data_DUP
# 
_chem_comp.id                                    DUP 
_chem_comp.name                                  
;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H16 N3 O13 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2003-12-17 
_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                        467.157 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     DUP 
_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        1RN8 
_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 
DUP O4     O4   O 0 1 N N N -4.608  33.070 2.415 -2.207 -0.898 8.166  O4     DUP 1  
DUP C4     C4   C 0 1 Y N N -5.557  32.595 3.067 -1.444 -0.540 7.287  C4     DUP 2  
DUP C5     C5   C 0 1 Y N N -6.573  33.399 3.592 -0.684 0.644  7.441  C5     DUP 3  
DUP C6     C6   C 0 1 Y N N -7.586  32.789 4.301 0.154  1.019  6.451  C6     DUP 4  
DUP N3     N3   N 0 1 Y N N -5.596  31.268 3.283 -1.314 -1.267 6.160  N3     DUP 5  
DUP C2     C2   C 0 1 Y N N -6.575  30.671 3.981 -0.474 -0.867 5.187  C2     DUP 6  
DUP O2     O2   O 0 1 N N N -6.536  29.438 4.169 -0.368 -1.534 4.175  O2     DUP 7  
DUP N1     N1   N 0 1 Y N N -7.610  31.446 4.498 0.256  0.253  5.322  N1     DUP 8  
DUP "C1'"  C1*  C 0 1 N N R -8.677  30.796 5.271 1.166  0.660  4.249  "C1'"  DUP 9  
DUP "C2'"  C2*  C 0 1 N N N -8.503  31.067 6.753 2.229  -0.432 4.002  "C2'"  DUP 10 
DUP "C3'"  C3*  C 0 1 N N S -9.491  32.167 7.069 2.432  -0.420 2.470  "C3'"  DUP 11 
DUP "O3'"  O3*  O 0 1 N N N -9.921  32.128 8.439 3.782  -0.084 2.146  "O3'"  DUP 12 
DUP "O4'"  O4*  O 0 1 N N N -9.921  31.364 4.899 0.453  0.771  2.998  "O4'"  DUP 13 
DUP "C4'"  C4*  C 0 1 N N R -10.597 31.928 6.041 1.466  0.677  1.969  "C4'"  DUP 14 
DUP "C5'"  C5*  C 0 1 N N N -11.423 33.160 5.672 0.835  0.273  0.635  "C5'"  DUP 15 
DUP "O5'"  O5*  O 0 1 N N N -10.593 34.233 5.217 -0.105 1.270  0.232  "O5'"  DUP 16 
DUP PA     PA   P 0 1 N N S -11.226 35.542 4.503 -0.727 0.783  -1.170 PA     DUP 17 
DUP O1A    O1A  O 0 1 N N N -12.301 36.064 5.415 -1.394 -0.525 -0.986 O1A    DUP 18 
DUP O2A    O2A  O 0 1 N N N -10.043 36.415 4.161 -1.802 1.865  -1.685 O2A    DUP 19 
DUP N3A    N3A  N 0 1 N N N -11.874 34.943 3.064 0.504  0.630  -2.306 N3A    DUP 20 
DUP PB     PB   P 0 1 N N R -13.457 35.135 2.564 -0.219 0.121  -3.738 PB     DUP 21 
DUP O1B    O1B  O 0 1 N N N -14.032 36.396 3.198 -0.893 -1.177 -3.515 O1B    DUP 22 
DUP O2B    O2B  O 0 1 N N N -13.443 35.114 1.080 -1.302 1.214  -4.210 O2B    DUP 23 
DUP O3B    O3B  O 0 1 N N N -14.204 33.801 3.087 0.905  -0.046 -4.877 O3B    DUP 24 
DUP PG     PG   P 0 1 N N N -15.321 33.739 4.265 0.147  -0.533 -6.212 PG     DUP 25 
DUP O2G    O2G  O 0 1 N N N -15.085 34.759 5.355 -0.854 0.481  -6.608 O2G    DUP 26 
DUP O1G    O1G  O 0 1 N N N -16.672 33.993 3.614 1.218  -0.722 -7.399 O1G    DUP 27 
DUP O3G    O3G  O 0 1 N N N -15.188 32.344 4.831 -0.592 -1.934 -5.928 O3G    DUP 28 
DUP H5     H5   H 0 1 N N N -6.575  34.492 3.449 -0.774 1.240  8.337  H5     DUP 29 
DUP H6     H6   H 0 1 N N N -8.404  33.395 4.724 0.742  1.920  6.551  H6     DUP 30 
DUP HN3    HN3  H 0 1 N N N -4.849  30.688 2.900 -1.831 -2.080 6.047  HN3    DUP 31 
DUP "H1'"  H1*  H 0 1 N N N -8.637  29.700 5.068 1.645  1.607  4.497  "H1'"  DUP 32 
DUP "H2'1" 1H2* H 0 0 N N N -8.615  30.161 7.393 1.862  -1.404 4.330  "H2'1" DUP 33 
DUP "H2'2" 2H2* H 0 0 N N N -7.454  31.303 7.048 3.160  -0.182 4.512  "H2'2" DUP 34 
DUP H1     H1   H 0 1 N N N -9.073  33.197 6.987 2.166  -1.386 2.042  H1     DUP 35 
DUP "H3'"  H3*  H 0 1 N N N -10.541 32.819 8.637 4.339  -0.786 2.508  "H3'"  DUP 36 
