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                    2008-10-15 
_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 InChI            InChI                1.02b InChI=1/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/f/h10,15-16H 
DU InChIKey         InChI                1.02b JSRLJPSBLDHEIO-KGOHLMIXDS                                                                                                                               
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                                                                                                                  
# 
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" 
# 
