data_GDG # _chem_comp.id GDG _chem_comp.name GDP-ALPHA-D-GLUCOSE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H25 N5 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms GDP-ALPHA-D-GLUCOSE _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-09-05 _chem_comp.pdbx_modified_date 2020-06-17 _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 605.341 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GDG _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 5K42 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 GDG C21 C1 C 0 1 N N R 164.955 118.572 36.676 5.981 -0.173 -0.644 C21 GDG 1 GDG C22 C2 C 0 1 N N R 165.849 117.380 37.067 6.247 -1.113 -1.823 C22 GDG 2 GDG C24 C3 C 0 1 N N S 165.050 116.102 35.052 5.913 -3.033 -0.265 C24 GDG 3 GDG C01 C4 C 0 1 Y N N 170.171 122.987 28.693 -4.468 -0.786 1.614 C01 GDG 4 GDG N02 N1 N 0 1 Y N N 170.879 124.057 28.299 -5.246 -1.758 1.997 N02 GDG 5 GDG C03 C5 C 0 1 Y N N 170.187 124.699 27.312 -6.146 -2.016 1.020 C03 GDG 6 GDG C04 C6 C 0 1 Y N N 169.010 123.966 27.116 -5.891 -1.136 -0.024 C04 GDG 7 GDG N05 N2 N 0 1 Y N N 169.048 122.926 27.981 -4.838 -0.369 0.369 N05 GDG 8 GDG C06 C7 C 0 1 N N R 167.984 121.968 28.065 -4.210 0.704 -0.407 C06 GDG 9 GDG C07 C8 C 0 1 N N R 168.384 120.760 27.850 -4.925 2.047 -0.143 C07 GDG 10 GDG C08 C9 C 0 1 N N S 167.359 119.955 28.583 -3.782 3.087 -0.141 C08 GDG 11 GDG C09 C10 C 0 1 N N R 167.039 120.840 29.822 -2.512 2.249 -0.405 C09 GDG 12 GDG O10 O1 O 0 1 N N N 167.378 122.013 29.547 -2.852 0.916 0.036 O10 GDG 13 GDG C11 C11 C 0 1 N N N 167.885 120.326 31.022 -1.336 2.794 0.408 C11 GDG 14 GDG O12 O2 O 0 1 N N N 167.257 119.107 31.351 -0.147 2.080 0.064 O12 GDG 15 GDG P13 P1 P 0 1 N N N 167.620 118.391 32.724 1.286 2.392 0.728 P13 GDG 16 GDG O14 O3 O 0 1 N N N 167.425 116.919 32.497 1.612 3.825 0.551 O14 GDG 17 GDG O15 O4 O 0 1 N N N 169.033 118.707 33.111 1.237 2.043 2.299 O15 GDG 18 GDG O16 O5 O 0 1 N N N 166.620 118.877 33.875 2.415 1.493 0.014 O16 GDG 19 GDG P17 P2 P 0 1 N N N 166.923 119.797 35.156 4.024 1.536 -0.018 P17 GDG 20 GDG O18 O6 O 0 1 N N N 167.154 121.212 34.693 4.540 1.752 1.353 O18 GDG 21 GDG O19 O7 O 0 1 N N N 168.154 119.335 35.941 4.510 2.741 -0.969 O19 GDG 22 GDG O20 O8 O 0 1 N N N 165.607 119.741 36.123 4.588 0.140 -0.589 O20 GDG 23 GDG C23 C12 C 0 1 N N S 166.217 116.491 35.893 5.484 -2.423 -1.603 C23 GDG 24 GDG C25 C13 C 0 1 N N R 164.144 117.281 34.675 5.660 -2.019 0.853 C25 GDG 25 GDG O26 O9 O 0 1 N N N 163.807 118.167 35.834 6.373 -0.813 0.572 O26 GDG 26 GDG C27 C14 C 0 1 N N N 162.869 116.820 34.094 6.142 -2.598 2.185 C27 GDG 27 GDG O28 O10 O 0 1 N N N 162.070 116.205 35.084 5.800 -1.702 3.245 O28 GDG 28 GDG O29 O11 O 0 1 N N N 165.539 115.476 33.854 5.157 -4.219 -0.016 O29 GDG 29 GDG O30 O12 O 0 1 N N N 166.862 115.270 36.360 5.785 -3.334 -2.662 O30 GDG 30 