1.2959   -0.6307 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5925    0.2610    0.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4462   -0.8077    1.4821 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2073    0.2296   -1.4053 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4710    0.1849   -1.5214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1741   -2.3697   -0.5457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0830   -0.4053    1.4698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1655    1.6315    1.6460 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5708    1.3795    1.1299 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4026    2.1862   -1.2765 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  3  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  6
  5 15  1  0
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  1
 10 20  1  0
M  END
Download

3D SDF for NP0001055 (D-Ribose)


  Mrv1652305271900072D          

 10 10  0  0  1  0            999 V2000
   12.9398   -2.8516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0424   -4.7885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8374   -4.7885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3163   -2.2746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5274   -4.1211    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.2725   -3.3365    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.3524   -4.1211    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.6075   -3.3365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4878   -3.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3920   -3.0816    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  1  8  1  0  0  0  0
  5  2  1  6  0  0  0
  7  3  1  6  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  9  1  1  0  0  0
  7  8  1  0  0  0  0
  8 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001055

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1OC(O)[C@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1

> <INCHI_KEY>
HMFHBZSHGGEWLO-SOOFDHNKSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.681345802838806

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol

> <ALOGPS_LOGP>
-2.65

> <JCHEM_LOGP>
-2.302204276

> <ALOGPS_LOGS>
0.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.899514700313038

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.30569577774193

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811390578102284

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
29.9609

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.07e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-ribofuranoside

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001055 (D-Ribose)

HMDB0000283
     RDKit          3D
D-Ribose
 20 20  0  0  0  0  0  0  0  0999 V2000
    2.5759   -1.6543   -0.0424 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8696   -0.5817    0.4914 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7707   -0.1109   -0.4628 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1386   -1.1041   -0.7295 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4117   -0.5249   -0.6620 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4202   -1.4315   -0.6017 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2545    0.2758    0.6333 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3100    1.1436    0.8199 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0327    0.9985    0.2672 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3235    1.9954   -0.6558 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2839   -1.2959   -0.6307 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5925    0.2610    0.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4462   -0.8077    1.4821 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2073    0.2296   -1.4053 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4710    0.1849   -1.5214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1741   -2.3697   -0.5457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0830   -0.4053    1.4698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1655    1.6315    1.6460 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5708    1.3795    1.1299 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4026    2.1862   -1.2765 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  3  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  6
  5 15  1  0
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  1
 10 20  1  0
M  END
Download

PDB for NP0001055 (D-Ribose)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      24.154  -5.323   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      22.479  -8.939   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      25.830  -8.939   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      21.124  -4.246   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      23.384  -7.693   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      22.909  -6.228   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      24.924  -7.693   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      25.401  -6.228   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.444  -5.752   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      26.865  -5.752   0.000  0.00  0.00           O+0
CONECT    1    6    8                                                       
CONECT    2    5                                                            
CONECT    3    7                                                            
CONECT    4    9                                                            
CONECT    5    2    6    7                                                  
CONECT    6    1    5    9                                                  
CONECT    7    3    5    8                                                  
CONECT    8    1    7   10                                                  
CONECT    9    4    6                                                       
CONECT   10    8                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for NP0001055 (D-Ribose)

COMPND    HMDB0000283
HETATM    1  O1  UNL     1       2.576  -1.654  -0.042  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.870  -0.582   0.491  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.771  -0.111  -0.463  1.00  0.00           C  
HETATM    4  O2  UNL     1      -0.139  -1.104  -0.730  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.412  -0.525  -0.662  1.00  0.00           C  
HETATM    6  O3  UNL     1      -2.420  -1.432  -0.602  1.00  0.00           O  
HETATM    7  C4  UNL     1      -1.255   0.276   0.633  1.00  0.00           C  
HETATM    8  O4  UNL     1      -2.310   1.144   0.820  1.00  0.00           O  
HETATM    9  C5  UNL     1       0.033   0.998   0.267  1.00  0.00           C  
HETATM   10  O5  UNL     1      -0.323   1.995  -0.656  1.00  0.00           O  
HETATM   11  H1  UNL     1       3.284  -1.296  -0.631  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.592   0.261   0.594  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.446  -0.808   1.482  1.00  0.00           H  
HETATM   14  H4  UNL     1       1.207   0.230  -1.405  1.00  0.00           H  
HETATM   15  H5  UNL     1      -1.471   0.185  -1.521  1.00  0.00           H  
HETATM   16  H6  UNL     1      -2.174  -2.370  -0.546  1.00  0.00           H  
HETATM   17  H7  UNL     1      -1.083  -0.405   1.470  1.00  0.00           H  
HETATM   18  H8  UNL     1      -2.165   1.631   1.646  1.00  0.00           H  
HETATM   19  H9  UNL     1       0.571   1.380   1.130  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.403   2.186  -1.277  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3   12   13
CONECT    3    4    9   14
CONECT    4    5
CONECT    5    6    7   15
CONECT    6   16
CONECT    7    8    9   17
CONECT    8   18
CONECT    9   10   19
CONECT   10   20
END
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SMILES for NP0001055 (D-Ribose)

OC[C@H]1OC(O)[C@H](O)[C@@H]1O
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INCHI for NP0001055 (D-Ribose)

InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1
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View in JSmol
Synonyms
ValueSource
(3R,4S,5R)-5-(Hydroxymethyl)tetrahydrofuran-2,3,4-triolChEBI
RiboseChEBI
WURCS=2.0/1,1,0/[a222h-1x_1-4]/1/ChEBI
D-RibofuranosideHMDB
D-​RibofuranoseHMDB
RibofuranosideHMDB
RibofuranoseHMDB
Chemical FormulaC5H10O5
Average Mass150.1299 Da
Monoisotopic Mass150.05282 Da
IUPAC Name(3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
Traditional NameD-ribofuranoside
CAS Registry Number613-83-2
SMILES
OC[C@H]1OC(O)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1
InChI KeyHMFHBZSHGGEWLO-SOOFDHNKSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Allium cepaFooDB
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Arabidopsis thalianaPlant
Artemisia dracunculusFooDB
Averrhoa carambolaKNApSAcK Database
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
Codonopsis pilosulaPlant
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Mycoplasmopsis bovisLOTUS Database
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Phoenix dactyliferaFooDB
Prunus aviumPlant
Psidium guajavaPlant
Solanum lycopersicumFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Triticum aestivumPlant
Vigna radiataFooDB
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
  • Tetrahydrofuran
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point95 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP-2.32Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility1070 g/LALOGPS
logP-2.6ALOGPS
logP-2.3ChemAxon
logS0.85ALOGPS
pKa (Strongest Acidic)11.31ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.96 m³·mol⁻¹ChemAxon
Polarizability13.68 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000283
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB031292
KNApSAcK IDC00053746
Chemspider ID5575
KEGG Compound IDC00121
BioCyc IDNot Available
BiGG ID33936
Wikipedia LinkRibose
METLIN ID313
PubChem Compound5779
PDB IDNot Available
ChEBI ID47013
Good Scents IDNot Available
References
General References
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