DUP "H4'"  H4*  H 0 1 N N N -11.371 31.249 6.469 1.992  1.626  1.867  "H4'"  DUP 37 
DUP "H5'1" 1H5* H 0 0 N N N -12.213 32.911 4.925 1.614  0.181  -0.121 "H5'1" DUP 38 
DUP "H5'2" 2H5* H 0 0 N N N -12.076 33.480 6.516 0.325  -0.683 0.749  "H5'2" DUP 39 
DUP H2A    H2A  H 0 1 N N N -10.414 37.182 3.742 -1.328 2.701  -1.791 H2A    DUP 40 
DUP H3A    H3A  H 0 1 N N N -11.684 33.940 3.053 0.859  1.559  -2.475 H3A    DUP 41 
DUP H2B    H2B  H 0 1 N N N -14.342 35.223 0.795 -0.822 2.043  -4.344 H2B    DUP 42 
DUP H1G    H1G  H 0 1 N N N -17.325 33.956 4.302 0.723  -1.013 -8.177 H1G    DUP 43 
DUP H3G    H3G  H 0 1 N N N -15.841 32.307 5.519 0.093  -2.566 -5.673 H3G    DUP 44 
# 
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 
DUP O4    C4     DOUB N N 1  
DUP C4    C5     SING Y N 2  
DUP C4    N3     SING Y N 3  
DUP C5    C6     DOUB Y N 4  
DUP C5    H5     SING N N 5  
DUP C6    N1     SING Y N 6  
DUP C6    H6     SING N N 7  
DUP N3    C2     SING Y N 8  
DUP N3    HN3    SING N N 9  
DUP C2    O2     DOUB N N 10 
DUP C2    N1     SING Y N 11 
DUP N1    "C1'"  SING N N 12 
DUP "C1'" "C2'"  SING N N 13 
DUP "C1'" "O4'"  SING N N 14 
DUP "C1'" "H1'"  SING N N 15 
DUP "C2'" "C3'"  SING N N 16 
DUP "C2'" "H2'1" SING N N 17 
DUP "C2'" "H2'2" SING N N 18 
DUP "C3'" "O3'"  SING N N 19 
DUP "C3'" "C4'"  SING N N 20 
DUP "C3'" H1     SING N N 21 
DUP "O3'" "H3'"  SING N N 22 
DUP "O4'" "C4'"  SING N N 23 
DUP "C4'" "C5'"  SING N N 24 
DUP "C4'" "H4'"  SING N N 25 
DUP "C5'" "O5'"  SING N N 26 
DUP "C5'" "H5'1" SING N N 27 
DUP "C5'" "H5'2" SING N N 28 
DUP "O5'" PA     SING N N 29 
DUP PA    O1A    DOUB N N 30 
DUP PA    O2A    SING N N 31 
DUP PA    N3A    SING N N 32 
DUP O2A   H2A    SING N N 33 
DUP N3A   PB     SING N N 34 
DUP N3A   H3A    SING N N 35 
DUP PB    O1B    DOUB N N 36 
DUP PB    O2B    SING N N 37 
DUP PB    O3B    SING N N 38 
DUP O2B   H2B    SING N N 39 
DUP O3B   PG     SING N N 40 
DUP PG    O2G    DOUB N N 41 
DUP PG    O1G    SING N N 42 
DUP PG    O3G    SING N N 43 
DUP O1G   H1G    SING N N 44 
DUP O3G   H3G    SING N N 45 
# 
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 
DUP SMILES           ACDLabs              10.04 "O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O"                                                                                                                                 
DUP SMILES_CANONICAL CACTVS               3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)N[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                             
DUP SMILES           CACTVS               3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                                    
DUP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O"                                                                                                             
DUP SMILES           "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                                 
DUP InChI            InChI                1.03  "InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1" 
DUP InChIKey         InChI                1.03  XZLLMTSKYYYJLH-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 
DUP "SYSTEMATIC NAME" ACDLabs              10.04 "2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine"                                     
DUP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methoxy-N-(hydroxy-phosphonooxy-phosphoryl)phosphonamidic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
DUP "Create component"  2003-12-17 RCSB 
DUP "Modify descriptor" 2011-06-04 RCSB 
# 
