data_UGF # _chem_comp.id UGF _chem_comp.name ;(2~{R},3~{S},4~{R},5~{R},6~{R})-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidany l)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-fluoranyl-4,5-bis(oxidanyl)oxane-2-carboxylic acid ; _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H21 F N2 O17 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "UDP-4-Deoxy-4-Fluoro-Glucuronic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-06-01 _chem_comp.pdbx_modified_date 2020-07-24 _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 582.276 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UGF _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 6Z76 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 UGF O2 O1 O 0 1 N N N -4.654 17.681 -7.777 -5.845 -2.020 -2.223 O2 UGF 1 UGF C2 C1 C 0 1 N N N -3.638 16.989 -7.674 -5.862 -2.218 -1.024 C2 UGF 2 UGF N3 N1 N 0 1 N N N -2.377 17.599 -7.736 -6.267 -3.413 -0.555 N3 UGF 3 UGF C4 C2 C 0 1 N N N -1.211 16.898 -7.658 -6.292 -3.649 0.772 C4 UGF 4 UGF O4 O2 O 0 1 N N N -0.121 17.486 -7.760 -6.658 -4.730 1.198 O4 UGF 5 UGF C5 C3 C 0 1 N N N -1.315 15.511 -7.513 -5.889 -2.628 1.667 C5 UGF 6 UGF C6 C4 C 0 1 N N N -2.564 14.908 -7.431 -5.488 -1.439 1.169 C6 UGF 7 UGF N1 N2 N 0 1 N N N -3.720 15.648 -7.515 -5.472 -1.242 -0.184 N1 UGF 8 UGF C1D C5 C 0 1 N N R -5.035 15.018 -7.406 -5.031 0.047 -0.725 C1D UGF 9 UGF O4D O3 O 0 1 N N N -5.077 14.713 -5.984 -3.726 0.388 -0.209 O4D UGF 10 UGF C2D C6 C 0 1 N N R -5.186 13.754 -8.165 -5.958 1.181 -0.235 C2D UGF 11 UGF O2D O4 O 0 1 N N N -5.783 14.107 -9.448 -6.927 1.503 -1.234 O2D UGF 12 UGF C3D C7 C 0 1 N N S -6.181 12.986 -7.273 -5.003 2.373 -0.002 C3D UGF 13 UGF O3D O5 O 0 1 N N N -7.581 13.292 -7.681 -5.353 3.468 -0.852 O3D UGF 14 UGF C4D C8 C 0 1 N N R -5.907 13.504 -5.869 -3.612 1.818 -0.380 C4D UGF 15 UGF C5D C9 C 0 1 N N N -5.114 12.554 -4.972 -2.541 2.382 0.556 C5D UGF 16 UGF O5D O6 O 0 1 N N N -4.076 12.026 -5.755 -1.258 1.890 0.164 O5D UGF 17 UGF PA P1 P 0 1 N N N -2.843 11.132 -5.013 0.102 2.281 0.931 PA UGF 18 UGF O1A O7 O 0 1 N N N -1.763 10.818 -5.990 0.235 3.754 0.982 O1A UGF 19 UGF O2A O8 O 0 1 N N N -2.678 11.566 -3.592 0.062 1.693 2.429 O2A UGF 20 UGF O3A O9 O 0 1 N N N -3.653 9.727 -4.749 1.360 1.656 0.143 O3A UGF 21 UGF PB P2 P 0 1 N N N -4.517 8.824 -5.800 2.949 1.913 0.190 PB UGF 22 UGF O1B O10 O 0 1 N N N -5.871 8.758 -5.220 3.290 3.302 -0.550 O1B UGF 23 UGF O2B O11 O 0 1 N N N -4.292 9.124 -7.232 3.396 1.983 1.599 O2B UGF 24 UGF O3B O12 O 0 1 N N N -3.678 7.474 -5.731 3.710 0.706 -0.555 O3B UGF 25 UGF "C1'" C10 C 0 1 N N R -3.235 6.912 -4.479 5.134 0.590 -0.593 "C1'" UGF 26 UGF "O5'" O13 O 0 1 N N N -4.182 6.079 -3.895 5.580 -0.170 0.532 "O5'" UGF 27 UGF "C5'" C11 C 0 1 N N R -4.573 5.024 -4.748 5.030 -1.487 0.602 "C5'" UGF 28 UGF "C6'" C12 C 0 1 N N N -5.689 4.217 -4.047 5.544 -2.183 1.836 "C6'" UGF 29 UGF "O'P" O14 O 0 1 N N N -6.238 4.715 -3.041 5.082 -3.400 2.162 "O'P" UGF 30 UGF "O'Q" O15 O 0 1 N N N -5.973 3.121 -4.550 6.373 -1.645 2.531 "O'Q" UGF 31 UGF "C4'" C13 C 0 1 N N S -3.346 4.122 -4.994 5.446 -2.279 -0.641 "C4'" UGF 32 UGF "F4'" F1 F 0 1 N N N -3.758 3.138 -5.881 4.863 -3.550 -0.603 "F4'" UGF 33 UGF "C3'" C14 C 0 1 N N R -2.141 4.937 -5.500 4.971 -1.535 -1.893 "C3'" UGF 34 UGF "O3'" O16 O 0 1 N N N -0.949 4.154 -5.328 5.419 -2.228 -3.060 "O3'" UGF 35 UGF "C2'" C15 C 0 1 N N R -1.937 6.145 -4.678 5.554 -0.118 -1.883 "C2'" UGF 36 UGF "O2'" O17 O 0 1 N N N -1.009 7.014 -5.367 5.060 0.609 -3.010 "O2'" UGF 37 UGF H1 H1 H 0 1 N N N -2.331 18.592 -7.842 -6.541 -4.107 -1.174 H1 UGF 38 UGF H2 H2 H 0 1 N N N -0.421 14.906 -7.465 -5.903 -2.799 2.734 H2 UGF 39 UGF H3 H3 H 0 1 N N N -2.628 13.838 -7.299 -5.177 -0.649 1.837 H3 UGF 40 UGF H4 H4 H 0 1 N N N -5.831 15.727 -7.678 -5.013 0.014 -1.814 H4 UGF 41 UGF H5 H5 H 0 1 N N N -4.235 13.211 -8.271 -6.449 0.898 0.697 H5 UGF 42 UGF H6 H6 H 0 1 N N N -5.899 13.322 -9.971 -7.536 2.210 -0.979 H6 UGF 43 UGF H7 H7 H 0 1 N N N -5.984 11.905 -7.329 -5.021 2.679 1.044 H7 UGF 44 UGF H8 H8 H 0 1 N N N -8.185 12.814 -7.125 -6.241 3.816 -0.698 H8 UGF 45 UGF H9 H9 H 0 1 N N N -6.861 13.749 -5.380 -3.376 2.059 -1.416 H9 UGF 46 UGF H10 H10 H 0 1 N N N -4.699 13.102 -4.113 -2.546 3.470 0.500 H10 UGF 47 UGF H11 H11 H 0 1 N N N -5.764 11.744 -4.610 -2.753 2.070 1.579 H11 UGF 48 UGF H12 H12 H 0 1 N N N -1.753 11.618 -3.382 -0.024 0.731 2.472 H12 UGF 49 UGF H13 H13 H 0 1 N N N -6.515 8.933 -5.897 3.024 3.327 -1.480 H13 UGF 50 UGF H14 H14 H 0 1 N N N -3.019 7.741 -3.790 5.581 1.583 -0.561 H14 UGF 51 UGF H15 H15 H 0 1 N N N -4.946 5.405 -5.710 3.942 -1.426 0.646 H15 UGF 52 UGF H16 H16 H 0 1 N N N -6.908 4.123 -2.720 5.442 -3.806 2.963 H16 UGF 53 UGF H17 H17 H 0 1 N N N -3.065 3.666 -4.033 6.531 -2.376 -0.665 H17 UGF 54 UGF H18 H18 H 0 1 N N N -2.292 5.207 -6.556 3.882 -1.482 -1.895 H18 UGF 55 UGF H19 H19 H 0 1 N N N -0.198 4.647 -5.637 5.093 -3.136 -3.127 H19 UGF 56 UGF H20 H20 H 0 1 N N N -1.532 5.861 -3.695 6.642 -0.172 -1.932 H20 UGF 57 UGF H21 H21 H 0 1 N N N -0.866 7.798 -4.851 5.389 1.517 -3.067 H21 UGF 58 # # 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 UGF O2D C2D SING N N 1 UGF C2D C1D SING N N 2 UGF C2D C3D SING N N 3 UGF O2 C2 DOUB N N 4 UGF O4 C4 DOUB N N 5 UGF N3 C2 SING N N 6 UGF N3 C4 SING N N 7 