data_URX # _chem_comp.id URX _chem_comp.name "[(1R,3R,4R,5R,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]hept-1-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H17 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-10-11 _chem_comp.pdbx_modified_date 2011-06-04 _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 348.246 _chem_comp.one_letter_code ? _chem_comp.three_letter_code URX _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 3OZ4 _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 URX P P P 0 1 N N N 10.353 4.544 2.733 4.307 0.932 0.238 P URX 1 URX N1 N1 N 0 1 N N N 6.125 6.136 5.636 -2.412 0.221 0.331 N1 URX 2 URX C2 C2 C 0 1 N N N 5.153 6.238 6.595 -3.695 -0.067 0.614 C2 URX 3 URX O2 O2 O 0 1 N N N 4.257 7.177 6.537 -3.975 -1.148 1.095 O2 URX 4 URX N3 N3 N 0 1 N N N 5.083 5.357 7.598 -4.674 0.826 0.374 N3 URX 5 URX C4 C4 C 0 1 N N N 5.994 4.398 7.735 -4.379 2.030 -0.158 C4 URX 6 URX O4 O4 O 0 1 N N N 5.895 3.603 8.696 -5.264 2.838 -0.375 O4 URX 7 URX C5 C5 C 0 1 N N N 6.998 4.254 6.785 -3.033 2.345 -0.461 C5 URX 8 URX C6 C6 C 0 1 N N N 7.035 5.138 5.714 -2.072 1.431 -0.210 C6 URX 9 URX "C1'" "C1'" C 0 1 N N R 6.124 7.053 4.512 -1.368 -0.769 0.610 "C1'" URX 10 URX "C2'" "C2'" C 0 1 N N R 6.913 8.332 4.821 -1.279 -1.803 -0.557 "C2'" URX 11 URX "C3'" "C3'" C 0 1 N N S 8.261 7.869 4.540 -0.288 -1.022 -1.495 "C3'" URX 12 URX "O3'" "O3'" O 0 1 N N N 9.194 8.987 4.490 0.243 -1.850 -2.532 "O3'" URX 13 URX "C4'" "C4'" C 0 1 N N R 7.934 7.381 3.172 0.760 -0.738 -0.362 "C4'" URX 14 URX "O4'" "O4'" O 0 1 N N N 6.829 6.465 3.400 -0.078 -0.131 0.659 "O4'" URX 15 URX "C5'" "C5'" C 0 1 N N N 9.082 6.725 2.473 1.989 0.073 -0.777 "C5'" URX 16 URX "O5'" "O5'" O 0 1 N N N 9.632 5.756 3.358 2.902 0.151 0.320 "O5'" URX 17 URX "C6'" "C6'" C 0 1 N N R 6.699 9.268 3.663 -0.347 -2.919 0.012 "C6'" URX 18 URX "C7'" "C7'" C 0 1 N N N 5.288 9.599 3.384 -0.866 -3.416 1.363 "C7'" URX 19 URX "C8'" "C8'" C 0 1 N N N 7.371 8.597 2.507 1.031 -2.184 0.154 "C8'" URX 20 URX OP1 OP1 O 0 1 N N N 11.413 5.090 1.690 5.094 0.414 -0.903 OP1 URX 21 URX OP2 OP2 O 0 1 N N N 11.038 3.688 3.887 4.035 2.506 0.032 OP2 URX 22 URX OP3 OP3 O 0 1 N Y N 9.397 3.783 1.700 5.128 0.704 1.604 OP3 URX 23 URX H5 H5 H 0 1 N N N 7.735 3.470 6.878 -2.778 3.303 -0.888 H5 URX 24 URX H6 H6 H 0 1 N N N 7.787 5.029 4.947 -1.039 1.654 -0.434 H6 URX 25 URX "H1'" "H1'" H 0 1 N N N 5.067 7.270 4.296 -1.574 -1.279 1.551 "H1'" URX 26 URX "H2'" "H2'" H 0 1 N N N 6.685 8.778 5.800 -2.222 -2.130 -0.995 "H2'" URX 27 URX "H3'" "H3'" H 0 1 N N N 8.731 7.166 5.244 -0.728 -0.106 -1.890 "H3'" URX 28 URX "HO3'" "HO3'" H 0 0 N Y N 10.068 8.663 4.305 -0.426 -2.207 -3.131 "HO3'" URX 29 URX "H5'" "H5'" H 0 1 N N N 8.733 6.238 1.550 2.478 -0.413 -1.622 "H5'" URX 30 URX "H5'A" "H5'A" H 0 0 N N N 9.844 7.475 2.214 1.681 1.078 -1.066 "H5'A" URX 31 URX "H6'" "H6'" H 0 1 N N N 7.125 10.257 3.887 -0.266 -3.746 -0.693 "H6'" URX 32 URX "H7'" "H7'" H 0 1 N N N 5.235 10.285 