data_GDR
# 
_chem_comp.id                                    GDR 
_chem_comp.name                                  "GUANOSINE-5'-DIPHOSPHATE-RHAMNOSE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C16 H25 N5 O15 P2" 
_chem_comp.mon_nstd_parent_comp_id               DG 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2002-11-21 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        589.342 
_chem_comp.one_letter_code                       G 
_chem_comp.three_letter_code                     GDR 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1N7G 
_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 
GDR PB     PB     P 0 1 N N R 1.891  27.721 40.142 -0.849 0.214  -3.683 PB     GDR 1  
GDR O3A    O3A    O 0 1 N N N 1.355  26.197 40.344 -0.694 -0.609 -2.309 O3A    GDR 2  
GDR O1B    O1B    O 0 1 N N N 2.643  28.152 41.394 -0.321 1.584  -3.498 O1B    GDR 3  
GDR O2B    O2B    O 0 1 N N N 0.696  28.638 39.895 -2.405 0.290  -4.090 O2B    GDR 4  
GDR O3B    O3B    O 0 1 N N N 2.822  27.720 38.933 -0.024 -0.526 -4.849 O3B    GDR 5  
GDR PA     PA     P 0 1 N N S 0.964  25.246 41.609 -1.540 0.183  -1.192 PA     GDR 6  
GDR O1A    O1A    O 0 1 N N N -0.037 24.259 41.132 -1.001 1.553  -1.046 O1A    GDR 7  
GDR O2A    O2A    O 0 1 N N N 2.213  24.754 42.250 -3.084 0.259  -1.641 O2A    GDR 8  
GDR O5D    O5*    O 0 1 N N N 0.263  26.219 42.661 -1.428 -0.590 0.215  O5D    GDR 9  
GDR C5D    C5*    C 0 1 N N N -0.937 26.916 42.331 -2.195 0.159  1.160  C5D    GDR 10 
GDR C4D    C4*    C 0 1 N N R -1.467 27.658 43.537 -2.131 -0.525 2.526  C4D    GDR 11 
GDR O4D    O4*    O 0 1 N N N -1.966 26.698 44.519 -0.771 -0.561 2.992  O4D    GDR 12 
GDR C1D    C1*    C 0 1 N N R -1.264 26.869 45.733 -0.813 -0.422 4.428  C1D    GDR 13 
GDR N9     N9     N 0 1 Y N N -1.190 25.582 46.425 0.475  0.050  4.939  N9     GDR 14 
GDR C4     C4     C 0 1 Y N N -0.229 24.602 46.260 0.995  -0.200 6.179  C4     GDR 15 
GDR N3     N3     N 0 1 N N N 0.667  24.527 45.251 0.577  -0.895 7.243  N3     GDR 16 
GDR C2     C2     C 0 1 N N N 1.446  23.460 45.361 1.307  -0.973 8.333  C2     GDR 17 
GDR N2     N2     N 0 1 N N N 2.385  23.220 44.438 0.834  -1.693 9.402  N2     GDR 18 
GDR N1     N1     N 0 1 N N N 1.362  22.548 46.383 2.521  -0.361 8.433  N1     GDR 19 
GDR C6     C6     C 0 1 N N N 0.453  22.604 47.431 3.012  0.353  7.396  C6     GDR 20 
GDR O6     O6     O 0 1 N N N 0.467  21.726 48.304 4.096  0.904  7.476  O6     GDR 21 
GDR C5     C5     C 0 1 Y N N -0.399 23.737 47.324 2.236  0.446  6.217  C5     GDR 22 
GDR N7     N7     N 0 1 Y N N -1.441 24.157 48.138 2.408  1.058  5.020  N7     GDR 23 
GDR C8     C8     C 0 1 Y N N -1.881 25.247 47.566 1.373  0.827  4.266  C8     GDR 24 
GDR C2D    C2*    C 0 1 N N R 0.052  27.532 45.348 -1.918 0.639  4.656  C2D    GDR 25 
GDR O2D    O2*    O 0 1 N N N 0.593  28.202 46.468 -2.495 0.505  5.957  O2D    GDR 26 
GDR C3D    C3*    C 0 1 N N S -0.442 28.507 44.286 -2.949 0.278  3.555  C3D    GDR 27 
GDR O3D    O3*    O 0 1 N N N -1.095 29.600 44.915 -4.004 -0.518 4.099  O3D    GDR 28 
