data_UP1 # _chem_comp.id UP1 _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 ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-12-22 _chem_comp.pdbx_modified_date 2011-06-04 _chem_comp.pdbx_ambiguous_flag ? _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 UP1 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 UP1 N1 N1 N 0 1 N N N -4.474 9.098 -10.661 1.969 -1.518 1.997 N1 UP1 1 UP1 C2 C2 C 0 1 N N N -4.375 8.899 -12.150 1.579 -1.865 3.312 C2 UP1 2 UP1 N3 N3 N 0 1 N N N -4.476 10.039 -12.973 0.214 -1.713 3.588 N3 UP1 3 UP1 C4 C4 C 0 1 N N N -4.659 11.307 -12.408 -0.765 -1.266 2.715 C4 UP1 4 UP1 C5 C5 C 0 1 N N N -4.733 11.390 -11.074 -0.276 -0.925 1.364 C5 UP1 5 UP1 C6 C6 C 0 1 N N N -4.639 10.354 -10.403 1.022 -1.065 1.085 C6 UP1 6 UP1 O2 O2 O 0 1 N N N -4.220 7.812 -12.673 2.362 -2.274 4.172 O2 UP1 7 UP1 O4 O4 O 0 1 N N N -4.737 12.246 -13.091 -1.952 -1.149 3.003 O4 UP1 8 UP1 "C1'" C1* C 0 1 N N R -4.364 7.882 -9.678 3.334 -1.624 1.571 "C1'" UP1 9 UP1 "C2'" C2* C 0 1 N N R -2.935 7.225 -9.652 3.626 -2.952 0.890 "C2'" UP1 10 UP1 "O2'" O2* O 0 1 N N N -2.865 5.872 -9.916 4.153 -3.886 1.815 "O2'" UP1 11 UP1 "C3'" C3* C 0 1 N N R -2.354 7.431 -8.396 4.651 -2.555 -0.149 "C3'" UP1 12 UP1 "C4'" C4* C 0 1 N N R -3.403 8.169 -7.653 4.128 -1.196 -0.577 "C4'" UP1 13 UP1 "O4'" O4* O 0 1 N N N -4.563 8.314 -8.375 3.606 -0.588 0.614 "O4'" UP1 14 UP1 "O3'" O3* O 0 1 N N N -1.188 8.061 -8.657 4.680 -3.456 -1.239 "O3'" UP1 15 UP1 "C5'" C5* C 0 1 N N N -3.273 8.852 -6.364 5.196 -0.303 -1.183 "C5'" UP1 16 UP1 "O5'" O5* O 0 1 N N N -2.982 10.138 -6.859 4.609 0.930 -1.558 "O5'" UP1 17 UP1 PA PA P 0 1 N N S -1.808 11.024 -6.577 5.525 2.263 -1.526 PA UP1 18 UP1 O1A O1A O 0 1 N N N -2.267 11.981 -7.417 4.850 3.540 -1.933 O1A UP1 19 UP1 O2A O2A O 0 1 N N N -0.626 10.269 -6.944 6.830 1.872 -2.398 O2A UP1 20 UP1 O3A O3A O 0 1 N N N -2.064 11.767 -5.328 6.069 2.231 -0.004 O3A UP1 21 UP1 PB PB P 0 1 N N R -1.097 11.979 -3.968 7.146 3.166 0.758 PB UP1 22 UP1 O1B O1B O 0 1 N N N 0.318 11.865 -4.215 8.536 2.845 -0.005 O1B UP1 23 UP1 O2B O2B O 0 1 N N N -1.490 13.196 -3.478 6.788 4.623 0.806 O2B UP1 24 UP1 O3B O3B O 0 1 N N N -1.373 10.795 -3.548 7.292 2.455 2.201 O3B UP1 25 UP1 C1 C1 C 0 1 N N R -1.821 10.349 -2.231 7.630 1.070 2.278 C1 UP1 26 UP1 C23 C23 C 0 1 N N S -2.005 8.783 -2.303 6.982 0.514 3.540 C23 UP1 27 UP1 C3 C3 C 0 1 N N R -3.449 8.249 -2.128 7.433 -0.909 3.842 C3 UP1 28 UP1 C45 C45 C 0 1 N N R -4.649 9.155 -2.370 8.953 -1.018 3.777 C45 UP1 29 UP1 C56 C56 C 0 1 N N R -4.236 10.600 -2.837 9.509 -0.420 2.480 C56 UP1 30 UP1 C67 C67 C 0 1 N N N -5.372 11.606 -3.037 9.244 -1.257 1.227 C67 UP1 31 UP1 F2 F2 F 0 1 N N N -1.278 8.261 -1.340 5.630 0.494 3.352 F2 UP1 32 UP1 O3 O3 O 0 1 N N N -3.742 7.189 -2.954 7.012 -1.257 5.161 O3 UP1 33 UP1 O45 O45 O 0 1 N N N -5.259 9.040 -1.149 9.352 -2.379 3.893 O45 UP1 34 UP1 O5 O5 O 0 1 N N N -3.129 11.053 -1.892 9.047 0.923 2.316 O5 UP1 35 UP1 O6 O6 O 0 1 N N N -5.274 12.844 -2.311 9.798 -0.586 0.110 O6 UP1 36 UP1 H6 H6 H 0 1 N N N -4.721 10.608 -9.333 1.402 -0.820 0.099 H6 UP1 37 UP1 "H1'" H1* H 0 1 N N N -5.124 7.150 -10.038 3.962 -1.457 2.453 "H1'" UP1 38 UP1 H3 H3 H 0 1 N N N -4.416 9.945 -13.987 -0.090 -1.956 4.527 H3 UP1 39 UP1 H5 H5 H 0 1 N N N -4.874 12.331 -10.516 -0.985 -0.569 0.627 H5 UP1 40 UP1 "H2'" H2* H 0 1 N N N -2.398 7.729 -10.489 2.737 -3.396 0.426 "H2'" UP1 41 UP1 HA HA H 0 1 N N N -2.002 5.475 -9.900 4.632 -3.378 2.491 HA UP1 42 UP1 "H3'" H3* H 0 1 N N N -2.076 6.556 -7.764 5.655 -2.499 0.286 "H3'" UP1 43 UP1 "H4'" H4* H 0 1 N N N -3.091 7.687 -6.697 3.306 -1.294 -1.297 "H4'" UP1 44 UP1 HB HB H 0 1 N N N -0.794 8.201 -7.804 5.403 -4.085 -1.072 HB UP1 45 UP1 "H5'1" 1H5* H 0 0 N N N -2.547 8.418 -5.637 5.629 -0.772 -2.072 "H5'1" UP1 46 UP1 "H5'2" 2H5* H 0 0 N N N -4.135 8.768 -5.662 5.991 -0.109 -0.457 "H5'2" UP1 47 UP1 H2A H2A H 0 1 N N N 0.119 10.831 -6.765 7.517 2.554 -2.558 H2A UP1 48 UP1 H1B H1B H 0 1 N N N 0.864 11.985 -3.447 8.713 3.273 -0.869 H1B UP1 49 UP1 H1 H1 H 0 1 N N N -1.084 10.597 -1.432 7.226 0.591 1.380 H1 UP1 50 UP1 H2 H2 H 0 1 N N N -1.701 8.493 -3.336 7.169 1.169 4.399 H2 UP1 51 UP1 H33 H33 H 0 1 N N N -3.363 8.038 -1.037 6.953 -1.623 3.163 H33 UP1 52 UP1 H4 H4 H 0 1 N N N -5.327 8.887 -3.214 9.383 -0.485 4.634 H4 UP1 53 UP1 HC HC H 0 1 N N N -4.627 6.862 -2.847 6.954 -0.428 5.661 HC UP1 54 UP1 H56 H56 H 0 1 N N N -3.864 10.552 -3.887 10.600 -0.365 2.576 H56 UP1 55 UP1 HD HD H 0 1 N N N -6.008 9.605 -1.300 10.117 -2.392 4.489 HD UP1 56 UP1 H61 1H6 H 0 1 N N N -6.349 11.117 -2.812 8.170 -1.376 1.079 H61 UP1 57 UP1 H62 2H6 H 0 1 N N N -5.496 11.819 -4.125 9.712 -2.237 1.327 H62 UP1 58 UP1 H66 H66 H 0 1 N N N -5.979 13.468 -2.435 9.306 -0.884 -0.674 H66 UP1 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 UP1 N1 C2 SING N