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Showing NP-Card for Ribose 1-phosphate (NP0086801)

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Record Information
Version2.0
Created at2022-05-11 16:31:24 UTC
Updated at2022-05-11 16:31:24 UTC
NP-MRD IDNP0086801
Secondary Accession NumbersNone
Natural Product Identification
Common NameRibose 1-phosphate
DescriptionRibose 1-phosphate, also known as D-ribose-1P, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. The 1-phospho derivative of alpha-D-ribose. Ribose 1-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Ribose 1-phosphate exists in all living species, ranging from bacteria to humans. Within humans, ribose 1-phosphate participates in a number of enzymatic reactions. In particular, guanine and ribose 1-phosphate can be biosynthesized from guanosine; which is mediated by the enzyme purine nucleoside phosphorylase. In addition, xanthine and ribose 1-phosphate can be biosynthesized from xanthosine; which is mediated by the enzyme purine nucleoside phosphorylase. In humans, ribose 1-phosphate is involved in the metabolic disorder called the gout or kelley-seegmiller syndrome pathway. Outside of the human body, Ribose 1-phosphate has been detected, but not quantified in, several different foods, such as cauliflowers, grass pea, vaccinium (blueberry, cranberry, huckleberry), star anises, and lemons. Ribose 1-phosphate was first documented in 1997 (PMID: 9133638). This could make ribose 1-phosphate a potential biomarker for the consumption of these foods.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086801 (Ribose 1-phosphate)

439236
  Mrv0541 02231216412D          

 14 14  0  0  1  0            999 V2000
    2.6150    1.0082    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.2386    0.4311    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7865    0.2011    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1360   -1.5059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3412   -1.5059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8622    1.0082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4435    1.8151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8081    0.8366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4220    1.1797    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6511   -0.8384    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8261   -0.8384    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9060   -0.0538    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5712   -0.0538    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6907    0.2011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  1  9  2  0  0  0  0
  2 12  1  0  0  0  0
  2 13  1  0  0  0  0
 13  3  1  1  0  0  0
 10  4  1  1  0  0  0
 11  5  1  1  0  0  0
  6 14  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  6  0  0  0
M  END
Download

3D MOL for NP0086801 (Ribose 1-phosphate)

     RDKit          3D

 25 25  0  0  0  0  0  0  0  0999 V2000
    2.8045   -0.3472    1.6598 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1215    0.3689    0.3509 P   0  0  2  0  0  5  0  0  0  0  0  0
    4.4101   -0.4249   -0.3633 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6397    1.9456    0.7419 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7562    0.4218   -0.6442 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6704    0.0237    0.0832 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3444    0.9613    0.1451 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5438    0.3604   -0.1198 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7040    0.9497    0.6317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8322    2.2920    0.2957 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3237   -1.0981    0.2228 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2719   -1.9333   -0.2938 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0373   -1.2594   -0.4727 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1834   -1.1284   -1.8198 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8639    0.0945   -1.0723 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1749    2.5904    0.1405 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9499   -0.2313    1.1297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7858    0.4379   -1.2167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6259    0.4316    0.2976 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6073    0.7965    1.7211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1441    2.3574   -0.6336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1788   -1.1857    1.3112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6708   -2.4481    0.4548 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5612   -2.1542   -0.1654 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2262   -1.8210   -2.3842 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  2  5  1  6
  2  3  1  0
  2  4  1  0
  2  1  2  0
  6 13  1  0
 13 14  1  0
 13 11  1  0
 11 12  1  0
 11  8  1  0
 10 21  1  0
  9 19  1  0
  9 20  1  0
  8 18  1  6
  6 17  1  1
  3 15  1  0
  4 16  1  0
 13 24  1  6
 14 25  1  0
 11 22  1  1
 12 23  1  0
M  END
Download

3D SDF for NP0086801 (Ribose 1-phosphate)

439236
  Mrv0541 02231216412D          

 14 14  0  0  1  0            999 V2000
    2.6150    1.0082    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.2386    0.4311    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7865    0.2011    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1360   -1.5059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3412   -1.5059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8622    1.0082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4435    1.8151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8081    0.8366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4220    1.1797    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6511   -0.8384    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8261   -0.8384    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9060   -0.0538    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5712   -0.0538    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6907    0.2011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  1  9  2  0  0  0  0
  2 12  1  0  0  0  0
  2 13  1  0  0  0  0
 13  3  1  1  0  0  0
 10  4  1  1  0  0  0
 11  5  1  1  0  0  0
  6 14  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0086801

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-1-2-3(7)4(8)5(12-2)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1

> <INCHI_KEY>
YXJDFQJKERBOBM-TXICZTDVSA-N

> <FORMULA>
C5H11O8P

> <MOLECULAR_WEIGHT>
230.1098

> <EXACT_MASS>
230.01915384

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
18.165952447471312

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-2.04

> <JCHEM_LOGP>
-2.425770307333333

> <ALOGPS_LOGS>
-0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.218897432342067

