data_DKX # _chem_comp.id DKX _chem_comp.name "1-(3-deoxy-3-fluoro-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 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;1-(3-deoxy-3-fluoro-beta-D-glucosyl)pyrimidine-2,4(1H,3H)-dione; 1-(3-deoxy-3-fluoro-D-glucosyl)pyrimidine-2,4(1H,3H)-dione; 1-(3-deoxy-3-fluoro-glucosyl)pyrimidine-2,4(1H,3H)-dione ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-01-11 _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 276.218 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DKX _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 3L79 _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 DKX "1-(3-deoxy-3-fluoro-beta-D-glucosyl)pyrimidine-2,4(1H,3H)-dione" PDB ? 2 DKX "1-(3-deoxy-3-fluoro-D-glucosyl)pyrimidine-2,4(1H,3H)-dione" PDB ? 3 DKX "1-(3-deoxy-3-fluoro-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 DKX C1 C1 C 0 1 N N R 33.379 22.865 27.777 -0.090 0.083 0.421 C1 DKX 1 DKX N1 N1 N 0 1 N N N 34.269 23.577 28.722 1.327 -0.045 0.074 N1 DKX 2 DKX C2 C2 C 0 1 N N S 33.762 23.057 26.297 -0.654 1.363 -0.202 C2 DKX 3 DKX N2 N2 N 0 1 N N N 34.467 24.899 30.729 3.567 -0.107 0.753 N2 DKX 4 DKX O2 O2 O 0 1 N N N 33.846 24.457 25.989 0.024 2.497 0.341 O2 DKX 5 DKX C3 C3 C 0 1 N N S 32.741 22.352 25.386 -2.150 1.459 0.115 C3 DKX 6 DKX F3 F3 F 0 1 N N N 33.203 22.339 24.083 -2.689 2.589 -0.511 F3 DKX 7 DKX C4 C4 C 0 1 N N R 32.451 20.918 25.874 -2.853 0.201 -0.405 C4 DKX 8 DKX O4 O4 O 0 1 N N N 31.263 20.454 25.238 -4.237 0.247 -0.051 O4 DKX 9 DKX C5 C5 C 0 1 N N R 32.291 20.821 27.418 -2.204 -1.033 0.226 C5 DKX 10 DKX O5 O5 O 0 1 N N N 33.395 21.461 28.093 -0.808 -1.046 -0.081 O5 DKX 11 DKX C6 C6 C 0 1 N N N 32.267 19.373 27.932 -2.861 -2.297 -0.333 C6 DKX 12 DKX O6 O6 O 0 1 N N N 33.351 18.657 27.319 -2.337 -3.444 0.340 O6 DKX 13 DKX C7 C7 C 0 1 N N N 35.673 23.618 28.552 1.692 -0.218 -1.234 C7 DKX 14 DKX C8 C8 C 0 1 N N N 36.473 24.297 29.474 2.998 -0.336 -1.553 C8 DKX 15 DKX C9 C9 C 0 1 N N N 35.858 24.946 30.555 3.967 -0.278 -0.523 C9 DKX 16 DKX O9 O9 O 0 1 N N N 36.529 25.565 31.379 5.152 -0.382 -0.787 O9 DKX 17 DKX C10 C10 C 0 1 N N N 33.666 24.210 29.814 2.258 0.013 1.043 C10 DKX 18 DKX O10 O10 O 0 1 N N N 32.443 24.169 29.956 1.913 0.171 2.198 O10 DKX 19 DKX H1 H1 H 0 1 N N N 32.374 23.297 27.897 -0.197 0.129 1.505 H1 DKX 20 DKX H2 H2 H 0 1 N N N 34.748 22.604 26.119 -0.512 1.336 -1.282 H2 DKX 21 DKX HO2 HO2 H 0 1 N Y N 34.082 24.567 25.075 -0.283 3.345 -0.010 HO2 DKX 22 DKX H3 H3 H 0 1 N N N 31.796 22.914 25.426 -2.290 1.537 1.193 H3 DKX 23 DKX H4 H4 H 0 1 N N N 33.316 20.292 25.608 -2.755 0.150 -1.489 H4 DKX 24 DKX HO4 HO4 H 0 1 N Y N 31.072 19.570 25.530 -4.710 1.008 -0.413 HO4 DKX 25 