N 1 UP1 N1 C6 SING N N 2 UP1 N1 "C1'" SING N N 3 UP1 C2 N3 SING N N 4 UP1 C2 O2 DOUB N N 5 UP1 N3 C4 SING N N 6 UP1 N3 H3 SING N N 7 UP1 C4 C5 SING N N 8 UP1 C4 O4 DOUB N N 9 UP1 C5 C6 DOUB N N 10 UP1 C5 H5 SING N N 11 UP1 C6 H6 SING N N 12 UP1 "C1'" "C2'" SING N N 13 UP1 "C1'" "O4'" SING N N 14 UP1 "C1'" "H1'" SING N N 15 UP1 "C2'" "O2'" SING N N 16 UP1 "C2'" "C3'" SING N N 17 UP1 "C2'" "H2'" SING N N 18 UP1 "O2'" HA SING N N 19 UP1 "C3'" "C4'" SING N N 20 UP1 "C3'" "O3'" SING N N 21 UP1 "C3'" "H3'" SING N N 22 UP1 "C4'" "O4'" SING N N 23 UP1 "C4'" "C5'" SING N N 24 UP1 "C4'" "H4'" SING N N 25 UP1 "O3'" HB SING N N 26 UP1 "C5'" "O5'" SING N N 27 UP1 "C5'" "H5'1" SING N N 28 UP1 "C5'" "H5'2" SING N N 29 UP1 "O5'" PA SING N N 30 UP1 PA O1A DOUB N N 31 UP1 PA O2A SING N N 32 UP1 PA O3A SING N N 33 UP1 O2A H2A SING N N 34 UP1 O3A PB SING N N 35 UP1 PB O1B SING N N 36 UP1 PB O2B DOUB N N 37 UP1 PB O3B SING N N 38 UP1 O1B H1B SING N N 39 UP1 O3B C1 SING N N 40 UP1 C1 C23 SING N N 41 UP1 C1 O5 SING N N 42 UP1 C1 H1 SING N N 43 UP1 C23 C3 SING N N 44 UP1 C23 F2 SING N N 45 UP1 C23 H2 SING N N 46 UP1 C3 C45 SING N N 47 UP1 C3 O3 SING N N 48 UP1 C3 H33 SING N N 49 UP1 C45 C56 SING N N 50 UP1 C45 O45 SING N N 51 UP1 C45 H4 SING N N 52 UP1 C56 C67 SING N N 53 UP1 C56 O5 SING N N 54 UP1 C56 H56 SING N N 55 UP1 C67 O6 SING N N 56 UP1 C67 H61 SING N N 57 UP1 C67 H62 SING N N 58 UP1 O3 HC SING N N 59 UP1 O45 HD SING N N 60 UP1 O6 H66 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 UP1 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" UP1 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" UP1 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" UP1 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H](C(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" UP1 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" UP1 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" UP1 InChIKey InChI 1.03 NGTCPFGWXMBZEP-ASADWNOXSA-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 UP1 "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3R,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5R,6R)-3-fluoro-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" UP1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3S,4R,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 UP1 "Create component" 2006-12-22 PDBJ UP1 "Modify descriptor" 2011-06-04 RCSB #