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Showing NP-Card for β-d-ribofuranoside (NP0175729)

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Record Information
Version1.0
Created at2022-09-03 13:16:08 UTC
Updated at2022-09-03 13:16:09 UTC
NP-MRD IDNP0175729
Secondary Accession NumbersNone
Natural Product Identification
Common Nameβ-d-ribofuranoside
Description β-d-ribofuranoside is found in Daphnia pulex.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0175729 (β-d-ribofuranoside)

            
  Mrv1652305161817372D          

 10 10  0  0  1  0            999 V2000
   12.9393   -2.8516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0419   -4.7884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8368   -4.7884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.3915   -3.0815    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3158   -2.2746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5269   -4.1210    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.2721   -3.3364    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.3518   -4.1210    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.6070   -3.3364    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.4874   -3.0815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  1  9  1  0  0  0  0
  6  2  1  6  0  0  0
  8  3  1  6  0  0  0
  5 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7 10  1  1  0  0  0
  8  9  1  0  0  0  0
  9  4  1  1  0  0  0
M  END
Download

3D MOL for NP0175729 (β-d-ribofuranoside)

     RDKit          3D

 20 20  0  0  0  0  0  0  0  0999 V2000
    2.2784    0.5494   -0.7176 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9634    0.3539    0.6231 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4766    0.2417    0.7380 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2086    1.3449    0.3042 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3821    0.9567   -0.2845 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2673    1.2482   -1.6634 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4744   -0.5527   -0.1903 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9202   -0.9407    1.0714 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0308   -0.8623   -0.2298 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3212   -2.1141    0.2259 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0234   -0.0578   -0.9622 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3217    1.2501    1.1783 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4287   -0.5333    1.0534 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1519   -0.0899    1.7572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2626    1.4604    0.1368 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2534    2.2009   -1.8460 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0124   -1.0155   -1.0109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2349   -0.1624    1.5977 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4212   -0.6075   -1.2161 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5986   -2.6701   -0.5653 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  1
  5 15  1  1
  6 16  1  0
  7 17  1  6
  8 18  1  0
  9 19  1  6
 10 20  1  0
M  END
Download

3D SDF for NP0175729 (β-d-ribofuranoside)

            
  Mrv1652305161817372D          

 10 10  0  0  1  0            999 V2000
   12.9393   -2.8516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0419   -4.7884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8368   -4.7884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.3915   -3.0815    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3158   -2.2746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5269   -4.1210    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.2721   -3.3364    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.3518   -4.1210    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.6070   -3.3364    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.4874   -3.0815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  1  9  1  0  0  0  0
  6  2  1  6  0  0  0
  8  3  1  6  0  0  0
  5 10  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7 10  1  1  0  0  0
  8  9  1  0  0  0  0
  9  4  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0175729

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](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-TXICZTDVSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.621018245765843

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,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>
29.96089999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.07e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-D-ribofuranoside

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0175729 (β-d-ribofuranoside)

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PDB for NP0175729 (β-d-ribofuranoside)
HEADER    PROTEIN                                 16-MAY-18   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-18         0                                  
HETATM    1  O   UNK     0      24.153  -5.323   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      22.478  -8.938   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      25.829  -8.938   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      26.864  -5.752   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      21.123  -4.246   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      23.384  -7.693   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.908  -6.228   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      24.923  -7.693   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      25.400  -6.228   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      21.443  -5.752   0.000  0.00  0.00           C+0
CONECT    1    7    9                                                       
CONECT    2    6                                                            
CONECT    3    8                                                            
CONECT    4    9                                                            
CONECT    5   10                                                            
CONECT    6    2    7    8                                                  
CONECT    7    1    6   10                                                  
CONECT    8    3    6    9                                                  
CONECT    9    1    8    4                                                  
CONECT   10    5    7                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0175729 (β-d-ribofuranoside)
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SMILES for NP0175729 (β-d-ribofuranoside)
OC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O
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INCHI for NP0175729 (β-d-ribofuranoside)
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
beta-D-RibChEBI
BETA-D-RIBOFURANOSYLChEBI
b-D-RibGenerator
Β-D-ribGenerator
b-D-RIBOFURANOSYLGenerator
Β-D-ribofuranosylGenerator
b-D-RibofuranoseGenerator
Β-D-ribofuranoseGenerator
Chemical FormulaC5H10O5
Average Mass150.1299 Da
Monoisotopic Mass150.05282 Da
IUPAC Name(2R,3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
Traditional Nameβ-D-ribofuranoside
CAS Registry NumberNot Available
SMILES
OC[C@H]1O[C@@H](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-TXICZTDVSA-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
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
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.6ALOGPS
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
Polarizability13.62 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 IDNot Available
Chemspider IDNot Available
KEGG Compound IDC16639  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound447347  
PDB IDNot Available
ChEBI ID47002  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]