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Showing NP-Card for ribose (NP0214433)

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Record Information
Version2.0
Created at2022-09-05 13:43:55 UTC
Updated at2022-09-05 13:43:56 UTC
NP-MRD IDNP0214433
Secondary Accession NumbersNone
Natural Product Identification
Common Nameribose
DescriptionD-Ribose belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. The “d-” in the name d-ribose refers to the stereochemistry of the chiral carbon atom farthest away from the aldehyde group (C4'). Ribose is an aldopentose (a monosaccharide containing five carbon atoms) that, in its open chain form, has an aldehyde functional group at one end. Ribose is a carbohydrate with the formula C5H10O5; specifically, it is a pentose monosaccharide (simple sugar) with linear form H−(CO)−(CHOH)4−H, which has all the hydroxyl groups on the same side in the Fischer projection. D-Ribose is an extremely weak basic (essentially neutral) compound (based on its pKa). In humans, D-ribose is involved in the metabolic disorder called the purine nucleoside phosphorylase deficiency pathway. Outside of the human body, D-Ribose has been detected, but not quantified in, several different foods, such as garden onions, mung beans, tarragons, garden tomato, and milk (cow). This could make D-ribose a potential biomarker for the consumption of these foods. Once converted, d-ribose-5-phosphate is available for the manufacturing of the amino acids tryptophan and histidine, or for use in the pentose phosphate pathway. The ribose β-d-ribofuranose forms part of the backbone of RNA. ribose is found in Arabidopsis thaliana, Cannabis sativa, Streptomyces sporangiiformans and Tamarix aphylla. Its synthetic mirror image, l-ribose, is not found in nature.D-Ribose was first reported in 1891 by Emil Fischer.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0214433 (ribose)


  Mrv1652305221920162D          

 13 12  0  0  1  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  1  0  0  0  0  0  0  0  0  0
    0.9059    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1914    0.7145    0.0000 C   0  0  1  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
   -0.5230    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914    1.5395    0.0000 H   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  2  0  0  0  0
  7  2  1  0  0  0  0
  3  8  1  1  0  0  0
  4  9  1  1  0  0  0
  5 10  1  6  0  0  0
  3 11  1  1  0  0  0
  4 12  1  1  0  0  0
  5 13  1  6  0  0  0
M  END
Download

3D MOL for NP0214433 (ribose)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
    2.0619    0.9220    1.7909 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7214   -0.0764    1.1716 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4017    0.0110   -0.2752 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4486    1.3046   -0.7503 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2149   -0.7790   -0.7138 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2778   -0.8406   -2.1411 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1189   -0.1747   -0.4213 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2886    1.1129   -0.9299 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5966   -0.3278    0.9950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9526    0.5260    1.8801 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6696   -1.0019    1.7308 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3049   -0.4911   -0.7769 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5279    1.9548   -0.0073 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2216   -1.8195   -0.3747 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3468    0.1114   -2.4110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8953   -0.7734   -1.0301 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3993    1.7806   -0.2032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5179   -1.3895    1.3450 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6905   -0.0999    1.0943 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7375    0.0505    2.7052 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  7  5  1  0
  5  6  1  0
  5  3  1  0
  3  4  1  0
  3  2  1  0
  2  1  2  0
  7 16  1  6
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  0
  5 14  1  1
  6 15  1  0
  3 12  1  6
  4 13  1  0
  2 11  1  0
M  END
Download

3D SDF for NP0214433 (ribose)


  Mrv1652305221920162D          

 13 12  0  0  1  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  1  0  0  0  0  0  0  0  0  0
    0.9059    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1914    0.7145    0.0000 C   0  0  1  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
   -0.5230    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914    1.5395    0.0000 H   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  2  0  0  0  0
  7  2  1  0  0  0  0
  3  8  1  1  0  0  0
  4  9  1  1  0  0  0
  5 10  1  6  0  0  0
  3 11  1  1  0  0  0
  4 12  1  1  0  0  0
  5 13  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0214433

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@](O)(CO)[C@@]([H])(O)[C@@]([H])(O)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4+,5-/m0/s1

> <INCHI_KEY>
PYMYPHUHKUWMLA-LMVFSUKVSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.392671307669183

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R)-2,3,4,5-tetrahydroxypentanal

> <ALOGPS_LOGP>
-2.28

> <JCHEM_LOGP>
-2.9380256209999995

> <ALOGPS_LOGS>
0.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.420851692159264

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.332793333319174

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9744929158468105

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
31.383099999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.80e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ribose

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0214433 (ribose)

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PDB for NP0214433 (ribose)
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      -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
HETATM   11  H   UNK     0      -0.976   0.564   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       1.691   0.564   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       0.357   2.874   0.000  0.00  0.00           H+0
CONECT    1    3    6                                                       
CONECT    2    4    7                                                       
CONECT    3    1    5    8   11                                             
CONECT    4    2    5    9   12                                             
CONECT    5    3    4   10   13                                             
CONECT    6    1                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    3                                                            
CONECT   12    4                                                            
CONECT   13    5                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

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3D PDB for NP0214433 (ribose)
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SMILES for NP0214433 (ribose)
[H][C@@](O)(CO)[C@@]([H])(O)[C@@]([H])(O)C=O
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INCHI for NP0214433 (ribose)
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4+,5-/m0/s1
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View in JSmol
Synonyms
ValueSource
(2R,3R,4R)-2,3,4,5-TetrahydroxypentanalChEBI
D-Ribo-2,3,4,5-tetrahydroxyvaleraldehydeChEBI
D-RiboseChEBI
D RiboseMeSH
RiboseMeSH
Chemical FormulaC5H10O5
Average Mass150.1299 Da
Monoisotopic Mass150.05282 Da
IUPAC Name(2R,3R,4R)-2,3,4,5-tetrahydroxypentanal
Traditional Nameribose
CAS Registry NumberNot Available
SMILES
[H][C@@](O)(CO)[C@@]([H])(O)[C@@]([H])(O)C=O
InChI Identifier
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h1,3-5,7-10H,2H2/t3-,4+,5-/m0/s1
InChI KeyPYMYPHUHKUWMLA-LMVFSUKVSA-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
Arabidopsis thalianaLOTUS Database
Cannabis sativaLOTUS Database
Streptomyces sporangiiformansLOTUS Database
Tamarix aphyllaLOTUS 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 aldehyde
    • 

  • Alpha-hydroxyaldehyde
    • 

  • Secondary alcohol
    • 

  • Polyol
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Short-chain aldehyde
    • 

  • Primary alcohol
    • 

  • Carbonyl group
    • 

  • Aldehyde
    • 

  • 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-2.3ALOGPS
logP-2.9ChemAxon
logS0.4ALOGPS
pKa (Strongest Acidic)12.33ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.38 m³·mol⁻¹ChemAxon
Polarizability13.39 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 IDFDB011145  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkRibose  
METLIN IDNot Available
PubChem Compound5311110  
PDB IDNot Available
ChEBI ID47014  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]