data_UBR
# 
_chem_comp.id                                    UBR 
_chem_comp.name                                  
;5-bromo-2'-deoxyuridine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H12 Br 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                     2008-03-26 
_chem_comp.pdbx_modified_date                    2009-04-07 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   OBS 
_chem_comp.pdbx_replaced_by                      BRU 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        387.078 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     UBR 
_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        1FYL 
_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 
UBR "O1'"  "O1'"  O  0 1 N Y N -0.077 1.871  16.784 5.070  -1.706 1.210  "O1'"  UBR 1  
UBR P      P      P  0 1 N N N -0.164 2.315  18.323 5.184  -1.253 -0.194 P      UBR 2  
UBR OP1    OP1    O  0 1 N N N 0.980  3.203  18.624 6.491  -0.327 -0.355 OP1    UBR 3  
UBR OP2    OP2    O  0 1 N N N -0.407 1.140  19.198 5.310  -2.533 -1.162 OP2    UBR 4  
UBR "O5'"  "O5'"  O  0 1 N N N -1.469 3.229  18.286 3.874  -0.406 -0.592 "O5'"  UBR 5  
UBR "C5'"  "C5'"  C  0 1 N N N -1.567 4.304  17.343 3.427  0.731  0.148  "C5'"  UBR 6  
UBR "C4'"  "C4'"  C  0 1 N N R -2.987 4.812  17.240 2.161  1.296  -0.498 "C4'"  UBR 7  
UBR "O4'"  "O4'"  O  0 1 N N N -3.824 3.864  16.538 1.052  0.390  -0.308 "O4'"  UBR 8  
UBR "C3'"  "C3'"  C  0 1 N N S -3.696 5.109  18.562 1.731  2.600  0.211  "C3'"  UBR 9  
UBR "O3'"  "O3'"  O  0 1 N N N -3.682 6.444  19.072 2.179  3.740  -0.524 "O3'"  UBR 10 
UBR "C2'"  "C2'"  C  0 1 N N N -5.028 4.380  18.474 0.187  2.532  0.217  "C2'"  UBR 11 
UBR "C1'"  "C1'"  C  0 1 N N R -5.157 3.980  17.014 -0.133 1.196  -0.489 "C1'"  UBR 12 
UBR N1     N1     N  0 1 N N N -5.830 2.667  16.823 -1.288 0.551  0.140  N1     UBR 13 
UBR C2     C2     C  0 1 N N N -7.025 2.614  16.125 -1.227 0.188  1.434  C2     UBR 14 
UBR O2     O2     O  0 1 N N N -7.557 3.589  15.609 -0.211 0.399  2.068  O2     UBR 15 
UBR N3     N3     N  0 1 N N N -7.577 1.361  16.040 -2.273 -0.406 2.037  N3     UBR 16 
UBR C4     C4     C  0 1 N N N -7.070 0.179  16.543 -3.407 -0.647 1.348  C4     UBR 17 
UBR O4     O4     O  0 1 N N N -7.677 -0.884 16.347 -4.355 -1.184 1.893  O4     UBR 18 
UBR C5     C5     C  0 1 N N N -5.824 0.318  17.266 -3.486 -0.271 -0.015 C5     UBR 19 
UBR C6     C6     C  0 1 N N N -5.268 1.527  17.351 -2.423 0.328  -0.594 C6     UBR 20 
UBR BR     BR     BR 0 0 N N N -5.088 -1.170 18.053 -5.061 -0.595 -1.009 BR     UBR 21 
UBR HOP1   HOP1   H  0 0 N N N 1.453  3.393  17.822 6.628  0.006  -1.252 HOP1   UBR 22 
UBR HOP2   HOP2   H  0 0 N N N -0.459 0.354  18.667 6.079  -3.090 -0.979 HOP2   UBR 23 
UBR "H5'"  "H5'"  H  0 1 N N N -0.917 5.128  17.673 3.210  0.434  1.174  "H5'"  UBR 24 
UBR "H5'A" "H5'A" H  0 0 N N N -1.256 3.932  16.355 4.207  1.493  0.148  "H5'A" UBR 25 
UBR "H4'"  "H4'"  H  0 1 N N N -2.864 5.765  16.705 2.327  1.478  -1.560 "H4'"  UBR 26 
UBR "H3'"  "H3'"  H  0 1 N N N -3.099 4.722  19.401 2.118  2.626  1.229  "H3'"  UBR 27 
