NP-MRD: Showing NP-Card for GDP-α-D-glucose (NP0339735)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2024-09-11 23:17:54 UTC

Updated at

2024-09-11 23:17:55 UTC

NP-MRD ID

NP0339735

Secondary Accession Numbers

None

Natural Product Identification

Common Name

GDP-α-D-glucose

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05272301502D          

 39 42  0  0  0  0            999 V2000
   -5.7689    6.0490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4363    6.5339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0152    6.3846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9290    7.2050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5964    7.6900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1753    7.5406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0891    8.3611    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5079    7.0557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7542    7.3912    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5941    6.2352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3478    5.8996    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9267    5.7503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0129    4.9298    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8334    5.0160    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.1924    4.8436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0991    4.1093    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4317    3.6244    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9166    2.9569    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.9468    4.2918    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7643    3.1395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505    2.3190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    1.8341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    2.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.8736    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0865    1.4216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9115    1.4216    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    1.0091    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -2.3479    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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  3 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 17 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 22 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 29 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 35 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  2  0  0  0  0
 32 38  1  0  0  0  0
M  CHG  2  14  -1  18  -1
M  END


  Mrv2104 05272301502D          

 39 42  0  0  0  0            999 V2000
   -5.7689    6.0490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4363    6.5339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0152    6.3846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9290    7.2050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5964    7.6900    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1753    7.5406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0891    8.3611    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5079    7.0557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7542    7.3912    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5941    6.2352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3478    5.8996    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9267    5.7503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0129    4.9298    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8334    5.0160    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.1924    4.8436    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0991    4.1093    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4317    3.6244    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9166    2.9569    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.9468    4.2918    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7643    3.1395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505    2.3190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    1.8341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    2.0890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.8736    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0865    1.4216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9115    1.4216    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    1.0091    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -2.3479    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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  3 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 17 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 22 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 29 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 35 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  2  0  0  0  0
 32 38  1  0  0  0  0
M  CHG  2  14  -1  18  -1
M  END
> <DATABASE_ID>
NP0339735

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC2=C(N=CN2C2OC(COP([O-])(=O)OP([O-])(=O)OC3OC(CO)C(O)C(O)C3O)C(O)C2O)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/p-2

> <INCHI_KEY>
MVMSCBBUIHUTGJ-UHFFFAOYNA-L

> <FORMULA>
C16H23N5O16P2

> <MOLECULAR_WEIGHT>
603.328

> <EXACT_MASS>
603.062600836

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
50.781511965009955

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl {[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl phosphonato]oxy}phosphonate

> <JCHEM_LOGP>
-5.287584132999999

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.176324364365109

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7325998238285532

> <JCHEM_PKA_STRONGEST_BASIC>
-3.64840938010819

> <JCHEM_POLAR_SURFACE_AREA>
333.0899999999999

> <JCHEM_REFRACTIVITY>
116.2679

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl phosphonato]oxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$

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     -10.769  11.291   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0     -12.015  12.197   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -9.362  11.918   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -9.201  13.449   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0     -10.447  14.355   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -7.794  14.076   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -7.633  15.607   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -6.548  13.171   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -5.141  13.797   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -6.709  11.639   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -8.116  11.013   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -5.463  10.734   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0      -5.624   9.202   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      -7.156   9.363   0.000  0.00  0.00           O-1
HETATM   15  O   UNK     0      -4.093   9.041   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -5.785   7.671   0.000  0.00  0.00           O+0
HETATM   17  P   UNK     0      -4.539   6.766   0.000  0.00  0.00           P+0
HETATM   18  O   UNK     0      -5.444   5.520   0.000  0.00  0.00           O-1
HETATM   19  O   UNK     0      -3.634   8.011   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -3.293   5.860   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -3.454   4.329   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.208   3.424   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.744   3.899   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -0.268   5.364   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       0.161   2.654   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       1.701   2.654   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -0.744   1.408   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -2.208   1.884   0.000  0.00  0.00           O+0
HETATM   29  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0      -0.268  -2.549   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0       2.530   0.237   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0       3.864  -0.533   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0       5.198   0.237   0.000  0.00  0.00           N+0
HETATM   37  N   UNK     0       3.864  -2.073   0.000  0.00  0.00           N+0
HETATM   38  C   UNK     0       2.530  -2.843   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       2.530  -4.383   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1                                                            
CONECT    3    1    4   11                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10    3                                                       
CONECT   12   10   13                                                       
CONECT   13   12   14   15   16                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   13   17                                                       
CONECT   17   16   18   19   20                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   28                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27   22                                                       
CONECT   29   27   30   33                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   38                                                  
CONECT   33   32   29   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38                                                       
CONECT   38   37   39   32                                                  
CONECT   39   38                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₂₃N₅O₁₆P₂

Average Mass

603.3280 Da

Monoisotopic Mass

603.06260 Da

IUPAC Name

[5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl {[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl phosphonato]oxy}phosphonate

Traditional Name

[5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl phosphonato]oxyphosphonate

CAS Registry Number

Not Available

SMILES

NC1=NC2=C(N=CN2C2OC(COP([O-])(=O)OP([O-])(=O)OC3OC(CO)C(O)C(O)C3O)C(O)C2O)C(=O)N1

InChI Identifier

InChI=1/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/p-2

InChI Key

MVMSCBBUIHUTGJ-UHFFFAOYNA-L

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Classification

Not classified

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-5.3	ChemAxon
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	333.09 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	116.27 m³·mol⁻¹	ChemAxon
Polarizability	50.78 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

Not Available

References

General References

Not Available

Showing NP-Card for GDP-α-D-glucose (NP0339735)

MOL for NP0339735 (GDP-α-D-glucose)

3D MOL for NP0339735 (GDP-α-D-glucose)

3D SDF for NP0339735 (GDP-α-D-glucose)

3D-SDF for NP0339735 (GDP-α-D-glucose)

PDB for NP0339735 (GDP-α-D-glucose)

3D PDB for NP0339735 (GDP-α-D-glucose)

SMILES for NP0339735 (GDP-α-D-glucose)

INCHI for NP0339735 (GDP-α-D-glucose)

Structure for NP0339735 (GDP-α-D-glucose)

3D Structure for NP0339735 (GDP-α-D-glucose)