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Showing NP-Card for Adenosine diphosphate ribose (NP0334678)

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Record Information
Version2.0
Created at2024-09-10 19:28:51 UTC
Updated at2024-09-10 19:28:52 UTC
NP-MRD IDNP0334678
Secondary Accession NumbersNone
Natural Product Identification
Common NameAdenosine diphosphate ribose
DescriptionAdenosine diphosphate ribose belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group. Based on a literature review very few articles have been published on Adenosine diphosphate ribose.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0334678 (Adenosine diphosphate ribose)


  Mrv2104 05252322012D          

 36 39  0  0  0  0            999 V2000
   26.9197  -19.8564    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   28.3410  -19.7095    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   24.8285  -21.3121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.7922  -19.4457    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.7346  -20.8960    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   31.2307  -19.4882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.2513  -20.3402    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.1325  -21.3189    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   31.9173  -21.5096    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.0942  -20.0464    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   32.6501  -19.8711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.5879  -19.3726    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.4034  -20.5247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.4359  -19.1881    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.6779  -18.9564    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.0041  -20.4626    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.7872  -22.3499    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.7872  -23.6777    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.2920  -22.1888    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.5775  -23.4263    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.2920  -24.6638    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.0457  -20.2308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5596  -20.8974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.8300  -20.4871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.0434  -21.5656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.4982  -20.0033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.6857  -20.7067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.5155  -19.8994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.5060  -20.7944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.8429  -20.0413    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.7624  -19.5626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0065  -22.6013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2686  -23.0138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0065  -23.4263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.2920  -23.8388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.5775  -22.6013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  1 12  1  0  0  0  0
  1 13  1  0  0  0  0
  1 14  2  0  0  0  0
  2 10  1  0  0  0  0
  2 12  1  0  0  0  0
  2 15  1  0  0  0  0
  2 16  2  0  0  0  0
  3 24  1  0  0  0  0
  3 25  1  0  0  0  0
  4 22  1  0  0  0  0
  5 23  1  0  0  0  0
  6 28  1  0  0  0  0
  6 30  1  0  0  0  0
  7 26  1  0  0  0  0
  8 27  1  0  0  0  0
  9 29  1  0  0  0  0
 10 31  1  0  0  0  0
 11 30  1  0  0  0  0
 17 25  1  0  0  0  0
 17 32  1  0  0  0  0
 17 33  1  0  0  0  0
 18 33  2  0  0  0  0
 18 34  1  0  0  0  0
 19 32  2  0  0  0  0
 19 36  1  0  0  0  0
 20 35  1  0  0  0  0
 20 36  2  0  0  0  0
 21 35  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 23 25  1  0  0  0  0
 24 26  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 28 31  1  0  0  0  0
 29 30  1  0  0  0  0
 32 34  1  0  0  0  0
 34 35  2  0  0  0  0
M  END
Download

3D MOL for NP0334678 (Adenosine diphosphate ribose)

Download
3D SDF for NP0334678 (Adenosine diphosphate ribose)

