data_URX
# 
_chem_comp.id                                    URX 
_chem_comp.name                                  "[(1R,3R,4R,5R,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]hept-1-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H17 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                     2010-10-11 
_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                        348.246 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     URX 
_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        3OZ4 
_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 
URX P      P      P 0 1 N N N 10.353 4.544  2.733 4.307  0.932  0.238  P      URX 1  
URX N1     N1     N 0 1 N N N 6.125  6.136  5.636 -2.412 0.221  0.331  N1     URX 2  
URX C2     C2     C 0 1 N N N 5.153  6.238  6.595 -3.695 -0.067 0.614  C2     URX 3  
URX O2     O2     O 0 1 N N N 4.257  7.177  6.537 -3.975 -1.148 1.095  O2     URX 4  
URX N3     N3     N 0 1 N N N 5.083  5.357  7.598 -4.674 0.826  0.374  N3     URX 5  
URX C4     C4     C 0 1 N N N 5.994  4.398  7.735 -4.379 2.030  -0.158 C4     URX 6  
URX O4     O4     O 0 1 N N N 5.895  3.603  8.696 -5.264 2.838  -0.375 O4     URX 7  
URX C5     C5     C 0 1 N N N 6.998  4.254  6.785 -3.033 2.345  -0.461 C5     URX 8  
URX C6     C6     C 0 1 N N N 7.035  5.138  5.714 -2.072 1.431  -0.210 C6     URX 9  
URX "C1'"  "C1'"  C 0 1 N N R 6.124  7.053  4.512 -1.368 -0.769 0.610  "C1'"  URX 10 
URX "C2'"  "C2'"  C 0 1 N N R 6.913  8.332  4.821 -1.279 -1.803 -0.557 "C2'"  URX 11 
URX "C3'"  "C3'"  C 0 1 N N S 8.261  7.869  4.540 -0.288 -1.022 -1.495 "C3'"  URX 12 
URX "O3'"  "O3'"  O 0 1 N N N 9.194  8.987  4.490 0.243  -1.850 -2.532 "O3'"  URX 13 
URX "C4'"  "C4'"  C 0 1 N N R 7.934  7.381  3.172 0.760  -0.738 -0.362 "C4'"  URX 14 
URX "O4'"  "O4'"  O 0 1 N N N 6.829  6.465  3.400 -0.078 -0.131 0.659  "O4'"  URX 15 
URX "C5'"  "C5'"  C 0 1 N N N 9.082  6.725  2.473 1.989  0.073  -0.777 "C5'"  URX 16 
URX "O5'"  "O5'"  O 0 1 N N N 9.632  5.756  3.358 2.902  0.151  0.320  "O5'"  URX 17 
URX "C6'"  "C6'"  C 0 1 N N R 6.699  9.268  3.663 -0.347 -2.919 0.012  "C6'"  URX 18 
URX "C7'"  "C7'"  C 0 1 N N N 5.288  9.599  3.384 -0.866 -3.416 1.363  "C7'"  URX 19 
URX "C8'"  "C8'"  C 0 1 N N N 7.371  8.597  2.507 1.031  -2.184 0.154  "C8'"  URX 20 
URX OP1    OP1    O 0 1 N N N 11.413 5.090  1.690 5.094  0.414  -0.903 OP1    URX 21 
URX OP2    OP2    O 0 1 N N N 11.038 3.688  3.887 4.035  2.506  0.032  OP2    URX 22 
URX OP3    OP3    O 0 1 N Y N 9.397  3.783  1.700 5.128  0.704  1.604  OP3    URX 23 
URX H5     H5     H 0 1 N N N 7.735  3.470  6.878 -2.778 3.303  -0.888 H5     URX 24 
URX H6     H6     H 0 1 N N N 7.787  5.029  4.947 -1.039 1.654  -0.434 H6     URX 25 
URX "H1'"  "H1'"  H 0 1 N N N 5.067  7.270  4.296 -1.574 -1.279 1.551  "H1'"  URX 26 
URX "H2'"  "H2'"  H 0 1 N N N 6.685  8.778  5.800 -2.222 -2.130 -0.995 "H2'"  URX 27 
URX "H3'"  "H3'"  H 0 1 N N N 8.731  7.166  5.244 -0.728 -0.106 -1.890 "H3'"  URX 28 
URX "HO3'" "HO3'" H 0 0 N Y N 10.068 8.663  4.305 -0.426 -2.207 -3.131 "HO3'" URX 29 
URX "H5'"  "H5'"  H 0 1 N N N 8.733  6.238  1.550 2.478  -0.413 -1.622 "H5'"  URX 30 
URX "H5'A" "H5'A" H 0 0 N N N 9.844  7.475  2.214 1.681  1.078  -1.066 "H5'A" URX 31 
URX "H6'"  "H6'"  H 0 1 N N N 7.125  10.257 3.887 -0.266 -3.746 -0.693 "H6'"  URX 32 
URX "H7'"  "H7'"  H 0 1 N N N 5.235  10.285 2.526 -1.915 -3.699 1.267  "H7'"  URX 33 
URX "H7'A" "H7'A" H 0 0 N N N 4.734  8.677  3.152 -0.284 -4.282 1.680  "H7'A" URX 34 
URX "H7'B" "H7'B" H 0 0 N N N 4.843  10.082 4.267 -0.770 -2.623 2.103  "H7'B" URX 35 