2.526 -1.915 -3.699 1.267 "H7'" URX 33 URX "H7'A" "H7'A" H 0 0 N N N 4.734 8.677 3.152 -0.284 -4.282 1.680 "H7'A" URX 34 URX "H7'B" "H7'B" H 0 0 N N N 4.843 10.082 4.267 -0.770 -2.623 2.103 "H7'B" URX 35 URX "H8'" "H8'" H 0 1 N N N 8.151 9.226 2.053 1.792 -2.670 -0.456 "H8'" URX 36 URX "H8'A" "H8'A" H 0 0 N N N 6.666 8.346 1.700 1.337 -2.163 1.201 "H8'A" URX 37 URX HOP2 HOP2 H 0 0 N N N 11.977 3.656 3.743 3.524 2.913 0.744 HOP2 URX 38 URX HOP3 HOP3 H 0 0 N Y N 9.738 3.884 0.819 5.988 1.147 1.625 HOP3 URX 39 URX HN3 HN3 H 0 1 N N N 4.333 5.420 8.256 -5.594 0.603 0.585 HN3 URX 40 # 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 URX OP1 P DOUB N N 1 URX OP3 P SING N N 2 URX P "O5'" SING N N 3 URX P OP2 SING N N 4 URX "C1'" N1 SING N N 5 URX N1 C6 SING N N 6 URX N1 C2 SING N N 7 URX O2 C2 DOUB N N 8 URX C2 N3 SING N N 9 URX N3 C4 SING N N 10 URX C5 C4 SING N N 11 URX C4 O4 DOUB N N 12 URX C6 C5 DOUB N N 13 URX C5 H5 SING N N 14 URX C6 H6 SING N N 15 URX "O4'" "C1'" SING N N 16 URX "C1'" "C2'" SING N N 17 URX "C1'" "H1'" SING N N 18 URX "C6'" "C2'" SING N N 19 URX "C3'" "C2'" SING N N 20 URX "C2'" "H2'" SING N N 21 URX "C4'" "C3'" SING N N 22 URX "O3'" "C3'" SING N N 23 URX "C3'" "H3'" SING N N 24 URX "O3'" "HO3'" SING N N 25 URX "C5'" "C4'" SING N N 26 URX "C8'" "C4'" SING N N 27 URX "C4'" "O4'" SING N N 28 URX "C5'" "O5'" SING N N 29 URX "C5'" "H5'" SING N N 30 URX "C5'" "H5'A" SING N N 31 URX "C8'" "C6'" SING N N 32 URX "C7'" "C6'" SING N N 33 URX "C6'" "H6'" SING N N 34 URX "C7'" "H7'" SING N N 35 URX "C7'" "H7'A" SING N N 36 URX "C7'" "H7'B" SING N N 37 URX "C8'" "H8'" SING N N 38 URX "C8'" "H8'A" SING N N 39 URX OP2 HOP2 SING N N 40 URX OP3 HOP3 SING N N 41 URX N3 HN3 SING N N 42 # 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 URX SMILES ACDLabs 12.01 "O=P(O)(O)OCC23OC(N1C(=O)NC(=O)C=C1)C(C(C2)C)C3O" URX SMILES_CANONICAL CACTVS 3.370 "C[C@@H]1C[C@]2(CO[P](O)(O)=O)O[C@H]([C@H]1[C@@H]2O)N3C=CC(=O)NC3=O" URX SMILES CACTVS 3.370 "C[CH]1C[C]2(CO[P](O)(O)=O)O[CH]([CH]1[CH]2O)N3C=CC(=O)NC3=O" URX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C[C@@H]1C[C@]2([C@H]([C@@H]1[C@@H](O2)N3C=CC(=O)NC3=O)O)COP(=O)(O)O" URX SMILES "OpenEye OEToolkits" 1.7.0 "CC1CC2(C(C1C(O2)N3C=CC(=O)NC3=O)O)COP(=O)(O)O" URX InChI InChI 1.03 "InChI=1S/C12H17N2O8P/c1-6-4-12(5-21-23(18,19)20)9(16)8(6)10(22-12)14-3-2-7(15)13-11(14)17/h2-3,6,8-10,16H,4-5H2,1H3,(H,13,15,17)(H2,18,19,20)/t6-,8-,9+,10-,12-/m1/s1" URX InChIKey InChI 1.03 BIKPERMTZJFCSY-VOLLVAIWSA-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 URX "SYSTEMATIC NAME" ACDLabs 12.01 "[(1R,3R,4R,5R,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]hept-1-yl]methyl dihydrogen phosphate" URX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(1R,2R,4R,6R,7S)-6-(2,4-dioxopyrimidin-1-yl)-7-hydroxy-2-methyl-5-oxabicyclo[2.2.1]heptan-4-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 URX "Create component" 2010-10-11 RCSB URX "Modify descriptor" 2011-06-04 RCSB #