GDR "C1'"  "C1'"  C 0 1 N N R 2.512  26.939 37.779 -0.200 0.249  -6.037 "C1'"  GDR 29 
GDR "C2'"  "C2'"  C 0 1 N N S 3.799  26.358 37.174 -0.139 -0.671 -7.258 "C2'"  GDR 30 
GDR "O2'"  "O2'"  O 0 1 N N N 3.459  25.431 36.158 -0.286 0.104  -8.449 "O2'"  GDR 31 
GDR "C3'"  "C3'"  C 0 1 N N S 4.657  27.474 36.575 1.214  -1.389 -7.275 "C3'"  GDR 32 
GDR "O3'"  "O3'"  O 0 1 N N N 5.788  26.918 35.922 1.345  -2.137 -8.485 "O3'"  GDR 33 
GDR "C4'"  "C4'"  C 0 1 N N S 3.832  28.270 35.572 2.327  -0.337 -7.194 "C4'"  GDR 34 
GDR "O4'"  "O4'"  O 0 1 N N N 4.600  29.352 35.073 3.591  -0.989 -7.060 "O4'"  GDR 35 
GDR "C5'"  "C5'"  C 0 1 N N R 2.556  28.796 36.244 2.080  0.556  -5.977 "C5'"  GDR 36 
GDR "O5'"  "O5'"  O 0 1 N N N 1.788  27.697 36.794 0.831  1.230  -6.119 "O5'"  GDR 37 
GDR "C6'"  "C6'"  C 0 1 N N N 1.656  29.519 35.259 3.205  1.587  -5.867 "C6'"  GDR 38 
GDR HOB2   2HOB   H 0 0 N N N 1.008  29.527 39.777 -2.710 -0.620 -4.201 HOB2   GDR 39 
GDR HOA2   2HOA   H 0 0 N N N 1.985  24.199 42.987 -3.396 -0.652 -1.725 HOA2   GDR 40 
GDR "H5'"  1H5*   H 0 1 N N N -0.796 27.593 41.456 -1.790 1.167  1.239  "H5'"  GDR 41 
GDR "H5''" 2H5*   H 0 0 N N N -1.704 26.236 41.892 -3.232 0.209  0.827  "H5''" GDR 42 
GDR "H4'"  H4*    H 0 1 N N N -2.246 28.336 43.118 -2.524 -1.539 2.452  "H4'"  GDR 43 
GDR "H1'"  H1*    H 0 1 N N N -1.754 27.532 46.483 -1.087 -1.367 4.897  "H1'"  GDR 44 
GDR HN21   1HN2   H 0 0 N N N 2.984  22.399 44.522 -0.027 -2.134 9.346  HN21   GDR 45 
GDR HN22   2HN2   H 0 0 N N N 2.978  24.046 44.358 1.362  -1.761 10.213 HN22   GDR 46 
GDR HN1    HN1    H 0 1 N N N 2.023  21.771 46.362 3.035  -0.440 9.252  HN1    GDR 47 
GDR H8     H8     H 0 1 N N N -2.727 25.811 47.991 1.244  1.195  3.259  H8     GDR 48 
GDR "H2'"  H2*    H 0 1 N N N 0.861  26.849 44.997 -1.526 1.646  4.509  "H2'"  GDR 49 
GDR HO2A   HO2*   H 0 0 N N N 1.413  28.615 46.227 -3.171 1.191  6.035  HO2A   GDR 50 
GDR "H3'"  H3*    H 0 1 N N N 0.361  28.931 43.639 -3.352 1.182  3.098  "H3'"  GDR 51 
GDR HO3A   HO3*   H 0 0 N N N -0.457 30.128 45.380 -4.439 0.018  4.776  HO3A   GDR 52 
GDR "HC1'" "HC1'" H 0 0 N N N 1.849  26.103 38.103 -1.170 0.745  -6.005 "HC1'" GDR 53 
GDR "HC2'" "HC2'" H 0 0 N N N 4.380  25.848 37.977 -0.941 -1.406 -7.200 "HC2'" GDR 54 
GDR "HO2'" "HO2'" H 0 0 N N N 4.254  25.071 35.783 -1.146 0.542  -8.393 "HO2'" GDR 55 
GDR "HC3'" "HC3'" H 0 0 N N N 5.001  28.148 37.393 1.282  -2.061 -6.420 "HC3'" GDR 56 
GDR "HO3'" "HO3'" H 0 0 N Y N 6.320  27.611 35.550 0.619  -2.776 -8.498 "HO3'" GDR 57 
GDR "HC4'" "HC4'" H 0 0 N N N 3.544  27.605 34.724 2.322  0.268  -8.100 "HC4'" GDR 58 
GDR "HO4'" "HO4'" H 0 0 N N N 4.085  29.848 34.447 4.261  -0.292 -7.013 "HO4'" GDR 59 
GDR "HC5'" "HC5'" H 0 0 N N N 2.885  29.501 37.042 2.060  -0.055 -5.075 "HC5'" GDR 60 
GDR HC61   1HC6   H 0 0 N N N 0.729  29.901 35.747 3.031  2.223  -4.999 HC61   GDR 61 
GDR HC62   2HC6   H 0 0 N N N 2.203  30.335 34.733 4.159  1.073  -5.755 HC62   GDR 62 
GDR HC63   3HC6   H 0 0 N N N 1.416  28.875 34.380 3.225  2.200  -6.768 HC63   GDR 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 
GDR PB    O3A    SING N N 1  