URX "H8'"  "H8'"  H 0 1 N N N 8.151  9.226  2.053 1.792  -2.670 -0.456 "H8'"  URX 36 
URX "H8'A" "H8'A" H 0 0 N N N 6.666  8.346  1.700 1.337  -2.163 1.201  "H8'A" URX 37 
URX HOP2   HOP2   H 0 0 N N N 11.977 3.656  3.743 3.524  2.913  0.744  HOP2   URX 38 
URX HOP3   HOP3   H 0 0 N Y N 9.738  3.884  0.819 5.988  1.147  1.625  HOP3   URX 39 
URX HN3    HN3    H 0 1 N N N 4.333  5.420  8.256 -5.594 0.603  0.585  HN3    URX 40 
# 
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 
URX OP1   P      DOUB N N 1  
URX OP3   P      SING N N 2  
URX P     "O5'"  SING N N 3  
URX P     OP2    SING N N 4  
URX "C1'" N1     SING N N 5  
URX N1    C6     SING N N 6  
URX N1    C2     SING N N 7  
URX O2    C2     DOUB N N 8  
URX C2    N3     SING N N 9  
URX N3    C4     SING N N 10 
URX C5    C4     SING N N 11 
URX C4    O4     DOUB N N 12 
URX C6    C5     DOUB N N 13 
URX C5    H5     SING N N 14 
URX C6    H6     SING N N 15 
URX "O4'" "C1'"  SING N N 16 
URX "C1'" "C2'"  SING N N 17 
URX "C1'" "H1'"  SING N N 18 
URX "C6'" "C2'"  SING N N 19 
URX "C3'" "C2'"  SING N N 20 
URX "C2'" "H2'"  SING N N 21 
URX "C4'" "C3'"  SING N N 22 
URX "O3'" "C3'"  SING N N 23 
URX "C3'" "H3'"  SING N N 24 
URX "O3'" "HO3'" SING N N 25 
URX "C5'" "C4'"  SING N N 26 
URX "C8'" "C4'"  SING N N 27 
URX "C4'" "O4'"  SING N N 28 
URX "C5'" "O5'"  SING N N 29 
URX "C5'" "H5'"  SING N N 30 
URX "C5'" "H5'A" SING N N 31 
URX "C8'" "C6'"  SING N N 32 
URX "C7'" "C6'"  SING N N 33 
URX "C6'" "H6'"  SING N N 34 
URX "C7'" "H7'"  SING N N 35 
URX "C7'" "H7'A" SING N N 36 
URX "C7'" "H7'B" SING N N 37 
URX "C8'" "H8'"  SING N N 38 
URX "C8'" "H8'A" SING N N 39 
URX OP2   HOP2   SING N N 40 
URX OP3   HOP3   SING N N 41 
URX N3    HN3    SING N N 42 
# 
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 
URX SMILES           ACDLabs              12.01 "O=P(O)(O)OCC23OC(N1C(=O)NC(=O)C=C1)C(C(C2)C)C3O"                                                                                                                       
URX SMILES_CANONICAL CACTVS               3.370 "C[C@@H]1C[C@]2(CO[P](O)(O)=O)O[C@H]([C@H]1[C@@H]2O)N3C=CC(=O)NC3=O"                                                                                                    
URX SMILES           CACTVS               3.370 "C[CH]1C[C]2(CO[P](O)(O)=O)O[CH]([CH]1[CH]2O)N3C=CC(=O)NC3=O"                                                                                                           
URX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C[C@@H]1C[C@]2([C@H]([C@@H]1[C@@H](O2)N3C=CC(=O)NC3=O)O)COP(=O)(O)O"                                                                                                   
URX SMILES           "OpenEye OEToolkits" 1.7.0 "CC1CC2(C(C1C(O2)N3C=CC(=O)NC3=O)O)COP(=O)(O)O"                                                                                                                         
URX InChI            InChI                1.03  "InChI=1S/C12H17N2O8P/c1-6-4-12(5-21-23(18,19)20)9(16)8(6)10(22-12)14-3-2-7(15)13-11(14)17/h2-3,6,8-10,16H,4-5H2,1H3,(H,13,15,17)(H2,18,19,20)/t6-,8-,9+,10-,12-/m1/s1" 
URX InChIKey         InChI                1.03  BIKPERMTZJFCSY-VOLLVAIWSA-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 
URX "SYSTEMATIC NAME" ACDLabs              12.01 "[(1R,3R,4R,5R,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]hept-1-yl]methyl dihydrogen phosphate" 
URX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(1R,2R,4R,6R,7S)-6-(2,4-dioxopyrimidin-1-yl)-7-hydroxy-2-methyl-5-oxabicyclo[2.2.1]heptan-4-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 
URX "Create component"  2010-10-11 RCSB 
URX "Modify descriptor" 2011-06-04 RCSB 
# 