UGF O3D C3D SING N N 8 UGF C2 N1 SING N N 9 UGF C4 C5 SING N N 10 UGF N1 C6 SING N N 11 UGF N1 C1D SING N N 12 UGF C5 C6 DOUB N N 13 UGF C1D O4D SING N N 14 UGF C3D C4D SING N N 15 UGF O2B PB DOUB N N 16 UGF O1A PA DOUB N N 17 UGF O4D C4D SING N N 18 UGF "F4'" "C4'" SING N N 19 UGF C4D C5D SING N N 20 UGF PB O3B SING N N 21 UGF PB O1B SING N N 22 UGF PB O3A SING N N 23 UGF O5D PA SING N N 24 UGF O5D C5D SING N N 25 UGF O3B "C1'" SING N N 26 UGF "C3'" "O3'" SING N N 27 UGF "C3'" "C4'" SING N N 28 UGF "C3'" "C2'" SING N N 29 UGF "O2'" "C2'" SING N N 30 UGF PA O3A SING N N 31 UGF PA O2A SING N N 32 UGF "C4'" "C5'" SING N N 33 UGF "C5'" "C6'" SING N N 34 UGF "C5'" "O5'" SING N N 35 UGF "C2'" "C1'" SING N N 36 UGF "O'Q" "C6'" DOUB N N 37 UGF "C1'" "O5'" SING N N 38 UGF "C6'" "O'P" SING N N 39 UGF N3 H1 SING N N 40 UGF C5 H2 SING N N 41 UGF C6 H3 SING N N 42 UGF C1D H4 SING N N 43 UGF C2D H5 SING N N 44 UGF O2D H6 SING N N 45 UGF C3D H7 SING N N 46 UGF O3D H8 SING N N 47 UGF C4D H9 SING N N 48 UGF C5D H10 SING N N 49 UGF C5D H11 SING N N 50 UGF O2A H12 SING N N 51 UGF O1B H13 SING N N 52 UGF "C1'" H14 SING N N 53 UGF "C5'" H15 SING N N 54 UGF "O'P" H16 SING N N 55 UGF "C4'" H17 SING N N 56 UGF "C3'" H18 SING N N 57 UGF "O3'" H19 SING N N 58 UGF "C2'" H20 SING N N 59 UGF "O2'" H21 SING N N 60 # # 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 UGF InChI InChI 1.03 "InChI=1S/C15H21FN2O17P2/c16-6-8(21)10(23)14(33-11(6)13(24)25)34-37(29,30)35-36(27,28)31-3-4-7(20)9(22)12(32-4)18-2-1-5(19)17-15(18)26/h1-2,4,6-12,14,20-23H,3H2,(H,24,25)(H,27,28)(H,29,30)(H,17,19,26)/t4-,6+,7-,8+,9-,10-,11+,12-,14-/m1/s1" UGF InChIKey InChI 1.03 LVBLRZZISSCAOI-CTMYAEKBSA-N UGF SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1[C@@H](O)[C@H](O[C@@H]([C@H]1F)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O" UGF SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]([CH]1F)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O" UGF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)C(=O)O)F)O)O)O)O" UGF SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)C(=O)O)F)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id UGF _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(2~{R},3~{S},4~{R},5~{R},6~{R})-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-fluoranyl-4,5-bis(oxidanyl)oxane-2-carboxylic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UGF _pdbx_chem_comp_synonyms.name "UDP-4-Deoxy-4-Fluoro-Glucuronic acid" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site UGF "Create component" 2020-06-01 PDBE UGF "Modify synonyms" 2020-06-05 PDBE UGF "Initial release" 2020-07-29 RCSB ##