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Showing NP-Card for 2-deoxy-d-ribofuranose (NP0196340)

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Record Information
Version2.0
Created at2022-09-04 14:25:10 UTC
Updated at2022-09-04 14:25:10 UTC
NP-MRD IDNP0196340
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-deoxy-d-ribofuranose
Description2-Deoxy-D-ribofuranose, also known as 2-deoxy-D-arabinose or 2-deoxy-D-erythro-pentose, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. A deoxypentose that is D-ribofuranose in which the hydroxy group at position C-2 is replaced by hydrogen. 2-deoxy-d-ribofuranose was first documented in 2016 (PMID: 26506859). 2-Deoxy-D-ribofuranose is an extremely weak basic (essentially neutral) compound (based on its pKa) (PMID: 27212641).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0196340 (2-deoxy-d-ribofuranose)

 
  Mrv0541 07171215542D          
 
  9  9  0  0  1  0            999 V2000
   15.6143  -12.1062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.8787  -12.8859    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.2772  -11.6254    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.8243  -11.8590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7133  -12.8859    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3979  -13.5591    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.9606  -12.1199    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
   14.3332  -12.5218    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7437  -11.8658    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  2  6  1  6  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  7  9  1  4  0  0  0
  5  7  1  0  0  0  0
M  END
Download

3D MOL for NP0196340 (2-deoxy-d-ribofuranose)

     RDKit          3D

 19 19  0  0  0  0  0  0  0  0999 V2000
    2.6523   -1.3177   -0.3905 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0390   -0.1585    0.0803 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6083   -0.0634   -0.3954 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0913   -1.1824    0.0840 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4137   -0.8035   -0.1373 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3315   -1.6597    0.4229 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4704    0.5288    0.5905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0769    1.0734    0.3368 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1286    2.2302   -0.4422 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2284   -1.6388    0.3682 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0356   -0.1206    1.1895 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5975    0.7301   -0.3197 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5154   -0.0053   -1.4810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5817   -0.6226   -1.2128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2265   -2.5755    0.0606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6073    0.3159    1.6844 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2542    1.1872    0.1836 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4180    1.2882    1.3024 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9125    2.7942   -0.2031 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
  8  9  1  0
  8  3  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  6
  5 14  1  6
  6 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  1
  9 19  1  0
M  END
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3D SDF for NP0196340 (2-deoxy-d-ribofuranose)

 
  Mrv0541 07171215542D          
 
  9  9  0  0  1  0            999 V2000
   15.6143  -12.1062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.8787  -12.8859    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.2772  -11.6254    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.8243  -11.8590    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7133  -12.8859    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3979  -13.5591    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.9606  -12.1199    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
   14.3332  -12.5218    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7437  -11.8658    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  2  6  1  6  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  7  9  1  4  0  0  0
  5  7  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0196340

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O4/c6-2-4-3(7)1-5(8)9-4/h3-8H,1-2H2/t3-,4+,5?/m0/s1

> <INCHI_KEY>
PDWIQYODPROSQH-PYHARJCCSA-N

> <FORMULA>
C5H10O4

> <MOLECULAR_WEIGHT>
134.1305

> <EXACT_MASS>
134.057908808

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
12.847990824562936

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.06

> <JCHEM_LOGP>
-1.4015662129999997

> <ALOGPS_LOGS>
0.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.970472920803939

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.360977999134441

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9789221500650536

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
28.45019999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.05e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4S,5R)-5-(hydroxymethyl)oxolane-2,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0196340 (2-deoxy-d-ribofuranose)

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PDB for NP0196340 (2-deoxy-d-ribofuranose)
HEADER    PROTEIN                                 17-JUL-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUL-12         0                                  
HETATM    1  C   UNK     0      29.147 -22.598   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      29.640 -24.054   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      30.384 -21.701   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      27.672 -22.137   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      31.198 -24.054   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      28.743 -25.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      31.660 -22.624   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      26.755 -23.374   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      33.122 -22.150   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8                                                       
CONECT    5    2    7                                                       
CONECT    6    2                                                            
CONECT    7    3    9    5                                                  
CONECT    8    4                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0196340 (2-deoxy-d-ribofuranose)
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SMILES for NP0196340 (2-deoxy-d-ribofuranose)
OC[C@H]1OC(O)C[C@@H]1O
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INCHI for NP0196340 (2-deoxy-d-ribofuranose)
InChI=1S/C5H10O4/c6-2-4-3(7)1-5(8)9-4/h3-8H,1-2H2/t3-,4+,5?/m0/s1
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View in JSmol
Synonyms
ValueSource
2-Deoxy-D-arabinoseChEBI
2-Deoxy-D-riboseChEBI
2-DeoxyriboseChEBI
2-Deoxy-D-erythro-pentoseKegg
ThyminoseKegg
2'-Deoxy-D-riboseChEBI
Chemical FormulaC5H10O4
Average Mass134.1305 Da
Monoisotopic Mass134.05791 Da
IUPAC Name(4S,5R)-5-(hydroxymethyl)oxolane-2,4-diol
Traditional Name(4S,5R)-5-(hydroxymethyl)oxolane-2,4-diol
CAS Registry NumberNot Available
SMILES
OC[C@H]1OC(O)C[C@@H]1O
InChI Identifier
InChI=1S/C5H10O4/c6-2-4-3(7)1-5(8)9-4/h3-8H,1-2H2/t3-,4+,5?/m0/s1
InChI KeyPDWIQYODPROSQH-PYHARJCCSA-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 OriginNot Available
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
    • 

  • Oxolane
    • 

  • Secondary alcohol
    • 

  • Hemiacetal
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • 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-2.1ALOGPS
logP-1.4ChemAxon
logS0.89ALOGPS
pKa (Strongest Acidic)12.36ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.92 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity28.45 m³·mol⁻¹ChemAxon
Polarizability12.85 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00001115  
Chemspider IDNot Available
KEGG Compound IDC01801  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkDeoxyribose  
METLIN IDNot Available
PubChem Compound9828112  
PDB IDNot Available
ChEBI ID90761  
Good Scents IDNot Available
References
General References
  1. Soluch M, Grzeszczyk B, Staszewska-Krajewska O, Chmielewski M, Furman B: Synthesis of Thienamycin methyl ester from 2-deoxy-D-ribose via Kinugasa reaction. J Antibiot (Tokyo). 2016 Mar;69(3):164-8. doi: 10.1038/ja.2015.108. Epub 2015 Oct  28. [PubMed:26506859  ] 
  2. Vogt N, Demaison J, Cocinero EJ, Ecija P, Lesarri A, Rudolph HD, Vogt J: The equilibrium molecular structures of 2-deoxyribose and fructose by the semiexperimental mixed estimation method and coupled-cluster computations. Phys Chem Chem Phys. 2016 Jun 21;18(23):15555-63. doi: 10.1039/c6cp01842d. Epub  2016 May 23. [PubMed:27212641  ] 
  3. LOTUS database [Link]