data_GPD
# 
_chem_comp.id                                    GPD 
_chem_comp.name                                  "(2R,3S,5S,6R)-5-amino-3-hydroxy-6-methyl-oxan-2-yl" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H26 N6 O13 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2008-08-12 
_chem_comp.pdbx_modified_date                    2011-06-04 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        572.358 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     GPD 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        3DR7 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
GPD N4A    N4A    N 0 1 N N N 15.953 -2.774 -4.088  -5.754 3.732  -2.372 N4A    GPD 1  
GPD C4G    C4G    C 0 1 N N S 17.294 -2.678 -4.620  -6.409 2.794  -1.450 C4G    GPD 2  
GPD C5G    C5G    C 0 1 N N R 18.274 -3.343 -3.672  -5.597 2.698  -0.156 C5G    GPD 3  
GPD C6G    C6G    C 0 1 N N N 17.968 -4.820 -3.429  -5.565 4.065  0.530  C6G    GPD 4  
GPD O5G    O5G    O 0 1 N N N 19.657 -3.158 -3.973  -6.204 1.742  0.715  O5G    GPD 5  
GPD C3G    C3G    C 0 1 N N N 17.583 -1.191 -4.782  -6.486 1.409  -2.099 C3G    GPD 6  
GPD C2G    C2G    C 0 1 N N S 19.079 -0.962 -4.839  -7.099 0.423  -1.101 C2G    GPD 7  
GPD O2G    O2G    O 0 1 N N N 19.434 -0.165 -5.965  -8.437 0.822  -0.795 O2G    GPD 8  
GPD C1G    C1G    C 0 1 N N R 19.896 -2.224 -5.008  -6.261 0.418  0.180  C1G    GPD 9  
GPD O1G    O1G    O 0 1 N N N 21.181 -1.666 -4.831  -4.938 -0.033 -0.118 O1G    GPD 10 
GPD P2     P2     P 0 1 N N S 22.474 -1.954 -5.712  -4.018 -0.818 0.945  P2     GPD 11 
GPD O3P    O3P    O 0 1 N N N 22.606 -3.446 -5.825  -4.746 -2.007 1.443  O3P    GPD 12 
GPD O4P    O4P    O 0 1 N N N 23.530 -1.153 -4.987  -3.674 0.156  2.179  O4P    GPD 13 
GPD OPP    OPP    O 0 1 N N N 22.077 -1.240 -7.102  -2.653 -1.285 0.232  OPP    GPD 14 
GPD P      P      P 0 1 N N S 23.091 -1.036 -8.331  -1.542 -2.402 0.564  P      GPD 15 
GPD O1P    O1P    O 0 1 N N N 24.484 -1.441 -7.956  -2.071 -3.845 0.083  O1P    GPD 16 
GPD O2P    O2P    O 0 1 N N N 22.913 0.366  -8.811  -1.293 -2.430 2.023  O2P    GPD 17 
GPD "O5'"  "O5'"  O 0 1 N N N 22.509 -1.992 -9.489  -0.175 -2.046 -0.207 "O5'"  GPD 18 
GPD "C5'"  "C5'"  C 0 1 N N N 22.692 -3.401 -9.479  1.033  -2.790 -0.034 "C5'"  GPD 19 
GPD "C4'"  "C4'"  C 0 1 N N R 23.214 -3.807 -10.835 2.133  -2.188 -0.910 "C4'"  GPD 20 
GPD "O4'"  "O4'"  O 0 1 N N N 22.308 -3.345 -11.854 2.471  -0.874 -0.436 "O4'"  GPD 21 
GPD "C3'"  "C3'"  C 0 1 N N S 24.543 -3.109 -11.090 3.406  -3.052 -0.821 "C3'"  GPD 22 
GPD "O3'"  "O3'"  O 0 1 N N N 25.396 -4.062 -11.729 3.760  -3.556 -2.110 "O3'"  GPD 23 
GPD "C2'"  "C2'"  C 0 1 N N R 24.224 -2.027 -12.110 4.490  -2.078 -0.301 "C2'"  GPD 24 
GPD "O2'"  "O2'"  O 0 1 N N N 25.314 -1.866 -13.018 5.732  -2.288 -0.977 "O2'"  GPD 25 
GPD "C1'"  "C1'"  C 0 1 N N R 23.017 -2.598 -12.827 3.885  -0.694 -0.665 "C1'"  GPD 26 
GPD N9     N9     N 0 1 Y N N 22.166 -1.535 -13.392 4.420  0.353  0.209  N9     GPD 27 
GPD C8     C8     C 0 1 Y N N 21.343 -0.739 -12.715 3.887  0.765  1.396  C8     GPD 28 
GPD N7     N7     N 0 1 Y N N 20.759 0.105  -13.587 4.620  1.711  1.904  N7     GPD 29 
GPD C4     C4     C 0 1 Y N N 22.119 -1.212 -14.686 5.550  1.093  -0.013 C4     GPD 30 