  Mrv2104 05252322012D          

 36 39  0  0  0  0            999 V2000
   26.9197  -19.8564    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   28.3410  -19.7095    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   24.8285  -21.3121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.7922  -19.4457    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.7346  -20.8960    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   31.2307  -19.4882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.2513  -20.3402    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.1325  -21.3189    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   31.9173  -21.5096    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.0942  -20.0464    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   32.6501  -19.8711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.5879  -19.3726    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.4034  -20.5247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.4359  -19.1881    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.6779  -18.9564    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.0041  -20.4626    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.7872  -22.3499    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.7872  -23.6777    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.2920  -22.1888    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.5775  -23.4263    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.2920  -24.6638    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.0457  -20.2308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5596  -20.8974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.8300  -20.4871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.0434  -21.5656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.4982  -20.0033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.6857  -20.7067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.5155  -19.8994    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.5060  -20.7944    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.8429  -20.0413    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.7624  -19.5626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0065  -22.6013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2686  -23.0138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0065  -23.4263    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.2920  -23.8388    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.5775  -22.6013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  1 12  1  0  0  0  0
  1 13  1  0  0  0  0
  1 14  2  0  0  0  0
  2 10  1  0  0  0  0
  2 12  1  0  0  0  0
  2 15  1  0  0  0  0
  2 16  2  0  0  0  0
  3 24  1  0  0  0  0
  3 25  1  0  0  0  0
  4 22  1  0  0  0  0
  5 23  1  0  0  0  0
  6 28  1  0  0  0  0
  6 30  1  0  0  0  0
  7 26  1  0  0  0  0
  8 27  1  0  0  0  0
  9 29  1  0  0  0  0
 10 31  1  0  0  0  0
 11 30  1  0  0  0  0
 17 25  1  0  0  0  0
 17 32  1  0  0  0  0
 17 33  1  0  0  0  0
 18 33  2  0  0  0  0
 18 34  1  0  0  0  0
 19 32  2  0  0  0  0
 19 36  1  0  0  0  0
 20 35  1  0  0  0  0
 20 36  2  0  0  0  0
 21 35  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 23 25  1  0  0  0  0
 24 26  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 28 31  1  0  0  0  0
 29 30  1  0  0  0  0
 32 34  1  0  0  0  0
 34 35  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0334678

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=C2N=CN(C3OC(COP(O)(=O)OP(O)(=O)OCC4OC(O)C(O)C4O)C(O)C3O)C2=NC=N1

> <INCHI_IDENTIFIER>
InChI=1/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)

> <INCHI_KEY>
SRNWOUGRCWSEMX-UHFFFAOYNA-N

> <FORMULA>
C15H23N5O14P2

> <MOLECULAR_WEIGHT>
559.318

> <EXACT_MASS>
559.071674437

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
46.43901117692843

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(3,4,5-trihydroxyoxolan-2-yl)methoxy]phosphoryl}oxy)phosphinic acid

> <JCHEM_LOGP>
-6.1615488764215405

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.283027015166816

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8542479274454697

> <JCHEM_PKA_STRONGEST_BASIC>
4.930731259644615

> <JCHEM_POLAR_SURFACE_AREA>
291.52

> <JCHEM_REFRACTIVITY>
111.12330000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
adpribose

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0334678 (Adenosine diphosphate ribose)
Download
PDB for NP0334678 (Adenosine diphosphate ribose)
HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  P   UNK     0      50.250 -37.065   0.000  0.00  0.00           P+0
HETATM    2  P   UNK     0      52.903 -36.791   0.000  0.00  0.00           P+0
HETATM    3  O   UNK     0      46.347 -39.783   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      44.412 -36.299   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      42.438 -39.006   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      58.297 -36.378   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      49.002 -37.968   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      56.247 -39.795   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      59.579 -40.151   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      54.309 -37.420   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      60.947 -37.093   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      51.497 -36.162   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      51.153 -38.313   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      49.347 -35.818   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      53.532 -35.385   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      52.274 -38.197   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0      44.403 -41.720   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0      44.403 -44.198   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0      41.612 -41.419   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0      40.278 -43.729   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0      41.612 -46.039   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      44.885 -37.764   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      43.978 -39.008   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      46.349 -38.243   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      44.881 -40.256   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      47.597 -37.339   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      57.280 -38.653   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      56.962 -37.146   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      58.811 -38.816   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      59.440 -37.410   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      55.556 -36.517   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      42.945 -42.189   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      45.301 -42.959   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      42.945 -43.729   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      41.612 -44.499   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      40.278 -42.189   0.000  0.00  0.00           C+0
CONECT    1    7   12   13   14                                             
CONECT    2   10   12   15   16                                             
CONECT    3   24   25                                                       
CONECT    4   22                                                            
CONECT    5   23                                                            
CONECT    6   28   30                                                       
CONECT    7    1   26                                                       
CONECT    8   27                                                            
CONECT    9   29                                                            
CONECT   10    2   31                                                       
CONECT   11   30                                                            
CONECT   12    1    2                                                       
CONECT   13    1                                                            
CONECT   14    1                                                            
CONECT   15    2                                                            
CONECT   16    2                                                            
CONECT   17   25   32   33                                                  
CONECT   18   33   34                                                       
CONECT   19   32   36                                                       
CONECT   20   35   36                                                       
CONECT   21   35                                                            
CONECT   22    4   23   24                                                  
CONECT   23    5   22   25                                                  
CONECT   24    3   22   26                                                  
CONECT   25    3   17   23                                                  
CONECT   26    7   24                                                       
CONECT   27    8   28   29                                                  
CONECT   28    6   27   31                                                  
CONECT   29    9   27   30                                                  
CONECT   30    6   11   29                                                  
CONECT   31   10   28                                                       
CONECT   32   17   19   34                                                  
CONECT   33   17   18                                                       
CONECT   34   18   32   35                                                  
CONECT   35   20   21   34                                                  
CONECT   36   19   20                                                       
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

