data_GPK # _chem_comp.id GPK _chem_comp.name "5-fluoro-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C10 H13 F N2 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;5-fluoro-1-(beta-D-glucosyl)pyrimidine-2,4(1H,3H)-dione; 5-fluoro-1-(D-glucosyl)pyrimidine-2,4(1H,3H)-dione; 5-fluoro-1-(glucosyl)pyrimidine-2,4(1H,3H)-dione ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-08-10 _chem_comp.pdbx_modified_date 2020-07-17 _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 292.218 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GPK _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 3SYR _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 GPK "5-fluoro-1-(beta-D-glucosyl)pyrimidine-2,4(1H,3H)-dione" PDB ? 2 GPK "5-fluoro-1-(D-glucosyl)pyrimidine-2,4(1H,3H)-dione" PDB ? 3 GPK "5-fluoro-1-(glucosyl)pyrimidine-2,4(1H,3H)-dione" PDB ? # # 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 GPK C1A C1 C 0 1 N N N 35.503 23.491 28.595 -2.062 0.079 -1.168 C1A GPK 1 GPK F1 F1 F 0 1 N N N 37.610 24.155 29.411 -4.326 0.029 -1.775 F1 GPK 2 GPK C2A C2 C 0 1 N N N 36.275 24.181 29.518 -3.363 -0.042 -0.829 C2A GPK 3 GPK C3A C3 C 0 1 N N N 35.649 24.904 30.535 -3.706 -0.246 0.531 C3A GPK 4 GPK O3A O3 O 0 1 N N N 36.347 25.543 31.344 -4.873 -0.359 0.860 O3A GPK 5 GPK N4 N4 N 0 1 N N N 34.298 24.935 30.635 -2.728 -0.315 1.456 N4 GPK 6 GPK C5A C5 C 0 1 N N N 33.512 24.265 29.758 -1.438 -0.190 1.092 C5A GPK 7 GPK O5A O5 O 0 1 N N N 32.262 24.254 29.874 -0.568 -0.253 1.939 O5A GPK 8 GPK C1 "C1'" C 0 1 N N R 33.227 22.796 27.745 0.314 0.135 -0.561 C1 GPK 9 GPK "N1'" "N1'" N 0 1 N N N 34.099 23.454 28.771 -1.098 0.004 -0.195 "N1'" GPK 10 GPK C2 "C2'" C 0 1 N N R 33.657 23.040 26.293 0.889 1.406 0.071 C2 GPK 11 GPK O2 "O2'" O 0 1 N N N 33.760 24.449 26.045 0.206 2.549 -0.447 O2 GPK 12 GPK C3 "C3'" C 0 1 N N S 32.613 22.381 25.376 2.380 1.504 -0.266 C3 GPK 13 GPK O3 "O3'" O 0 1 N N N 33.022 22.450 24.024 2.942 2.648 0.381 O3 GPK 14 GPK C4 "C4'" C 0 1 N N S 32.364 20.929 25.760 3.089 0.238 0.226 C4 GPK 15 GPK O4 "O4'" O 0 1 N N N 31.255 20.457 24.976 4.467 0.287 -0.147 O4 GPK 16 GPK C5 "C5'" C 0 1 N N R 32.113 20.760 27.272 2.428 -0.987 -0.412 C5 GPK 17 GPK O5 "O5'" O 0 1 N N N 33.168 21.378 27.998 1.037 -1.002 -0.085 O5 GPK 18 GPK C6 "C6'" C 0 1 N N N 32.085 19.307 27.768 3.091 -2.259 0.120 C6 GPK 19 GPK O6 "O6'" O 0 1 N N N 33.175 18.551 27.212 2.556 -3.396 -0.561 O6 GPK 20 GPK H1A H1 H 0 1 N N N 35.965 22.991 27.757 -1.781 0.231 -2.199 H1A GPK 21 GPK HN4 HN4 H 0 1 N N N 33.873 25.463 31.370 -2.955 -0.454 2.389 HN4 GPK 22 GPK H1 "H1'" H 0 1 N N N 32.236 23.261 27.849 0.405 0.196 -1.645 H1 GPK 23 GPK H2 "H2'" H 0 1 N N N 34.646 22.600 26.095 0.761 1.364 1.153 H2 GPK 24 GPK HO2 "HO2'" H 0 1 N Y N 34.026 24.594 25.145 0.520 3.390 -0.089 HO2 GPK 25 GPK H3 "H3'" H 0 1 N N N 31.673 22.938 25.502 2.505 1.598 -1.345 H3 GPK 26 GPK HO3 "HO3'" H 0 1 N Y N 32.366 22.039 23.473 3.886 2.772 0.211 HO3 GPK 27 GPK H4 "H4'" H 0 1 N N N 33.261 