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 
# 