Download
3D PDB for NP0334678 (Adenosine diphosphate ribose)
Download
SMILES for NP0334678 (Adenosine diphosphate ribose)
NC1=C2N=CN(C3OC(COP(O)(=O)OP(O)(=O)OCC4OC(O)C(O)C4O)C(O)C3O)C2=NC=N1
Download
INCHI for NP0334678 (Adenosine diphosphate ribose)
InChI=1/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)
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View in JSmol
Synonyms
ValueSource
Adenosine diphosphoric acid riboseGenerator
Chemical FormulaC15H23N5O14P2
Average Mass559.3180 Da
Monoisotopic Mass559.07167 Da
IUPAC Name{[5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({hydroxy[(3,4,5-trihydroxyoxolan-2-yl)methoxy]phosphoryl}oxy)phosphinic acid
Traditional Nameadpribose
CAS Registry NumberNot Available
SMILES
NC1=C2N=CN(C3OC(COP(O)(=O)OP(O)(=O)OCC4OC(O)C(O)C4O)C(O)C3O)C2=NC=N1
InChI Identifier
InChI=1/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)
InChI KeySRNWOUGRCWSEMX-UHFFFAOYNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group.
KingdomOrganic compounds  
Super ClassNucleosides, nucleotides, and analogues  
ClassPurine nucleotides  
Sub ClassPurine nucleotide sugars  
Direct ParentPurine nucleotide sugars  
Alternative Parents
Substituents
  • Purine nucleotide sugar
    • 

  • Purine ribonucleoside diphosphate
    • 

  • Purine ribonucleoside monophosphate
    • 

  • Pentose phosphate
    • 

  • Pentose-5-phosphate
    • 

  • Glycosyl compound
    • 

  • N-glycosyl compound
    • 

  • 6-aminopurine
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  • Monosaccharide phosphate
    • 

  • Organic pyrophosphate
    • 

  • Imidazopyrimidine
    • 

  • Purine
    • 

  • Aminopyrimidine
    • 

  • Monoalkyl phosphate
    • 

  • Pyrimidine
    • 

  • Alkyl phosphate
    • 

  • Imidolactam
    • 

  • Phosphoric acid ester
    • 

  • Monosaccharide
    • 

  • N-substituted imidazole
    • 

  • Organic phosphoric acid derivative
    • 

  • Tetrahydrofuran
    • 

  • Azole
    • 

  • Imidazole
    • 

  • Heteroaromatic compound
    • 

  • Secondary alcohol
    • 

  • Hemiacetal
    • 

  • Organoheterocyclic compound
    • 

  • Polyol
    • 

  • Azacycle
    • 

  • Oxacycle
    • 

  • Organic oxide
    • 

  • Amine
    • 

  • Alcohol
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Primary amine
    • 

  • Hydrocarbon derivative
    • 

  • Organic nitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
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-6.2ChemAxon
pKa (Strongest Acidic)1.85ChemAxon
pKa (Strongest Basic)4.93ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area291.52 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity111.12 m³·mol⁻¹ChemAxon
Polarizability46.44 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
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 LinkAdenosine diphosphate ribose  
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References