data_GDR # _chem_comp.id GDR _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE-RHAMNOSE" _chem_comp.type "RNA 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 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 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 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" GDR InChI InChI 1.03 "InChI=1S/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" GDR InChIKey InChI 1.03 LQEBEXMHBLQMDB-GDJBGNAASA-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 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" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site GDR "Create component" 2002-11-21 RCSB GDR "Modify linking type" 2011-06-04 RCSB GDR "Modify descriptor" 2011-06-04 RCSB #