GPD C5     C5     C 0 1 Y N N 21.223 -0.165 -14.822 5.664  1.964  1.077  C5     GPD 31 
GPD C6     C6     C 0 1 N N N 20.986 0.367  -16.090 6.754  2.864  1.114  C6     GPD 32 
GPD O6     O6     O 0 1 N N N 20.186 1.285  -16.316 6.896  3.636  2.046  O6     GPD 33 
GPD N3     N3     N 0 1 N N N 22.748 -1.711 -15.773 6.466  1.128  -0.987 N3     GPD 34 
GPD C2     C2     C 0 1 N N N 22.512 -1.177 -16.984 7.478  1.966  -0.939 C2     GPD 35 
GPD N1     N1     N 0 1 N N N 21.640 -0.162 -17.130 7.636  2.846  0.090  N1     GPD 36 
GPD N2     N2     N 0 1 N N N 23.134 -1.643 -18.098 8.393  1.965  -1.962 N2     GPD 37 
GPD HN4A   HN4A   H 0 0 N N N 15.991 -2.796 -3.089  -6.272 3.813  -3.234 HN4A   GPD 38 
GPD HN4B   HN4B   H 0 0 N N N 15.420 -1.981 -4.384  -5.629 4.635  -1.940 HN4B   GPD 39 
GPD H4G    H4G    H 0 1 N N N 17.394 -3.192 -5.587  -7.415 3.148  -1.224 H4G    GPD 40 
GPD H5G    H5G    H 0 1 N N N 18.104 -2.791 -2.736  -4.579 2.384  -0.388 H5G    GPD 41 
GPD H6G    H6G    H 0 1 N N N 17.894 -5.343 -4.394  -6.583 4.379  0.762  H6G    GPD 42 
GPD H6GA   H6GA   H 0 0 N N N 18.775 -5.268 -2.830  -4.987 3.997  1.451  H6GA   GPD 43 
GPD H6GB   H6GB   H 0 0 N N N 17.014 -4.912 -2.888  -5.103 4.795  -0.136 H6GB   GPD 44 
GPD H3G    H3G    H 0 1 N N N 17.123 -0.830 -5.714  -7.110 1.459  -2.992 H3G    GPD 45 
GPD H3GA   H3GA   H 0 0 N N N 17.164 -0.644 -3.924  -5.485 1.078  -2.373 H3GA   GPD 46 
GPD H2G    H2G    H 0 1 N N N 19.301 -0.486 -3.873  -7.108 -0.577 -1.534 H2G    GPD 47 
GPD HO2G   HO2G   H 0 0 N N N 19.513 0.743  -5.698  -8.887 0.240  -0.167 HO2G   GPD 48 
GPD H1G    H1G    H 0 1 N N N 19.702 -2.772 -5.942  -6.716 -0.250 0.911  H1G    GPD 49 
GPD HO4P   HO4P   H 0 0 N N N 24.259 -0.985 -5.573  -3.195 0.958  1.926  HO4P   GPD 50 
GPD HO1P   HO1P   H 0 0 N N N 25.012 -1.527 -8.741  -2.256 -3.899 -0.865 HO1P   GPD 51 
GPD "H5'"  "H5'"  H 0 1 N N N 23.414 -3.682 -8.698  1.338  -2.750 1.012  "H5'"  GPD 52 
GPD "H5'A" "H5'A" H 0 0 N N N 21.740 -3.910 -9.266  0.865  -3.828 -0.323 "H5'A" GPD 53 
GPD "H4'"  "H4'"  H 0 1 N N N 23.321 -4.902 -10.860 1.794  -2.133 -1.945 "H4'"  GPD 54 
GPD "H3'"  "H3'"  H 0 1 N N N 25.010 -2.712 -10.177 3.261  -3.873 -0.118 "H3'"  GPD 55 
GPD "HO3'" "HO3'" H 0 0 N N N 25.585 -3.775 -12.615 4.554  -4.108 -2.113 "HO3'" GPD 56 
GPD "H2'"  "H2'"  H 0 1 N N N 24.045 -1.037 -11.665 4.616  -2.176 0.778  "H2'"  GPD 57 
GPD "HO2'" "HO2'" H 0 0 N N N 24.983 -1.830 -13.908 6.103  -3.172 -0.852 "HO2'" GPD 58 
GPD "H1'"  "H1'"  H 0 1 N N N 23.325 -3.223 -13.678 4.077  -0.457 -1.712 "H1'"  GPD 59 
GPD H8     H8     H 0 1 N N N 21.172 -0.765 -11.649 2.990  0.364  1.845  H8     GPD 60 
GPD HN1    HN1    H 0 1 N N N 21.476 0.208  -18.044 8.392  3.454  0.093  HN1    GPD 61 
GPD HN2    HN2    H 0 1 N N N 22.837 -1.129 -18.903 8.288  1.352  -2.706 HN2    GPD 62 
GPD HN2A   HN2A   H 0 0 N N N 23.795 -2.394 -18.112 9.145  2.577  -1.941 HN2A   GPD 63 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
GPD C4G   N4A    SING N N 1  
GPD N4A   HN4A   SING N N 2  
GPD N4A   HN4B   SING N N 3  
GPD C3G   C4G    SING N N 4  
GPD C4G   C5G    SING N N 5  
GPD C4G   H4G    SING N N 6  
GPD O5G   C5G    SING N N 7  
GPD C5G   C6G    SING N N 8  
GPD C5G   H5G    SING N N 9  