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1553760127282273

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811597090040385

> <JCHEM_POLAR_SURFACE_AREA>
136.68

> <JCHEM_REFRACTIVITY>
40.833800000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.52e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ribose 1-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0086801 (Ribose 1-phosphate)

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PDB for NP0086801 (Ribose 1-phosphate)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 439236                                            
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  P   UNK     0       4.881   1.882   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0       7.912   0.805   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       5.201   0.375   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       9.587  -2.811   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       6.237  -2.811   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      10.943   1.882   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.561   3.388   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       3.375   1.562   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       6.388   2.202   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       8.682  -1.565   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.142  -1.565   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.158  -0.100   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.666  -0.100   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.623   0.375   0.000  0.00  0.00           C+0
CONECT    1    3    7    8    9                                             
CONECT    2   12   13                                                       
CONECT    3    1   13                                                       
CONECT    4   10                                                            
CONECT    5   11                                                            
CONECT    6   14                                                            
CONECT    7    1                                                            
CONECT    8    1                                                            
CONECT    9    1                                                            
CONECT   10    4   11   12                                                  
CONECT   11    5   10   13                                                  
CONECT   12    2   10   14                                                  
CONECT   13    2    3   11                                                  
CONECT   14    6   12                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

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3D PDB for NP0086801 (Ribose 1-phosphate)
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SMILES for NP0086801 (Ribose 1-phosphate)
OC[C@H]1O[C@H](OP(O)(O)=O)[C@H](O)[C@@H]1O
Download
INCHI for NP0086801 (Ribose 1-phosphate)
InChI=1S/C5H11O8P/c6-1-2-3(7)4(8)5(12-2)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1
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View in JSmol
Synonyms
ValueSource
1-O-Phosphono-alpha-D-ribofuranoseChEBI
1-Phospho-alpha-D-ribofuranoseChEBI
D-Ribose 1-phosphateChEBI
1-O-Phosphono-a-D-ribofuranoseGenerator
1-O-Phosphono-α-D-ribofuranoseGenerator
1-Phospho-a-D-ribofuranoseGenerator
1-Phospho-α-D-ribofuranoseGenerator
D-Ribose 1-phosphoric acidGenerator
Ribose 1-phosphoric acidGenerator
1-O-Phosphono-D-ribofuranoseHMDB
a-D-Ribofuranose 1-(dihydrogen phosphate)HMDB
a-D-Ribose 1-phosphateHMDB
alpha-D-Ribofuranose 1-(dihydrogen phosphate)HMDB
alpha-D-Ribofuranose 1-phosphateHMDB
alpha-D-Ribose 1-phosphateHMDB
D-Ribofuranose 1-(dihydrogen phosphate)HMDB
D-Ribofuranose 1-phosphateHMDB
D-Ribose-1-phosphateHMDB
D-Ribose-1PHMDB
Ribofuranose 1-phosphateHMDB
Ribose 1-phosphate, (beta-D)-isomerHMDB
Ribose 1-phosphate, (alpha-D)-isomerHMDB
Chemical FormulaC5H11O8P
Average Mass230.1098 Da
Monoisotopic Mass230.01915 Da
IUPAC Name{[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid
Traditional Nameribose 1-phosphate
CAS Registry NumberNot Available
SMILES
OC[C@H]1O[C@H](OP(O)(O)=O)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H11O8P/c6-1-2-3(7)4(8)5(12-2)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1
InChI KeyYXJDFQJKERBOBM-TXICZTDVSA-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
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
    • 

  • Monoalkyl phosphate
    • 

  • Alkyl phosphate
    • 

  • Phosphoric acid ester
    • 

  • Organic phosphoric acid derivative
    • 

  • Tetrahydrofuran
    • 

  • Secondary alcohol
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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-2ALOGPS
logP-2.4ChemAxon
logS-0.82ALOGPS
pKa (Strongest Acidic)1.16ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area136.68 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity40.83 m³·mol⁻¹ChemAxon
Polarizability18.17 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001489  
DrugBank IDDB03101  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB031271  
KNApSAcK IDNot Available
Chemspider ID388373  
KEGG Compound IDC00620  
BioCyc IDRIBOSE-1P  
BiGG ID34994  
Wikipedia LinkNot Available
METLIN ID6273  
PubChem Compound439236  
PDB IDNot Available
ChEBI ID16300  
Good Scents IDNot Available
References
General References
  1. Giorgelli F, Bottai C, Mascia L, Scolozzi C, Camici M, Ipata PL: Recycling of alpha-D-ribose 1-phosphate for nucleoside interconversion. Biochim Biophys Acta. 1997 Apr 17;1335(1-2):6-22. [PubMed:9133638  ]