data_UPF # _chem_comp.id UPF _chem_comp.name "URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H23 F N2 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE 2-DEOXY-2-FLUORO-GALACTOPYRANOSYL-MONOPHOSPHATE ESTER" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-11-30 _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 568.293 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UPF _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 1GA8 _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 UPF N1 N1 N 0 1 N N N 27.246 44.476 57.859 0.858 -0.674 5.805 N1 UPF 1 UPF C2 C2 C 0 1 N N N 27.632 43.844 56.664 1.590 0.372 5.383 C2 UPF 2 UPF N3 N3 N 0 1 N N N 26.736 44.095 55.610 2.870 0.523 5.772 N3 UPF 3 UPF C4 C4 C 0 1 N N N 25.543 44.905 55.653 3.444 -0.383 6.588 C4 UPF 4 UPF C5 C5 C 0 1 N N N 25.233 45.520 56.910 2.686 -1.493 7.036 C5 UPF 5 UPF C6 C6 C 0 1 N N N 26.052 45.309 57.942 1.403 -1.617 6.634 C6 UPF 6 UPF O2 O2 O 0 1 N N N 28.633 43.138 56.565 1.086 1.198 4.647 O2 UPF 7 UPF O4 O4 O 0 1 N N N 24.868 45.022 54.645 4.603 -0.250 6.936 O4 UPF 8 UPF C1D C1* C 0 1 N N R 27.946 44.427 59.222 -0.533 -0.809 5.369 C1D UPF 9 UPF C2D C2* C 0 1 N N R 29.213 45.245 59.123 -1.346 0.460 5.726 C2D UPF 10 UPF "O2'" O2* O 0 1 N N N 30.325 44.490 59.591 -1.858 0.381 7.058 "O2'" UPF 11 UPF C3D C3* C 0 1 N N S 28.928 46.470 59.974 -2.497 0.412 4.687 C3D UPF 12 UPF C4D C4* C 0 1 N N R 28.177 45.825 61.135 -1.951 -0.493 3.566 C4D UPF 13 UPF O4D O4* O 0 1 N N N 27.357 44.776 60.451 -0.611 -0.866 3.929 O4D UPF 14 UPF O3D O3* O 0 1 N N N 30.009 47.247 60.450 -3.673 -0.155 5.270 O3D UPF 15 UPF C5D C5* C 0 1 N N N 26.869 46.225 61.745 -1.938 0.270 2.241 C5D UPF 16 UPF O5D O5* O 0 1 N N N 26.298 47.578 61.483 -1.424 -0.574 1.209 O5D UPF 17 UPF PA PA P 0 1 N N R 26.766 49.099 61.249 -1.438 0.288 -0.149 PA UPF 18 UPF O1A O1A O 0 1 N N N 28.222 49.272 61.261 -2.825 0.704 -0.454 O1A UPF 19 UPF O2A O2A O 0 1 N N N 26.106 49.694 60.059 -0.514 1.593 0.033 O2A UPF 20 UPF O3A O3A O 0 1 N N N 26.011 49.279 62.643 -0.869 -0.607 -1.359 O3A UPF 21 UPF PB PB P 0 1 N N S 25.737 50.507 63.615 -0.912 0.313 -2.680 PB UPF 22 UPF O1B O1B O 0 1 N N N 27.073 51.140 63.723 -2.307 0.729 -2.946 O1B UPF 23 UPF O2B O2B O 0 1 N N N 24.752 51.397 62.959 0.003 1.618 -2.454 O2B UPF 24 UPF O3B O3B O 0 1 N N N 25.283 49.976 64.989 -0.352 -0.523 -3.936 O3B UPF 25 UPF "C1'" "C1'" C 0 1 N N R 25.663 49.782 66.526 -0.416 0.342 -5.071 "C1'" UPF 26 UPF "C2'" "C2'" C 0 1 N N R 27.142 49.349 66.499 -0.643 -0.491 -6.334 "C2'" UPF 27 UPF "C3'" "C3'" C 0 1 N N S 27.570 48.162 65.500 0.503 -1.496 -6.482 "C3'" UPF 28 UPF "C4'" "C4'" C 0 1 N N R 26.580 46.942 65.687 1.832 -0.733 -6.435 "C4'" UPF 29 UPF "C5'" "C5'" C 0 1 N N R 25.091 47.558 