data_8XU # _chem_comp.id 8XU _chem_comp.name "1-(5-O-phosphono-beta-D-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-07-16 _chem_comp.pdbx_modified_date 2015-07-24 _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 324.181 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8XU _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 2N4J _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 8XU P P P 0 1 N N N 78.668 107.071 -13.170 4.155 0.864 0.130 P 8XU 1 8XU OP1 OP1 O 0 1 N N N 77.280 107.479 -12.870 3.839 1.820 -0.954 OP1 8XU 2 8XU OP2 OP2 O 0 1 N N N 79.391 106.217 -12.203 4.706 1.668 1.412 OP2 8XU 3 8XU "O5'" "O5'" O 0 1 N N N 78.691 106.347 -14.613 2.824 0.054 0.536 "O5'" 8XU 4 8XU "C5'" "C5'" C 0 1 N N N 79.699 105.386 -14.941 2.038 -0.676 -0.408 "C5'" 8XU 5 8XU "C4'" "C4'" C 0 1 N N R 79.825 105.178 -16.449 0.851 -1.323 0.308 "C4'" 8XU 6 8XU "O4'" "O4'" O 0 1 N N N 81.194 105.162 -16.836 -0.083 -0.317 0.755 "O4'" 8XU 7 8XU "C1'" "C1'" C 0 1 N N R 81.447 103.998 -17.614 -1.349 -0.972 0.939 "C1'" 8XU 8 8XU N1 N1 N 0 1 N N N 82.335 103.078 -16.877 -2.439 -0.055 0.595 N1 8XU 9 8XU C6 C6 C 0 1 N N N 82.294 103.026 -15.516 -3.442 0.174 1.496 C6 8XU 10 8XU C2 C2 C 0 1 N N N 83.227 102.311 -17.600 -2.441 0.558 -0.603 C2 8XU 11 8XU O2 O2 O 0 1 N N N 83.266 102.329 -18.825 -1.536 0.344 -1.387 O2 8XU 12 8XU N3 N3 N 0 1 N N N 84.070 101.506 -16.858 -3.429 1.405 -0.945 N3 8XU 13 8XU C4 C4 C 0 1 N N N 84.098 101.402 -15.481 -4.439 1.653 -0.087 C4 8XU 14 8XU O4 O4 O 0 1 N N N 84.904 100.662 -14.926 -5.334 2.419 -0.395 O4 8XU 15 8XU C5 C5 C 0 1 N N N 83.127 102.235 -14.812 -4.446 1.019 1.179 C5 8XU 16 8XU "C2'" "C2'" C 0 1 N N R 80.118 103.329 -17.947 -1.374 -2.192 -0.002 "C2'" 8XU 17 8XU "O2'" "O2'" O 0 1 N N N 79.667 103.681 -19.261 -1.552 -3.397 0.746 "O2'" 8XU 18 8XU "C3'" "C3'" C 0 1 N N R 79.174 103.862 -16.867 0.020 -2.180 -0.680 "C3'" 8XU 19 8XU "O3'" "O3'" O 0 1 N N N 79.073 102.954 -15.762 -0.043 -1.556 -1.964 "O3'" 8XU 20 8XU O1 O1 O 0 1 N Y N 79.548 108.398 -13.434 5.279 -0.171 -0.377 O1 8XU 21 8XU H1 H1 H 0 1 N N N 78.827 106.029 -11.462 5.508 2.180 1.240 H1 8XU 22 8XU "H5''" "H5''" H 0 0 N N N 79.440 104.426 -14.471 1.672 0.004 -1.178 "H5''" 8XU 23 8XU "H5'" "H5'" H 0 1 N N N 80.665 105.737 -14.549 2.651 -1.450 -0.869 "H5'" 8XU 24 8XU "H4'" "H4'" H 0 1 N N N 79.303 106.001 -16.958 1.194 -1.929 1.146 "H4'" 8XU 25 8XU "H1'" "H1'" H 0 1 N N N 81.935 104.284 -18.558 -1.452 -1.297 1.974 "H1'" 8XU 26 8XU H6 H6 H 0 1 N N N 81.575 103.635 -14.988 -3.431 -0.319 2.457 H6 8XU 27 8XU H3 H3 H 0 1 N N N 84.723 100.945 -17.367 -3.415 1.838 -1.813 H3 8XU 28 8XU H5 H5 H 0 1 N N N 83.068 102.224 -13.734 -5.245 1.208 1.881 H5 8XU 29 8XU "H2'" "H2'" H 0 1 N N N 80.217 102.238 -17.844 -2.163 -2.084 -0.747 "H2'" 8XU 30 8XU "HO2'" "HO2'" H 0 0 N N N 78.839 103.250 -19.438 -1.576 -4.197 0.203 "HO2'" 8XU 31 8XU "H3'" "H3'" H 0 1 N N N 78.185 104.061 -17.306 0.422 -3.190 -0.760 "H3'" 8XU 32 8XU H2 H2 H 0 1 N N N 78.482 103.312 -15.110 -0.627 -2.004 -2.591 H2 8XU 33 8XU H4 H4 H 0 1 N N N 78.997 109.167 -13.343 5.536 -0.828 0.284 H4 8XU 34 # 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 8XU "O2'" "C2'" SING N N 1 8XU O2 C2 DOUB N N 2 8XU "C2'" "C1'" SING N N 3 8XU "C2'" "C3'" SING N N 4 8XU "C1'" N1 SING N N 5 8XU "C1'" "O4'" SING N N 6 8XU C2 N1 SING N N 7 8XU C2 N3 SING N N 8 8XU N1 C6 SING N N 9 8XU "C3'" "C4'" SING N N 10 8XU "C3'" "O3'" SING N N 11 8XU N3 C4 SING N N 12 8XU "O4'" "C4'" SING N N 13 8XU "C4'" "C5'" SING N N 14 8XU C6 C5 DOUB N N 15 8XU C4 O4 DOUB N N 16 8XU C4 C5 SING N N 17 8XU "C5'" "O5'" SING N N 18 8XU "O5'" P SING N N 19 8XU P OP1 DOUB N N 20 8XU P OP2 SING N N 21 8XU P O1 SING N N 22 8XU OP2 H1 SING N N 23 8XU "C5'" "H5''" SING N N 24 8XU "C5'" "H5'" SING N N 25 8XU "C4'" "H4'" SING N N 26 8XU "C1'" "H1'" SING N N 27 8XU C6 H6 SING N N 28 8XU N3 H3 SING N N 29 8XU C5 H5 SING N N 30 8XU "C2'" "H2'" SING N N 31 8XU "O2'" "HO2'" SING N N 32 8XU "C3'" "H3'" SING N N 33 8XU "O3'" H2 SING N N 34 8XU O1 H4 SING N N 35 # 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 8XU SMILES ACDLabs 12.01 "P(=O)(O)(O)OCC2OC(N1C=CC(NC1=O)=O)C(C2O)O" 8XU InChI InChI 1.03 "InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6+,7-,8-/m1/s1" 8XU InChIKey InChI 1.03 DJJCXFVJDGTHFX-PXBUCIJWSA-N 8XU SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" 8XU SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" 8XU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@H](O2)COP(=O)(O)O)O)O" 8XU SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O" # 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 8XU "SYSTEMATIC NAME" ACDLabs 12.01 "1-(5-O-phosphono-beta-D-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione" 8XU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen 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 8XU "Create component" 2015-07-16 RCSB 8XU "Initial release" 2015-07-29 RCSB #