GDR PB    O1B    DOUB N N 2  
GDR PB    O2B    SING N N 3  
GDR PB    O3B    SING N N 4  
GDR O3A   PA     SING N N 5  
GDR O2B   HOB2   SING N N 6  
GDR O3B   "C1'"  SING N N 7  
GDR PA    O1A    DOUB N N 8  
GDR PA    O2A    SING N N 9  
GDR PA    O5D    SING N N 10 
GDR O2A   HOA2   SING N N 11 
GDR O5D   C5D    SING N N 12 
GDR C5D   C4D    SING N N 13 
GDR C5D   "H5'"  SING N N 14 
GDR C5D   "H5''" SING N N 15 
GDR C4D   O4D    SING N N 16 
GDR C4D   C3D    SING N N 17 
GDR C4D   "H4'"  SING N N 18 
GDR O4D   C1D    SING N N 19 
GDR C1D   N9     SING N N 20 
GDR C1D   C2D    SING N N 21 
GDR C1D   "H1'"  SING N N 22 
GDR N9    C4     SING Y N 23 
GDR N9    C8     SING Y N 24 
GDR C4    N3     SING N N 25 
GDR C4    C5     DOUB Y N 26 
GDR N3    C2     DOUB N N 27 
GDR C2    N2     SING N N 28 
GDR C2    N1     SING N N 29 
GDR N2    HN21   SING N N 30 
GDR N2    HN22   SING N N 31 
GDR N1    C6     SING N N 32 
GDR N1    HN1    SING N N 33 
GDR C6    O6     DOUB N N 34 
GDR C6    C5     SING N N 35 
GDR C5    N7     SING Y N 36 
GDR N7    C8     DOUB Y N 37 
GDR C8    H8     SING N N 38 
GDR C2D   O2D    SING N N 39 
GDR C2D   C3D    SING N N 40 
GDR C2D   "H2'"  SING N N 41 
GDR O2D   HO2A   SING N N 42 
GDR C3D   O3D    SING N N 43 
GDR C3D   "H3'"  SING N N 44 
GDR O3D   HO3A   SING N N 45 
GDR "C1'" "C2'"  SING N N 46 
GDR "C1'" "O5'"  SING N N 47 
GDR "C1'" "HC1'" SING N N 48 
GDR "C2'" "O2'"  SING N N 49 
GDR "C2'" "C3'"  SING N N 50 
GDR "C2'" "HC2'" SING N N 51 
GDR "O2'" "HO2'" SING N N 52 
GDR "C3'" "O3'"  SING N N 53 
GDR "C3'" "C4'"  SING N N 54 
GDR "C3'" "HC3'" SING N N 55 
GDR "O3'" "HO3'" SING N N 56 
GDR "C4'" "O4'"  SING N N 57 
GDR "C4'" "C5'"  SING N N 58 
GDR "C4'" "HC4'" SING N N 59 
GDR "O4'" "HO4'" SING N N 60 
GDR "C5'" "O5'"  SING N N 61 
GDR "C5'" "C6'"  SING N N 62 
GDR "C5'" "HC5'" SING N N 63 
GDR "C6'" HC61   SING N N 64 
GDR "C6'" HC62   SING N N 65 
GDR "C6'" HC63   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 
GDR SMILES           ACDLabs              10.04 "O=P(OC1OC(C(O)C(O)C1O)C)(O)OP(=O)(O)OCC4OC(n2c3N=C(N)NC(=O)c3nc2)C(O)C4O" 
GDR InChI            InChI                1.02b 
;InChI=1/C16H25N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,7-11,14-15,22-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5-,7-,8-,9+,10-,11+,14-,15-/m1/s1/f/h20,28,30H,17H2
;
GDR InChIKey         InChI                1.02b LQEBEXMHBLQMDB-DPIAHOHUDM 
GDR 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@@H](O)[C@@H]1O" 
GDR 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)[CH](O)[CH]1O" 
GDR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@@H]1[C@H]([C@@H]([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)O)O" 
GDR SMILES           "OpenEye OEToolkits" 1.5.0 "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)O)O)O)O" 
# 
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 
GDR "SYSTEMATIC NAME" ACDLabs              10.04 
"[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" 
GDR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyl-oxan-2-yl] hydrogen phosphate" 
# 
