data_DU # _chem_comp.id DU _chem_comp.name "2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-06-01 _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 308.182 _chem_comp.one_letter_code U _chem_comp.three_letter_code DU _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _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 DU OP3 O3P O 0 1 N Y N ? ? ? -3.912 -2.311 1.636 OP3 DU 1 DU P P P 0 1 N N N 12.190 -12.289 0.399 -3.968 -1.665 3.118 P DU 2 DU OP1 O1P O 0 1 N N N 12.477 -13.576 -0.294 -4.406 -2.599 4.208 OP1 DU 3 DU OP2 O2P O 0 1 N N N 13.315 -11.490 0.952 -4.901 -0.360 2.920 OP2 DU 4 DU "O5'" O5* O 0 1 N N N 11.149 -12.592 1.572 -2.493 -1.028 3.315 "O5'" DU 5 DU "C5'" C5* C 0 1 N N N 10.832 -11.580 2.548 -2.005 -0.136 2.327 "C5'" DU 6 DU "C4'" C4* C 0 1 N N R 10.441 -12.214 3.863 -0.611 0.328 2.728 "C4'" DU 7 DU "O4'" O4* O 0 1 N N N 9.125 -12.814 3.763 0.247 -0.829 2.764 "O4'" DU 8 DU "C3'" C3* C 0 1 N N S 11.363 -13.310 4.399 0.008 1.286 1.720 "C3'" DU 9 DU "O3'" O3* O 0 1 N N N 11.383 -13.192 5.818 0.965 2.121 2.368 "O3'" DU 10 DU "C2'" C2* C 0 1 N N N 10.645 -14.591 3.996 0.710 0.360 0.754 "C2'" DU 11 DU "C1'" C1* C 0 1 N N R 9.182 -14.190 4.131 1.157 -0.778 1.657 "C1'" DU 12 DU N1 N1 N 0 1 N N N 8.265 -14.921 3.249 1.164 -2.047 0.989 N1 DU 13 DU C2 C2 C 0 1 N N N 7.200 -15.588 3.823 2.334 -2.545 0.374 C2 DU 14 DU O2 O2 O 0 1 N N N 7.004 -15.607 5.027 3.412 -1.946 0.363 O2 DU 15 DU N3 N3 N 0 1 N N N 6.374 -16.236 2.929 2.195 -3.797 -0.241 N3 DU 16 DU C4 C4 C 0 1 N N N 6.516 -16.285 1.561 1.046 -4.570 -0.300 C4 DU 17 DU O4 O4 O 0 1 N N N 5.711 -16.929 0.891 0.971 -5.663 -0.852 O4 DU 18 DU C5 C5 C 0 1 N N N 7.641 -15.573 1.051 -0.130 -3.976 0.367 C5 DU 19 DU C6 C6 C 0 1 N N N 8.456 -14.933 1.890 -0.013 -2.784 0.958 C6 DU 20 DU HOP3 3HOP H 0 0 N N N -0.183 0.821 0.442 -4.684 -2.823 1.313 HOP3 DU 21 DU HOP2 2HOP H 0 0 N N N 13.036 -10.589 1.070 -5.874 -0.475 2.871 HOP2 DU 22 DU "H5'" 1H5* H 0 1 N N N 9.987 -10.981 2.177 -1.971 -0.654 1.366 "H5'" DU 23 DU "H5''" 2H5* H 0 0 N N N 11.714 -10.942 2.704 -2.683 0.718 2.254 "H5''" DU 24 DU "H4'" H4* H 0 1 N N N 10.496 -11.368 4.564 -0.644 0.753 3.736 "H4'" DU 25 DU "H3'" H3* H 0 1 N N N 12.397 -13.269 4.027 -0.722 1.941 1.236 "H3'" DU 26 DU "HO3'" H3T H 0 0 N Y N 12.283 -13.166 6.121 0.743 3.042 2.146 "HO3'" DU 27 DU "H2'" 1H2* H 0 1 N N N 10.921 -15.462 4.608 -0.003 -0.001 0.003 "H2'" DU 28 DU "H2''" 2H2* H 0 0 N N N 10.896 -14.899 2.970 1.556 0.818 0.232 "H2''" DU 29 DU "H1'" H1* H 0 1 N N N 8.861 -14.411 5.160 2.163 -0.604 2.054 "H1'" DU 30 DU H3 H3 H 0 1 N N N 5.590 -16.721 3.315 3.023 -4.177 -0.691 H3 DU 31 DU H5 H5 H 0 1 N N N 7.832 -15.552 -0.012 -1.065 -4.523 0.362 H5 DU 32 DU H6 H6 H 0 1 N N N 9.303 -14.401 1.483 -0.864 -2.330 1.454 H6 DU 33 # 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 DU OP3 P SING N N 1 DU OP3 HOP3 SING N N 2 DU P OP1 DOUB N N 3 DU P OP2 SING N N 4 DU P "O5'" SING N N 5 DU OP2 HOP2 SING N N 6 DU "O5'" "C5'" SING N N 7 DU "C5'" "C4'" SING N N 8 DU "C5'" "H5'" SING N N 9 DU "C5'" "H5''" SING N N 10 DU "C4'" "O4'" SING N N 11 DU "C4'" "C3'" SING N N 12 DU "C4'" "H4'" SING N N 13 DU "O4'" "C1'" SING N N 14 DU "C3'" "O3'" SING N N 15 DU "C3'" "C2'" SING N N 16 DU "C3'" "H3'" SING N N 17 DU "O3'" "HO3'" SING N N 18 DU "C2'" "C1'" SING N N 19 DU "C2'" "H2'" SING N N 20 DU "C2'" "H2''" SING N N 21 DU "C1'" N1 SING N N 22 DU "C1'" "H1'" SING N N 23 DU N1 C2 SING N N 24 DU N1 C6 SING N N 25 DU C2 O2 DOUB N N 26 DU C2 N3 SING N N 27 DU N3 C4 SING N N 28 DU N3 H3 SING N N 29 DU C4 O4 DOUB N N 30 DU C4 C5 SING N N 31 DU C5 C6 DOUB N N 32 DU C5 H5 SING N N 33 DU C6 H6 SING N N 34 # 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 DU SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2)COP(=O)(O)O" DU SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" DU SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" DU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" DU SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" DU InChI InChI 1.03 "InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1" DU InChIKey InChI 1.03 JSRLJPSBLDHEIO-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 DU "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-5'-uridylic acid ; DU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-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 DU "Create component" 2001-06-01 PDBJ DU "Modify descriptor" 2011-06-04 RCSB #