20.329 25.547 3.007 0.173 1.311 H4 GPK 28 GPK HO4 "HO4'" H 0 1 N Y N 31.075 19.550 25.195 4.947 1.042 0.219 HO4 GPK 29 GPK H5 "H5'" H 0 1 N N N 31.122 21.209 27.436 2.547 -0.941 -1.495 H5 GPK 30 GPK H61 "H6'" H 0 1 N N N 32.169 19.302 28.865 4.167 -2.207 -0.050 H61 GPK 31 GPK H62 "H6'A" H 0 1 N N N 31.136 18.843 27.462 2.896 -2.350 1.189 H62 GPK 32 GPK HO6 "HO6'" H 0 1 N Y N 33.137 17.657 27.532 2.931 -4.239 -0.273 HO6 GPK 33 # # 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 GPK C1A C2A DOUB N N 1 GPK C1A "N1'" SING N N 2 GPK F1 C2A SING N N 3 GPK C2A C3A SING N N 4 GPK C3A O3A DOUB N N 5 GPK C3A N4 SING N N 6 GPK N4 C5A SING N N 7 GPK C5A O5A DOUB N N 8 GPK C5A "N1'" SING N N 9 GPK C1 "N1'" SING N N 10 GPK C1 C2 SING N N 11 GPK C1 O5 SING N N 12 GPK C2 O2 SING N N 13 GPK C2 C3 SING N N 14 GPK C3 O3 SING N N 15 GPK C3 C4 SING N N 16 GPK C4 O4 SING N N 17 GPK C4 C5 SING N N 18 GPK C5 O5 SING N N 19 GPK C5 C6 SING N N 20 GPK C6 O6 SING N N 21 GPK C1A H1A SING N N 22 GPK N4 HN4 SING N N 23 GPK C1 H1 SING N N 24 GPK C2 H2 SING N N 25 GPK O2 HO2 SING N N 26 GPK C3 H3 SING N N 27 GPK O3 HO3 SING N N 28 GPK C4 H4 SING N N 29 GPK O4 HO4 SING N N 30 GPK C5 H5 SING N N 31 GPK C6 H61 SING N N 32 GPK C6 H62 SING N N 33 GPK O6 HO6 SING N N 34 # # 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 GPK SMILES ACDLabs 12.01 "FC1=CN(C(=O)NC1=O)C2OC(C(O)C(O)C2O)CO" GPK InChI InChI 1.03 "InChI=1S/C10H13FN2O7/c11-3-1-13(10(19)12-8(3)18)9-7(17)6(16)5(15)4(2-14)20-9/h1,4-7,9,14-17H,2H2,(H,12,18,19)/t4-,5-,6+,7-,9-/m1/s1" GPK InChIKey InChI 1.03 YHWGRVDTEORPPJ-XSEHCYKFSA-N GPK SMILES_CANONICAL CACTVS 3.370 "OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)N2C=C(F)C(=O)NC2=O" GPK SMILES CACTVS 3.370 "OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)N2C=C(F)C(=O)NC2=O" GPK SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)F" GPK SMILES "OpenEye OEToolkits" 1.7.2 "C1=C(C(=O)NC(=O)N1C2C(C(C(C(O2)CO)O)O)O)F" # # 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 GPK "SYSTEMATIC NAME" ACDLabs 12.01 "5-fluoro-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione" GPK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "5-fluoranyl-1-[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]pyrimidine-2,4-dione" # # loop_ _pdbx_chem_comp_feature.comp_id _pdbx_chem_comp_feature.type _pdbx_chem_comp_feature.value _pdbx_chem_comp_feature.source _pdbx_chem_comp_feature.support GPK "CARBOHYDRATE ISOMER" D PDB ? GPK "CARBOHYDRATE RING" pyranose PDB ? GPK "CARBOHYDRATE ANOMER" beta PDB ? GPK "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose PDB ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site GPK "Create component" 2011-08-10 RCSB GPK "Other modification" 2020-07-03 RCSB GPK "Modify synonyms" 2020-07-17 RCSB GPK "Modify internal type" 2020-07-17 RCSB GPK "Modify linking type" 2020-07-17 RCSB GPK "Modify atom id" 2020-07-17 RCSB GPK "Modify component atom id" 2020-07-17 RCSB GPK "Modify leaving atom flag" 2020-07-17 RCSB ##