GPD C6G   H6G    SING N N 10 
GPD C6G   H6GA   SING N N 11 
GPD C6G   H6GB   SING N N 12 
GPD C1G   O5G    SING N N 13 
GPD C2G   C3G    SING N N 14 
GPD C3G   H3G    SING N N 15 
GPD C3G   H3GA   SING N N 16 
GPD O2G   C2G    SING N N 17 
GPD C1G   C2G    SING N N 18 
GPD C2G   H2G    SING N N 19 
GPD O2G   HO2G   SING N N 20 
GPD C1G   O1G    SING N N 21 
GPD C1G   H1G    SING N N 22 
GPD P2    O1G    SING N N 23 
GPD OPP   P2     SING N N 24 
GPD O3P   P2     DOUB N N 25 
GPD P2    O4P    SING N N 26 
GPD O4P   HO4P   SING N N 27 
GPD P     OPP    SING N N 28 
GPD "O5'" P      SING N N 29 
GPD O2P   P      DOUB N N 30 
GPD P     O1P    SING N N 31 
GPD O1P   HO1P   SING N N 32 
GPD "O5'" "C5'"  SING N N 33 
GPD "C4'" "C5'"  SING N N 34 
GPD "C5'" "H5'"  SING N N 35 
GPD "C5'" "H5'A" SING N N 36 
GPD "O4'" "C4'"  SING N N 37 
GPD "C3'" "C4'"  SING N N 38 
GPD "C4'" "H4'"  SING N N 39 
GPD "C1'" "O4'"  SING N N 40 
GPD "C2'" "C3'"  SING N N 41 
GPD "O3'" "C3'"  SING N N 42 
GPD "C3'" "H3'"  SING N N 43 
GPD "O3'" "HO3'" SING N N 44 
GPD "O2'" "C2'"  SING N N 45 
GPD "C1'" "C2'"  SING N N 46 
GPD "C2'" "H2'"  SING N N 47 
GPD "O2'" "HO2'" SING N N 48 
GPD N9    "C1'"  SING N N 49 
GPD "C1'" "H1'"  SING N N 50 
GPD C4    N9     SING Y N 51 
GPD N9    C8     SING Y N 52 
GPD N7    C8     DOUB Y N 53 
GPD C8    H8     SING N N 54 
GPD C5    N7     SING Y N 55 
GPD N3    C4     SING N N 56 
GPD C5    C4     DOUB Y N 57 
GPD C6    C5     SING N N 58 
GPD N1    C6     SING N N 59 
GPD O6    C6     DOUB N N 60 
GPD C2    N3     DOUB N N 61 
GPD N2    C2     SING N N 62 
GPD N1    C2     SING N N 63 
GPD N1    HN1    SING N N 64 
GPD N2    HN2    SING N N 65 
GPD N2    HN2A   SING N N 66 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
GPD SMILES           ACDLabs              10.04 "O=P(OC1OC(C(N)CC1O)C)(O)OP(=O)(O)OCC4OC(n2c3N=C(N)NC(=O)c3nc2)C(O)C4O" 
GPD SMILES_CANONICAL CACTVS               3.341 "C[C@H]1O[C@H](O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N)[C@@H](O)C[C@@H]1N" 
GPD SMILES           CACTVS               3.341 "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N)[CH](O)C[CH]1N" 
GPD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@@H]1[C@H](C[C@@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O)O)N" 
GPD SMILES           "OpenEye OEToolkits" 1.5.0 "CC1C(CC(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)O)O)N" 
GPD InChI            InChI                1.03  
"InChI=1S/C16H26N6O13P2/c1-5-6(17)2-7(23)15(32-5)34-37(29,30)35-36(27,28)31-3-8-10(24)11(25)14(33-8)22-4-19-9-12(22)20-16(18)21-13(9)26/h4-8,10-11,14-15,23-25H,2-3,17H2,1H3,(H,27,28)(H,29,30)(H3,18,20,21,26)/t5-,6+,7+,8-,10-,11-,14-,15-/m1/s1" 
GPD InChIKey         InChI                1.03  DRNSMVBRYJDNAT-CYCRINRGSA-N 
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
GPD "SYSTEMATIC NAME" ACDLabs              10.04 
"(2R,3S,5S,6R)-5-amino-3-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" 
GPD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5S,6R)-5-amino-3-hydroxy-6-methyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
GPD "Create component"     2008-08-12 RCSB 
GPD "Modify aromatic_flag" 2011-06-04 RCSB 
GPD "Modify descriptor"    2011-06-04 RCSB 
# 