65.670 1.873 0.117 -5.163 "C5'" UPF 30 UPF "C6'" "C6'" C 0 1 N N N 24.067 46.500 66.124 3.210 0.856 -5.089 "C6'" UPF 31 UPF "F2'" "F2'" F 0 1 N N N 28.007 50.445 66.303 -1.858 -1.177 -6.229 "F2'" UPF 32 UPF "O3'" "O3'" O 0 1 N N N 28.862 47.756 65.870 0.383 -2.180 -7.731 "O3'" UPF 33 UPF "O4'" "O4'" O 0 1 N N N 26.878 46.287 66.949 1.939 0.110 -7.583 "O4'" UPF 34 UPF "O5'" "O5'" O 0 1 N N N 24.823 48.627 66.707 0.808 1.065 -5.184 "O5'" UPF 35 UPF "O6'" "O6'" O 0 1 N N N 23.780 45.249 65.553 3.251 1.649 -3.901 "O6'" UPF 36 UPF HN3 HN3 H 0 1 N N N 26.975 43.644 54.726 3.382 1.285 5.461 HN3 UPF 37 UPF H5 H5 H 0 1 N N N 24.354 46.163 57.085 3.129 -2.229 7.690 H5 UPF 38 UPF H6 H6 H 0 1 N N N 25.741 45.824 58.866 0.810 -2.456 6.966 H6 UPF 39 UPF H1D H1* H 0 1 N N N 27.995 43.318 59.331 -0.989 -1.694 5.814 H1D UPF 40 UPF H2D H2* H 0 1 N N N 29.480 45.534 58.080 -0.741 1.358 5.596 H2D UPF 41 UPF "HO2'" *HO2 H 0 0 N N N 31.121 45.004 59.528 -2.351 1.198 7.216 "HO2'" UPF 42 UPF H3D H3* H 0 1 N N N 28.405 47.242 59.363 -2.707 1.410 4.303 H3D UPF 43 UPF H4D H4* H 0 1 N N N 29.017 45.834 61.868 -2.572 -1.384 3.474 H4D UPF 44 UPF "HO3'" *HO3 H 0 0 N N N 29.830 48.013 60.982 -3.930 0.423 6.000 "HO3'" UPF 45 UPF "H5'1" 1H5* H 0 0 N N N 26.104 45.462 61.466 -1.306 1.152 2.336 "H5'1" UPF 46 UPF "H5'2" 2H5* H 0 0 N N N 26.938 46.081 62.848 -2.953 0.576 1.987 "H5'2" UPF 47 UPF HOA2 2HOA H 0 0 N N N 26.382 50.592 59.920 0.378 1.278 0.230 HOA2 UPF 48 UPF HOB2 2HOB H 0 0 N N N 24.588 52.130 63.539 0.902 1.303 -2.284 HOB2 UPF 49 UPF "H1'" "H1'" H 0 1 N N N 25.544 50.610 67.262 -1.241 1.043 -4.946 "H1'" UPF 50 UPF "H2'" "H2'" H 0 1 N N N 27.251 48.908 67.517 -0.669 0.164 -7.204 "H2'" UPF 51 UPF "H3'" "H3'" H 0 1 N N N 27.539 48.503 64.439 0.465 -2.218 -5.666 "H3'" UPF 52 UPF "H4'" "H4'" H 0 1 N N N 26.681 46.177 64.881 2.659 -1.442 -6.424 "H4'" UPF 53 UPF "H5'" "H5'" H 0 1 N N N 25.004 47.940 64.626 1.767 -0.528 -4.292 "H5'" UPF 54 UPF "H6'1" "1H6'" H 0 0 N N N 24.310 46.290 67.191 3.317 1.502 -5.960 "H6'1" UPF 55 UPF "H6'2" "2H6'" H 0 0 N N N 23.089 47.034 66.173 4.025 0.132 -5.071 "H6'2" UPF 56 UPF HO3A "'HO3" H 0 0 N N N 29.114 47.055 65.280 -0.469 -2.634 -7.721 HO3A UPF 57 UPF "HO4'" "'HO4" H 0 0 N N N 26.283 45.554 67.061 1.903 -0.466 -8.358 "HO4'" UPF 58 UPF "HO6'" "'HO6" H 0 0 N N N 23.148 44.596 65.832 4.108 2.096 -3.893 "HO6'" UPF 59 # # 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 UPF N1 C2 SING N N 1 UPF N1 C6 SING N N 2 UPF N1 C1D SING N N 3 UPF C2 N3 SING N N 4 UPF C2 O2 DOUB N N 5 UPF N3 C4 SING N N 6 UPF N3 HN3 SING N N 7 UPF C4 C5 SING N N 8 UPF C4 O4 DOUB N N 9 UPF C5 C6 DOUB N N 10 UPF C5 H5 SING N N 11 UPF C6 H6 SING N N 12 UPF C1D C2D SING N N 13 UPF C1D O4D SING N N 14 UPF C1D H1D SING