data_DUR # _chem_comp.id DUR _chem_comp.name "2'-DEOXYURIDINE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H12 N2 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 228.202 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DUR _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 1BDU _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 DUR N1 N1 N 0 1 N N N -28.487 -8.988 20.192 -0.233 0.598 -1.002 N1 DUR 1 DUR C2 C2 C 0 1 N N N -27.488 -8.020 20.228 0.076 -0.682 -1.270 C2 DUR 2 DUR N3 N3 N 0 1 N N N -27.912 -6.723 20.094 0.313 -1.088 -2.532 N3 DUR 3 DUR C4 C4 C 0 1 N N N -29.228 -6.307 19.916 0.254 -0.207 -3.551 C4 DUR 4 DUR C5 C5 C 0 1 N N N -30.196 -7.393 19.876 -0.065 1.145 -3.282 C5 DUR 5 DUR C6 C6 C 0 1 N N N -29.770 -8.715 20.015 -0.303 1.523 -2.008 C6 DUR 6 DUR O2 O2 O 0 1 N N N -26.292 -8.259 20.326 0.133 -1.488 -0.361 O2 DUR 7 DUR O4 O4 O 0 1 N N N -29.516 -5.108 19.883 0.473 -0.572 -4.692 O4 DUR 8 DUR "C1'" C1* C 0 1 N N R -28.125 -10.401 20.419 -0.491 1.009 0.379 "C1'" DUR 9 DUR "C2'" C2* C 0 1 N N N -28.252 -10.829 21.873 -1.676 0.209 0.954 "C2'" DUR 10 DUR "C3'" C3* C 0 1 N N S -28.108 -12.332 21.793 -1.087 -0.502 2.199 "C3'" DUR 11 DUR "C4'" C4* C 0 1 N N R -29.083 -12.569 20.633 0.161 0.362 2.505 "C4'" DUR 12 DUR "O3'" O3* O 0 1 N N N -26.773 -12.637 21.378 -2.013 -0.474 3.287 "O3'" DUR 13 DUR "O4'" O4* O 0 1 N N N -28.834 -11.462 19.688 0.655 0.721 1.197 "O4'" DUR 14 DUR "C5'" C5* C 0 1 N N N -30.537 -12.526 21.144 1.206 -0.451 3.271 "C5'" DUR 15 DUR "O5'" O5* O 0 1 N N N -31.496 -12.761 20.106 2.365 0.352 3.496 "O5'" DUR 16 DUR HN3 HN3 H 0 1 N N N -27.186 -6.006 20.129 0.531 -2.016 -2.707 HN3 DUR 17 DUR H5 H5 H 0 1 N N N -31.274 -7.210 19.737 -0.118 1.864 -4.086 H5 DUR 18 DUR H6 H6 H 0 1 N N N -30.467 -9.568 19.984 -0.549 2.551 -1.785 H6 DUR 19 DUR "H1'" H1* H 0 1 N N N -27.082 -10.342 20.026 -0.712 2.076 0.414 "H1'" DUR 20 DUR "H2'1" 1H2* H 0 0 N N N -27.540 -10.328 22.570 -2.482 0.881 1.248 "H2'1" DUR 21 DUR "H2'2" 2H2* H 0 0 N N N -29.177 -10.475 22.384 -2.031 -0.520 0.228 "H2'2" DUR 22 DUR "H3'" H3* H 0 1 N N N -28.297 -12.918 22.722 -0.799 -1.526 1.961 "H3'" DUR 23 DUR "H4'" H4* H 0 1 N N N -28.934 -13.565 20.154 -0.117 1.253 3.068 "H4'" DUR 24 DUR "HO3'" *HO3 H 0 0 N N N -26.682 -13.581 21.327 -2.801 -0.953 2.996 "HO3'" DUR 25 DUR "H5'1" 1H5* H 0 0 N N N -30.683 -13.235 21.991 1.480 -1.330 2.688 "H5'1" DUR 26 DUR "H5'2" 2H5* H 0 0 N N N -30.746 -11.566 21.672 0.790 -0.765 4.229 "H5'2" DUR 27 DUR "HO5'" *HO5 H 0 0 N N N -32.391 -12.734 20.420 2.997 -0.196 3.980 "HO5'" DUR 28 # 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 DUR N1 C2 SING N N 1 DUR N1 C6 SING N N 2 DUR N1 "C1'" SING N N 3 DUR C2 N3 SING N N 4 DUR C2 O2 DOUB N N 5 DUR N3 C4 SING N N 6 DUR N3 HN3 SING N N 7 DUR C4 C5 SING N N 8 DUR C4 O4 DOUB N N 9 DUR C5 C6 DOUB N N 10 DUR C5 H5 SING N N 11 DUR C6 H6 SING N N 12 DUR "C1'" "C2'" SING N N 13 DUR "C1'" "O4'" SING N N 14 DUR "C1'" "H1'" SING N N 15 DUR "C2'" "C3'" SING N N 16 DUR "C2'" "H2'1" SING N N 17 DUR "C2'" "H2'2" SING N N 18 DUR "C3'" "C4'" SING N N 19 DUR "C3'" "O3'" SING N N 20 DUR "C3'" "H3'" SING N N 21 DUR "C4'" "O4'" SING N N 22 DUR "C4'" "C5'" SING N N 23 DUR "C4'" "H4'" SING N N 24 DUR "O3'" "HO3'" SING N N 25 DUR "C5'" "O5'" SING N N 26 DUR "C5'" "H5'1" SING N N 27 DUR "C5'" "H5'2" SING N N 28 DUR "O5'" "HO5'" SING N N 29 # 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 DUR SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CO" DUR SMILES_CANONICAL CACTVS 3.341 "OC[C@H]1O[C@H](C[C@@H]1O)N2C=CC(=O)NC2=O" DUR SMILES CACTVS 3.341 "OC[CH]1O[CH](C[CH]1O)N2C=CC(=O)NC2=O" DUR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO)O" DUR SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=O)NC2=O)CO)O" DUR InChI InChI 1.03 "InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)/t5-,6+,8+/m0/s1" DUR InChIKey InChI 1.03 MXHRCPNRJAMMIM-SHYZEUOFSA-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 DUR "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxyuridine" DUR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site DUR "Create component" 1999-07-08 RCSB DUR "Modify descriptor" 2011-06-04 RCSB #