GDG O31 O13 O 0 1 N N N 166.981 117.861 37.763 5.802 -0.498 -3.033 O31 GDG 31 GDG O32 O14 O 0 1 N N N 166.219 119.764 27.854 -3.975 4.045 -1.184 O32 GDG 32 GDG O33 O15 O 0 1 N N N 168.374 120.469 26.363 -5.859 2.331 -1.187 O33 GDG 33 GDG N34 N3 N 0 1 N N N 168.017 124.354 26.130 -6.675 -1.196 -1.148 N34 GDG 34 GDG C35 C15 C 0 1 N N N 168.249 125.550 25.311 -7.686 -2.099 -1.237 C35 GDG 35 GDG N36 N4 N 0 1 N N N 169.446 126.300 25.515 -7.961 -2.950 -0.271 N36 GDG 36 GDG C37 C16 C 0 1 N N N 170.417 125.923 26.469 -7.250 -2.969 0.867 C37 GDG 37 GDG O38 O16 O 0 1 N N N 171.419 126.596 26.595 -7.516 -3.763 1.755 O38 GDG 38 GDG N39 N5 N 0 1 N N N 167.317 125.960 24.353 -8.446 -2.126 -2.375 N39 GDG 39 GDG H1 H1 H 0 1 N N N 164.511 118.906 37.625 6.555 0.744 -0.774 H1 GDG 40 GDG H2 H2 H 0 1 N N N 165.260 116.762 37.761 7.315 -1.319 -1.890 H2 GDG 41 GDG H3 H3 H 0 1 N N N 164.443 115.377 35.615 6.975 -3.279 -0.301 H3 GDG 42 GDG H4 H4 H 0 1 N N N 170.465 122.289 29.463 -3.657 -0.372 2.194 H4 GDG 43 GDG H5 H5 H 0 1 N N N 167.178 122.257 27.374 -4.230 0.464 -1.470 H5 GDG 44 GDG H6 H6 H 0 1 N N N 169.384 120.555 28.260 -5.427 2.030 0.825 H6 GDG 45 GDG H7 H7 H 0 1 N N N 167.797 119.004 28.920 -3.719 3.583 0.827 H7 GDG 46 GDG H8 H8 H 0 1 N N N 165.972 120.735 30.068 -2.270 2.249 -1.467 H8 GDG 47 GDG H9 H9 H 0 1 N N N 168.932 120.165 30.727 -1.201 3.853 0.186 H9 GDG 48 GDG H10 H10 H 0 1 N N N 167.846 121.032 31.865 -1.540 2.669 1.472 H10 GDG 49 GDG H11 H11 H 0 1 N N N 169.541 117.905 33.139 1.028 1.118 2.490 H11 GDG 50 GDG H12 H12 H 0 1 N N N 168.795 120.036 35.967 4.208 2.665 -1.885 H12 GDG 51 GDG H13 H13 H 0 1 N N N 166.927 117.044 35.261 4.413 -2.223 -1.586 H13 GDG 52 GDG H14 H14 H 0 1 N N N 164.673 117.884 33.923 4.593 -1.804 0.915 H14 GDG 53 GDG H15 H15 H 0 1 N N N 162.329 117.682 33.676 5.664 -3.562 2.357 H15 GDG 54 GDG H16 H16 H 0 1 N N N 163.077 116.094 33.294 7.223 -2.729 2.155 H16 GDG 55 GDG H17 H17 H 0 1 N N N 161.253 115.913 34.696 6.076 -2.006 4.121 H17 GDG 56 GDG H18 H18 H 0 1 N N N 166.186 116.038 33.444 5.266 -4.904 -0.690 H18 GDG 57 GDG H19 H19 H 0 1 N N N 167.611 115.494 36.900 5.539 -3.012 -3.540 H19 GDG 58 GDG H20 H20 H 0 1 N N N 166.699 118.410 38.485 6.240 0.340 -3.233 H20 GDG 59 GDG H21 H21 H 0 1 N N N 165.601 119.249 28.360 -4.790 4.558 -1.101 H21 GDG 60 GDG H22 H22 H 0 1 N N N 168.669 119.579 26.212 -6.336 3.164 -1.072 H22 GDG 61 GDG H23 H23 H 0 1 N N N 167.185 123.813 26.010 -6.507 -0.587 -1.884 H23 GDG 62 GDG H24 H24 H 0 1 N N N 167.488 126.781 23.808 -9.172 -2.764 -2.458 H24 GDG 63 GDG H25 H25 H 0 1 N N N 166.479 125.432 24.212 -8.259 -1.508 -3.098 H25 GDG 64 # # 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 GDG N39 C35 SING N N 1 GDG C35 N36 DOUB N N 2 GDG C35 N34 SING N N 3 GDG N36 C37 SING N N 4 GDG N34 C04 SING N N 5 GDG O33 C07 SING N N 6 GDG C37 O38 