N N 15 UPF C2D "O2'" SING N N 16 UPF C2D C3D SING N N 17 UPF C2D H2D SING N N 18 UPF "O2'" "HO2'" SING N N 19 UPF C3D C4D SING N N 20 UPF C3D O3D SING N N 21 UPF C3D H3D SING N N 22 UPF C4D O4D SING N N 23 UPF C4D C5D SING N N 24 UPF C4D H4D SING N N 25 UPF O3D "HO3'" SING N N 26 UPF C5D O5D SING N N 27 UPF C5D "H5'1" SING N N 28 UPF C5D "H5'2" SING N N 29 UPF O5D PA SING N N 30 UPF PA O1A DOUB N N 31 UPF PA O2A SING N N 32 UPF PA O3A SING N N 33 UPF O2A HOA2 SING N N 34 UPF O3A PB SING N N 35 UPF PB O1B DOUB N N 36 UPF PB O2B SING N N 37 UPF PB O3B SING N N 38 UPF O2B HOB2 SING N N 39 UPF O3B "C1'" SING N N 40 UPF "C1'" "C2'" SING N N 41 UPF "C1'" "O5'" SING N N 42 UPF "C1'" "H1'" SING N N 43 UPF "C2'" "C3'" SING N N 44 UPF "C2'" "F2'" SING N N 45 UPF "C2'" "H2'" SING N N 46 UPF "C3'" "C4'" SING N N 47 UPF "C3'" "O3'" SING N N 48 UPF "C3'" "H3'" SING N N 49 UPF "C4'" "C5'" SING N N 50 UPF "C4'" "O4'" SING N N 51 UPF "C4'" "H4'" SING N N 52 UPF "C5'" "C6'" SING N N 53 UPF "C5'" "O5'" SING N N 54 UPF "C5'" "H5'" SING N N 55 UPF "C6'" "O6'" SING N N 56 UPF "C6'" "H6'1" SING N N 57 UPF "C6'" "H6'2" SING N N 58 UPF "O3'" HO3A SING N N 59 UPF "O4'" "HO4'" SING N N 60 UPF "O6'" "HO6'" SING N N 61 # # 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 UPF SMILES ACDLabs 10.04 "O=P(OC1OC(C(O)C(O)C1F)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O" UPF SMILES_CANONICAL CACTVS 3.341 "OC[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)N3C=CC(=O)NC3=O)[C@H](F)[C@@H](O)[C@H]1O" UPF SMILES CACTVS 3.341 "OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](F)[CH](O)[CH]1O" UPF SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)O)F)O)O" UPF SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)F)O)O" UPF InChI InChI 1.03 "InChI=1S/C15H23FN2O16P2/c16-8-11(23)9(21)5(3-19)32-14(8)33-36(28,29)34-35(26,27)30-4-6-10(22)12(24)13(31-6)18-2-1-7(20)17-15(18)25/h1-2,5-6,8-14,19,21-24H,3-4H2,(H,26,27)(H,28,29)(H,17,20,25)/t5-,6-,8-,9+,10-,11-,12-,13-,14-/m1/s1" UPF InChIKey InChI 1.03 NGTCPFGWXMBZEP-KBQKSTHMSA-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 UPF "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5R,6R)-3-fluoro-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" UPF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3R,4S,5R,6R)-3-fluoro-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-hydroxy-phosphoryl] 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 UPF "Create component" 2000-11-30 RCSB UPF "Modify descriptor" 2011-06-04 RCSB UPF "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UPF _pdbx_chem_comp_synonyms.name "URIDINE-5'-MONOPHOSPHATE 2-DEOXY-2-FLUORO-GALACTOPYRANOSYL-MONOPHOSPHATE ESTER" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##