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Showing NP-Card for 5-phospho-α-D-ribose 1-diphosphate (NP0339711)

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Record Information
Version2.0
Created at2024-09-11 23:10:44 UTC
Updated at2024-09-11 23:10:45 UTC
NP-MRD IDNP0339711
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-phospho-α-D-ribose 1-diphosphate
Description Based on a literature review very few articles have been published on 5-phospho-α-D-ribose 1-diphosphate.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0339711 (5-phospho-α-D-ribose 1-diphosphate)


  Mrv2104 05272301422D          

 22 22  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    3.1768    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    4.0018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9717    3.1768    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.6783    3.1768    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1296   -1.5764    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.3759   -1.2408    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8833   -1.9119    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7941   -2.3300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2790   -2.9975    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.7639   -3.6649    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6115   -3.4824    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.9464   -2.5126    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
  9 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
  7 21  1  0  0  0  0
M  CHG  5   5  -1   6  -1  13  -1  17  -1  18  -1
M  END
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3D MOL for NP0339711 (5-phospho-α-D-ribose 1-diphosphate)

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3D SDF for NP0339711 (5-phospho-α-D-ribose 1-diphosphate)

  Mrv2104 05272301422D          

 22 22  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    3.1768    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    4.0018    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9717    3.1768    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.6783    3.1768    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1296   -1.5764    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.3759   -1.2408    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8833   -1.9119    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7941   -2.3300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2790   -2.9975    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.7639   -3.6649    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6115   -3.4824    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.9464   -2.5126    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  1  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
  9 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
  7 21  1  0  0  0  0
M  CHG  5   5  -1   6  -1  13  -1  17  -1  18  -1
M  END
> <DATABASE_ID>
NP0339711

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1C(O)C(OP([O-])(=O)OP([O-])([O-])=O)OC1COP([O-])([O-])=O

> <INCHI_IDENTIFIER>
InChI=1/C5H13O14P3/c6-3-2(1-16-20(8,9)10)17-5(4(3)7)18-22(14,15)19-21(11,12)13/h2-7H,1H2,(H,14,15)(H2,8,9,10)(H2,11,12,13)/p-5

> <INCHI_KEY>
PQGCEDQWHSBAJP-UHFFFAOYNA-I

> <FORMULA>
C5H8O14P3

> <MOLECULAR_WEIGHT>
385.029

> <EXACT_MASS>
384.915433831

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
25.574593168632834

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-5

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({3,4-dihydroxy-5-[(phosphonatooxy)methyl]oxolan-2-yl phosphonato}oxy)phosphonate

> <JCHEM_LOGP>
-2.971134817666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.7946491011714985

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.089276744554774

> <JCHEM_PKA_STRONGEST_BASIC>
-3.680908173473228

> <JCHEM_POLAR_SURFACE_AREA>
243.89

> <JCHEM_REFRACTIVITY>
56.97110000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
{3,4-dihydroxy-5-[(phosphonatooxy)methyl]oxolan-2-yl phosphonato}oxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0339711 (5-phospho-α-D-ribose 1-diphosphate)
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PDB for NP0339711 (5-phospho-α-D-ribose 1-diphosphate)
HEADER    PROTEIN                                 27-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-23         0                                  
HETATM    1  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM    3  P   UNK     0      -0.274   5.930   0.000  0.00  0.00           P+0
HETATM    4  O   UNK     0      -0.274   7.470   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -1.814   5.930   0.000  0.00  0.00           O-1
HETATM    6  O   UNK     0       1.266   5.930   0.000  0.00  0.00           O-1
HETATM    7  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.306   1.175   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.735  -1.536   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0       2.109  -2.943   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0       0.702  -2.316   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       3.515  -3.569   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       1.482  -4.349   0.000  0.00  0.00           O+0
HETATM   15  P   UNK     0       2.387  -5.595   0.000  0.00  0.00           P+0
HETATM   16  O   UNK     0       3.293  -6.841   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.142  -6.500   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0       3.633  -4.690   0.000  0.00  0.00           O-1
HETATM   19  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3                                                            
CONECT    7    1    8   21                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   19                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11   15                                                       
CONECT   15   14   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   15                                                            
CONECT   19    9   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22    7                                                  
CONECT   22   21                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

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3D PDB for NP0339711 (5-phospho-α-D-ribose 1-diphosphate)
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SMILES for NP0339711 (5-phospho-α-D-ribose 1-diphosphate)
OC1C(O)C(OP([O-])(=O)OP([O-])([O-])=O)OC1COP([O-])([O-])=O
Download
INCHI for NP0339711 (5-phospho-α-D-ribose 1-diphosphate)
InChI=1/C5H13O14P3/c6-3-2(1-16-20(8,9)10)17-5(4(3)7)18-22(14,15)19-21(11,12)13/h2-7H,1H2,(H,14,15)(H2,8,9,10)(H2,11,12,13)/p-5
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Synonyms
ValueSource
5-Phospho-α-D-ribose 1-diphosphoric acidGenerator
Chemical FormulaC5H8O14P3
Average Mass385.0290 Da
Monoisotopic Mass384.91543 Da
IUPAC Name({3,4-dihydroxy-5-[(phosphonatooxy)methyl]oxolan-2-yl phosphonato}oxy)phosphonate
Traditional Name{3,4-dihydroxy-5-[(phosphonatooxy)methyl]oxolan-2-yl phosphonato}oxyphosphonate
CAS Registry NumberNot Available
SMILES
OC1C(O)C(OP([O-])(=O)OP([O-])([O-])=O)OC1COP([O-])([O-])=O
InChI Identifier
InChI=1/C5H13O14P3/c6-3-2(1-16-20(8,9)10)17-5(4(3)7)18-22(14,15)19-21(11,12)13/h2-7H,1H2,(H,14,15)(H2,8,9,10)(H2,11,12,13)/p-5
InChI KeyPQGCEDQWHSBAJP-UHFFFAOYNA-I
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
ClassificationNot classified
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-3ChemAxon
pKa (Strongest Acidic)1.09ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area243.89 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity56.97 m³·mol⁻¹ChemAxon
Polarizability25.57 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
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 IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References