DOUB N N 7 GDG C37 C03 SING N N 8 GDG C04 C03 DOUB Y N 9 GDG C04 N05 SING Y N 10 GDG C03 N02 SING Y N 11 GDG C07 C06 SING N N 12 GDG C07 C08 SING N N 13 GDG O32 C08 SING N N 14 GDG N05 C06 SING N N 15 GDG N05 C01 SING Y N 16 GDG C06 O10 SING N N 17 GDG N02 C01 DOUB Y N 18 GDG C08 C09 SING N N 19 GDG O10 C09 SING N N 20 GDG C09 C11 SING N N 21 GDG C11 O12 SING N N 22 GDG O12 P13 SING N N 23 GDG O14 P13 DOUB N N 24 GDG P13 O15 SING N N 25 GDG P13 O16 SING N N 26 GDG O29 C24 SING N N 27 GDG O16 P17 SING N N 28 GDG C27 C25 SING N N 29 GDG C27 O28 SING N N 30 GDG C25 C24 SING N N 31 GDG C25 O26 SING N N 32 GDG O18 P17 DOUB N N 33 GDG C24 C23 SING N N 34 GDG P17 O19 SING N N 35 GDG P17 O20 SING N N 36 GDG O26 C21 SING N N 37 GDG C23 O30 SING N N 38 GDG C23 C22 SING N N 39 GDG O20 C21 SING N N 40 GDG C21 C22 SING N N 41 GDG C22 O31 SING N N 42 GDG C21 H1 SING N N 43 GDG C22 H2 SING N N 44 GDG C24 H3 SING N N 45 GDG C01 H4 SING N N 46 GDG C06 H5 SING N N 47 GDG C07 H6 SING N N 48 GDG C08 H7 SING N N 49 GDG C09 H8 SING N N 50 GDG C11 H9 SING N N 51 GDG C11 H10 SING N N 52 GDG O15 H11 SING N N 53 GDG O19 H12 SING N N 54 GDG C23 H13 SING N N 55 GDG C25 H14 SING N N 56 GDG C27 H15 SING N N 57 GDG C27 H16 SING N N 58 GDG O28 H17 SING N N 59 GDG O29 H18 SING N N 60 GDG O30 H19 SING N N 61 GDG O31 H20 SING N N 62 GDG O32 H21 SING N N 63 GDG O33 H22 SING N N 64 GDG N34 H23 SING N N 65 GDG N39 H24 SING N N 66 GDG N39 H25 SING N N 67 # # 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 GDG SMILES ACDLabs 12.01 "C1(C(O)C(C(C(O1)CO)O)O)OP(OP(OCC4C(C(C(n2cnc3c2NC(=NC3=O)N)O4)O)O)(O)=O)(O)=O" GDG InChI InChI 1.03 "InChI=1S/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)/t4-,5-,7-,8-,9+,10-,11-,14-,15-/m1/s1" GDG InChIKey InChI 1.03 MVMSCBBUIHUTGJ-LRJDVEEWSA-N GDG SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O)[C@@H](O)[C@H]3O)c2N1" GDG SMILES CACTVS 3.385 "NC1=NC(=O)c2ncn([CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH](CO)[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O)c2N1" GDG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O[C@@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)O)O)NC(=NC2=O)N" GDG SMILES "OpenEye OEToolkits" 2.0.4 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)CO)O)O)O)O)O)NC(=NC2=O)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 GDG "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" GDG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)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 GDG "Create component" 2006-09-05 EBI GDG "Modify descriptor" 2011-06-04 RCSB GDG "Other modification" 2016-05-21 EBI GDG "Initial release" 2017-06-21 RCSB GDG "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id GDG _pdbx_chem_comp_synonyms.name GDP-ALPHA-D-GLUCOSE _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##