DKX H5 H5 H 0 1 N N N 31.331 21.313 27.633 -2.338 -1.002 1.308 H5 DKX 26 DKX H61 H6 H 0 1 N N N 32.384 19.363 29.026 -3.938 -2.245 -0.178 H61 DKX 27 DKX H62 H6A H 0 1 N N N 31.310 18.899 27.668 -2.650 -2.374 -1.400 H62 DKX 28 DKX HO6 HO6 H 0 1 N Y N 33.351 17.758 27.626 -2.710 -4.283 0.036 HO6 DKX 29 DKX H7 H7 H 0 1 N N N 36.128 23.123 27.707 0.938 -0.260 -2.006 H7 DKX 30 DKX H8 H8 H 0 1 N N N 37.546 24.322 29.357 3.300 -0.473 -2.581 H8 DKX 31 DKX HN2 HN2 H 0 1 N N N 34.047 25.360 31.511 4.225 -0.067 1.464 HN2 DKX 32 # # 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 DKX C2 C1 SING N N 1 DKX C1 O5 SING N N 2 DKX C1 N1 SING N N 3 DKX C1 H1 SING N N 4 DKX C7 N1 SING N N 5 DKX N1 C10 SING N N 6 DKX C3 C2 SING N N 7 DKX O2 C2 SING N N 8 DKX C2 H2 SING N N 9 DKX C10 N2 SING N N 10 DKX C9 N2 SING N N 11 DKX O2 HO2 SING N N 12 DKX F3 C3 SING N N 13 DKX C3 C4 SING N N 14 DKX C3 H3 SING N N 15 DKX O4 C4 SING N N 16 DKX C4 C5 SING N N 17 DKX C4 H4 SING N N 18 DKX O4 HO4 SING N N 19 DKX C5 C6 SING N N 20 DKX C5 O5 SING N N 21 DKX C5 H5 SING N N 22 DKX O6 C6 SING N N 23 DKX C6 H61 SING N N 24 DKX C6 H62 SING N N 25 DKX O6 HO6 SING N N 26 DKX C7 C8 DOUB N N 27 DKX C7 H7 SING N N 28 DKX C8 C9 SING N N 29 DKX C8 H8 SING N N 30 DKX C9 O9 DOUB N N 31 DKX C10 O10 DOUB N N 32 DKX N2 HN2 SING N N 33 # # 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 DKX SMILES_CANONICAL CACTVS 3.352 "OC[C@H]1O[C@H]([C@H](O)[C@@H](F)[C@@H]1O)N2C=CC(=O)NC2=O" DKX SMILES CACTVS 3.352 "OC[CH]1O[CH]([CH](O)[CH](F)[CH]1O)N2C=CC(=O)NC2=O" DKX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)F)O" DKX SMILES "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=O)NC1=O)C2C(C(C(C(O2)CO)O)F)O" DKX InChI InChI 1.03 "InChI=1S/C10H13FN2O6/c11-6-7(16)4(3-14)19-9(8(6)17)13-2-1-5(15)12-10(13)18/h1-2,4,6-9,14,16-17H,3H2,(H,12,15,18)/t4-,6+,7-,8-,9-/m1/s1" DKX InChIKey InChI 1.03 QGWLQEMDCINRKW-PMPOVCSBSA-N # _pdbx_chem_comp_identifier.comp_id DKX _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.6.1 _pdbx_chem_comp_identifier.identifier "1-[(2R,3S,4S,5R,6R)-4-fluoro-3,5-dihydroxy-6-(hydroxymethyl)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 DKX "CARBOHYDRATE ISOMER" D PDB ? DKX "CARBOHYDRATE RING" pyranose PDB ? DKX "CARBOHYDRATE ANOMER" beta PDB ? DKX "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 DKX "Create component" 2010-01-11 RCSB DKX "Modify descriptor" 2011-06-04 RCSB DKX "Other modification" 2020-07-03 RCSB DKX "Modify synonyms" 2020-07-17 RCSB DKX "Modify internal type" 2020-07-17 RCSB DKX "Modify linking type" 2020-07-17 RCSB DKX "Modify atom id" 2020-07-17 RCSB DKX "Modify component atom id" 2020-07-17 RCSB DKX "Modify leaving atom flag" 2020-07-17 RCSB ##