data_DUD # _chem_comp.id DUD _chem_comp.name "DEOXYURIDINE-5'-DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H14 N2 O11 P2" _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 388.162 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DUD _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 1DUC _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 DUD N1 N1 N 0 1 N N N 15.971 34.869 31.016 -0.011 0.492 3.888 N1 DUD 1 DUD C2 C2 C 0 1 N N N 15.469 33.803 31.734 -0.693 -0.664 3.803 C2 DUD 2 DUD N3 N3 N 0 1 N N N 15.844 32.533 31.335 -1.692 -0.943 4.662 N3 DUD 3 DUD C4 C4 C 0 1 N N N 16.696 32.335 30.245 -2.033 -0.056 5.618 C4 DUD 4 DUD C5 C5 C 0 1 N N N 17.212 33.481 29.541 -1.328 1.167 5.715 C5 DUD 5 DUD C6 C6 C 0 1 N N N 16.810 34.740 29.928 -0.326 1.418 4.844 C6 DUD 6 DUD O2 O2 O 0 1 N N N 14.745 33.970 32.698 -0.397 -1.474 2.946 O2 DUD 7 DUD O4 O4 O 0 1 N N N 17.000 31.184 29.970 -2.940 -0.305 6.392 O4 DUD 8 DUD "C1'" C1* C 0 1 N N R 15.524 36.224 31.504 1.074 0.764 2.943 "C1'" DUD 9 DUD "C2'" C2* C 0 1 N N N 16.715 36.952 32.187 2.176 -0.309 3.066 "C2'" DUD 10 DUD "C3'" C3* C 0 1 N N S 17.232 37.889 31.085 2.655 -0.525 1.613 "C3'" DUD 11 DUD "C4'" C4* C 0 1 N N R 15.949 38.265 30.363 1.784 0.442 0.781 "C4'" DUD 12 DUD "O4'" O4* O 0 1 N N N 15.202 36.991 30.338 0.600 0.653 1.583 "O4'" DUD 13 DUD "O3'" O3* O 0 1 N N N 17.846 39.084 31.564 4.038 -0.190 1.486 "O3'" DUD 14 DUD "C5'" C5* C 0 1 N N N 16.185 38.742 28.927 1.412 -0.186 -0.562 "C5'" DUD 15 DUD "O5'" O5* O 0 1 N N N 14.904 38.942 28.300 0.549 0.698 -1.280 "O5'" DUD 16 DUD PA PA P 0 1 N N S 14.863 39.921 27.025 0.200 -0.023 -2.676 PA DUD 17 DUD O1A O1A O 0 1 N N N 15.838 41.027 27.182 -0.474 -1.313 -2.409 O1A DUD 18 DUD O2A O2A O 0 1 N N N 13.467 40.373 26.847 1.558 -0.287 -3.498 O2A DUD 19 DUD O3A O3A O 0 1 N N N 15.202 38.979 25.752 -0.774 0.923 -3.540 O3A DUD 20 DUD PB PB P 0 1 N N N 16.433 38.746 24.791 -1.081 0.144 -4.915 PB DUD 21 DUD O1B O1B O 0 1 N N N 17.387 37.873 25.575 -1.736 -1.148 -4.614 O1B DUD 22 DUD O2B O2B O 0 1 N N N 17.074 40.020 24.393 -2.056 1.038 -5.833 O2B DUD 23 DUD O3B O3B O 0 1 N N N 15.787 37.949 23.639 0.298 -0.123 -5.700 O3B DUD 24 DUD HN3 HN3 H 0 1 N N N 15.486 31.730 31.852 -2.171 -1.783 4.589 HN3 DUD 25 DUD H5 H5 H 0 1 N N N 17.919 33.393 28.699 -1.586 1.889 6.475 H5 DUD 26 DUD H6 H6 H 0 1 N N N 17.154 35.630 29.375 0.222 2.346 4.903 H6 DUD 27 DUD "H1'" H1* H 0 1 N N N 14.671 36.116 32.214 1.489 1.756 3.120 "H1'" DUD 28 DUD "H2'1" 1H2* H 0 0 N N N 16.459 37.460 33.146 1.766 -1.233 3.474 "H2'1" DUD 29 DUD "H2'2" 2H2* H 0 0 N N N 17.487 36.273 32.619 2.995 0.052 3.688 "H2'2" DUD 30 DUD "H3'" H3* H 0 1 N N N 18.021 37.389 30.476 2.483 -1.556 1.303 "H3'" DUD 31 DUD "H4'" H4* H 0 1 N N N 15.427 39.110 30.870 2.310 1.384 0.625 "H4'" DUD 32 DUD "HO3'" *HO3 H 0 0 N N N 18.165 39.663 30.882 4.527 -0.805 2.049 "HO3'" DUD 33 DUD "H5'1" 1H5* H 0 0 N N N 16.833 39.647 28.876 2.317 -0.362 -1.144 "H5'1" DUD 34 DUD "H5'2" 2H5* H 0 0 N N N 16.842 38.052 28.348 0.900 -1.133 -0.391 "H5'2" DUD 35 DUD HOA2 2HOA H 0 0 N N N 13.442 40.951 26.093 1.965 0.575 -3.651 HOA2 DUD 36 DUD HOB2 2HOB H 0 0 N N N 17.814 39.879 23.814 -2.214 0.536 -6.644 HOB2 DUD 37 DUD HOB3 3HOB H 0 0 N N N 16.527 37.808 23.060 0.692 0.742 -5.876 HOB3 DUD 38 # 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 DUD N1 C2 SING N N 1 DUD N1 C6 SING N N 2 DUD N1 "C1'" SING N N 3 DUD C2 N3 SING N N 4 DUD C2 O2 DOUB N N 5 DUD N3 C4 SING N N 6 DUD N3 HN3 SING N N 7 DUD C4 C5 SING N N 8 DUD C4 O4 DOUB N N 9 DUD C5 C6 DOUB N N 10 DUD C5 H5 SING N N 11 DUD C6 H6 SING N N 12 DUD "C1'" "C2'" SING N N 13 DUD "C1'" "O4'" SING N N 14 DUD "C1'" "H1'" SING N N 15 DUD "C2'" "C3'" SING N N 16 DUD "C2'" "H2'1" SING N N 17 DUD "C2'" "H2'2" SING N N 18 DUD "C3'" "C4'" SING N N 19 DUD "C3'" "O3'" SING N N 20 DUD "C3'" "H3'" SING N N 21 DUD "C4'" "O4'" SING N N 22 DUD "C4'" "C5'" SING N N 23 DUD "C4'" "H4'" SING N N 24 DUD "O3'" "HO3'" SING N N 25 DUD "C5'" "O5'" SING N N 26 DUD "C5'" "H5'1" SING N N 27 DUD "C5'" "H5'2" SING N N 28 DUD "O5'" PA SING N N 29 DUD PA O1A DOUB N N 30 DUD PA O2A SING N N 31 DUD PA O3A SING N N 32 DUD O2A HOA2 SING N N 33 DUD O3A PB SING N N 34 DUD PB O1B DOUB N N 35 DUD PB O2B SING N N 36 DUD PB O3B SING N N 37 DUD O2B HOB2 SING N N 38 DUD O3B HOB3 SING N N 39 # 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 DUD SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O" DUD SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P@@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" DUD SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O" DUD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@](=O)(O)OP(=O)(O)O)O" DUD SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)OP(=O)(O)O)O" DUD InChI InChI 1.03 "InChI=1S/C9H14N2O11P2/c12-5-3-8(11-2-1-7(13)10-9(11)14)21-6(5)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1" DUD InChIKey InChI 1.03 QHWZTVCCBMIIKE-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 DUD "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxyuridine 5'-(trihydrogen diphosphate) ; DUD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl phosphono 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 DUD "Create component" 1999-07-08 RCSB DUD "Modify descriptor" 2011-06-04 RCSB #