UBR "HO3'" "HO3'" H  0 0 N N N -3.679 6.421  20.022 1.936  4.587  -0.124 "HO3'" UBR 28 
UBR "H2'"  "H2'"  H  0 1 N N N -5.038 3.496  19.128 -0.191 2.524  1.239  "H2'"  UBR 29 
UBR "H2'A" "H2'A" H  0 0 N N N -5.866 5.011  18.805 -0.234 3.370  -0.339 "H2'A" UBR 30 
UBR "H1'"  "H1'"  H  0 1 N N N -5.766 4.727  16.484 -0.320 1.362  -1.550 "H1'"  UBR 31 
UBR HN3    HN3    H  0 1 N N N -8.450 1.296  15.557 -2.211 -0.661 2.970  HN3    UBR 32 
UBR H6     H6     H  0 1 N N N -4.322 1.617  17.864 -2.466 0.626  -1.631 H6     UBR 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 
UBR "O1'" P      DOUB N N 1  
UBR "O5'" P      SING N N 2  
UBR P     OP1    SING N N 3  
UBR P     OP2    SING N N 4  
UBR OP1   HOP1   SING N N 5  
UBR OP2   HOP2   SING N N 6  
UBR "C5'" "O5'"  SING N N 7  
UBR "C4'" "C5'"  SING N N 8  
UBR "C5'" "H5'"  SING N N 9  
UBR "C5'" "H5'A" SING N N 10 
UBR "O4'" "C4'"  SING N N 11 
UBR "C4'" "C3'"  SING N N 12 
UBR "C4'" "H4'"  SING N N 13 
UBR "O4'" "C1'"  SING N N 14 
UBR "C2'" "C3'"  SING N N 15 
UBR "C3'" "O3'"  SING N N 16 
UBR "C3'" "H3'"  SING N N 17 
UBR "O3'" "HO3'" SING N N 18 
UBR "C1'" "C2'"  SING N N 19 
UBR "C2'" "H2'"  SING N N 20 
UBR "C2'" "H2'A" SING N N 21 
UBR N1    "C1'"  SING N N 22 
UBR "C1'" "H1'"  SING N N 23 
UBR C2    N1     SING N N 24 
UBR N1    C6     SING N N 25 
UBR O2    C2     DOUB N N 26 
UBR N3    C2     SING N N 27 
UBR N3    C4     SING N N 28 
UBR N3    HN3    SING N N 29 
UBR O4    C4     DOUB N N 30 
UBR C4    C5     SING N N 31 
UBR C5    C6     DOUB N N 32 
UBR C5    BR     SING N N 33 
UBR 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 
UBR SMILES           ACDLabs              10.04 "BrC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O"                                                                                              
UBR InChI            InChI                1.01  "InChI=1/C9H12BrN2O8P/c10-4-2-12(9(15)11-8(4)14)7-1-5(13)6(20-7)3-19-21(16,17)18/h2,5-7,13H,1,3H2,(H,11,14,15)(H2,16,17,18)/t5-,6+,7+/m0/s1" 
UBR SMILES_CANONICAL CACTVS               3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(Br)C(=O)NC2=O"                                                                                   
UBR SMILES           CACTVS               3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(Br)C(=O)NC2=O"                                                                                        
UBR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)Br)COP(=O)(O)O)O"                                                                                    
UBR SMILES           "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=C(C(=O)NC2=O)Br)COP(=O)(O)O)O"                                                                                                 
# 
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 
UBR "SYSTEMATIC NAME" ACDLabs              10.04 
;5-bromo-2'-deoxyuridine 5'-(dihydrogen phosphate)
;
UBR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(5-bromo-2,4-dioxo-pyrimidin-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 
UBR "Create component" 2008-03-26 RCSB 
# 
