data_DUN
# 
_chem_comp.id                                    DUN 
_chem_comp.name                                  
;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H15 N3 O10 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "2,4(1H,3H)-PYRIMIDINEDIONE; 1-[2-DEOXY-5-O-[HYDROXY(PHOSPHONOAMINO)PHOSPHINYL]-BETA-D-ERYTHRO-PENTOFURANOSYL]-" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2004-07-09 
_chem_comp.pdbx_modified_date                    2020-01-26 
_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                        387.177 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     DUN 
_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        1W2Y 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
DUN N1     N1   N 0 1 Y N N 60.018 56.627 17.009 0.151  0.295  3.767  N1     DUN 1  
DUN C2     C2   C 0 1 Y N N 60.190 55.256 17.026 -0.862 -0.546 3.493  C2     DUN 2  
DUN N3     N3   N 0 1 Y N N 59.766 54.570 18.098 -1.931 -0.629 4.306  N3     DUN 3  
DUN C4     C4   C 0 1 Y N N 59.166 55.137 19.179 -2.007 0.141  5.410  C4     DUN 4  
DUN C5     C5   C 0 1 Y N N 58.983 56.528 19.159 -0.950 1.035  5.707  C5     DUN 5  
DUN C6     C6   C 0 1 Y N N 59.435 57.215 18.077 0.112  1.094  4.876  C6     DUN 6  
DUN O2     O2   O 0 1 N N N 60.727 54.722 16.025 -0.807 -1.247 2.501  O2     DUN 7  
DUN O4     O4   O 0 1 N N N 58.799 54.461 20.150 -2.976 0.070  6.144  O4     DUN 8  
DUN "C1'"  C1*  C 0 1 N N R 60.506 57.403 15.868 1.304  0.360  2.865  "C1'"  DUN 9  
DUN "C2'"  C2*  C 0 1 N N N 59.881 57.057 14.533 1.997  -1.017 2.778  "C2'"  DUN 10 
DUN "C3'"  C3*  C 0 1 N N S 59.961 58.353 13.762 2.438  -1.123 1.301  "C3'"  DUN 11 
DUN "C4'"  C4*  C 0 1 N N R 60.321 59.436 14.798 1.960  0.201  0.667  "C4'"  DUN 12 
DUN "O4'"  O4*  O 0 1 N N N 60.317 58.800 16.080 0.874  0.643  1.516  "O4'"  DUN 13 
DUN "O3'"  O3*  O 0 1 N N N 61.018 58.241 12.781 3.860  -1.236 1.211  "O3'"  DUN 14 
DUN "C5'"  C5*  C 0 1 N N N 59.406 60.642 14.845 1.459  -0.032 -0.758 "C5'"  DUN 15 
DUN "O5'"  O5*  O 0 1 N N N 59.882 61.534 15.896 0.956  1.193  -1.294 "O5'"  DUN 16 
DUN PA     PA   P 0 1 N N R 59.191 62.959 16.078 0.449  0.875  -2.788 PA     DUN 17 
DUN O1A    O1A  O 0 1 N N N 57.729 62.872 15.691 -0.133 2.219  -3.455 O1A    DUN 18 
DUN O2A    O2A  O 0 1 N N N 59.537 63.307 17.502 1.583  0.374  -3.598 O2A    DUN 19 
DUN PB     PB   P 0 1 N N N 60.005 64.025 13.450 -1.235 -0.571 -4.324 PB     DUN 20 
DUN O1B    O1B  O 0 1 N N N 61.041 62.923 13.142 -2.397 -1.686 -4.349 O1B    DUN 21 
DUN O2B    O2B  O 0 1 N N N 60.464 65.360 12.986 -0.076 -1.050 -5.110 O2B    DUN 22 
DUN O3B    O3B  O 0 1 N N N 58.602 63.647 12.949 -1.790 0.796  -4.965 O3B    DUN 23 
DUN N3A    N3A  N 0 1 N N N 60.020 64.057 15.102 -0.759 -0.293 -2.734 N3A    DUN 24 
DUN H3     H3   H 0 1 N N N 59.902 53.559 18.103 -2.651 -1.243 4.096  H3     DUN 25 
DUN H5     H5   H 0 1 N N N 58.487 57.048 19.996 -0.992 1.660  6.586  H5     DUN 26 
DUN H6     H6   H 0 1 N N N 59.320 58.312 18.070 0.928  1.770  5.087  H6     DUN 27 
DUN "H1'"  H1*  H 0 1 N N N 61.603 57.222 15.783 2.009  1.118  3.206  "H1'"  DUN 28 
DUN "H2'1" 1H2* H 0 0 N N N 58.857 56.622 14.601 1.295  -1.814 3.025  "H2'1" DUN 29 
DUN "H2'2" 2H2* H 0 0 N N N 60.344 56.183 14.018 2.863  -1.052 3.439  "H2'2" DUN 30 
DUN "H3'"  H3*  H 0 1 N N N 58.987 58.583 13.271 1.957  -1.973 0.818  "H3'"  DUN 31 
DUN "H4'"  H4*  H 0 1 N N N 61.357 59.791 14.587 2.766  0.935  0.670  "H4'"  DUN 32 
DUN HA     HA   H 0 1 N N N 61.068 59.056 12.296 4.102  -2.064 1.647  HA     DUN 33 
DUN "H5'1" 1H5* H 0 0 N N N 58.334 60.363 14.970 2.282  -0.388 -1.378 "H5'1" DUN 34 
DUN "H5'2" 2H5* H 0 0 N N N 59.315 61.151 13.857 0.664  -0.777 -0.747 "H5'2" DUN 35 
DUN H1A    H1A  H 0 1 N N N 57.317 63.721 15.800 -0.867 2.511  -2.899 H1A    DUN 36 
DUN H1B    H1B  H 0 1 N N N 60.748 62.070 13.439 -2.640 -1.815 -5.276 H1B    DUN 37 
DUN H3B    H3B  H 0 1 N N N 57.964 64.325 13.139 -2.543 1.073  -4.425 H3B    DUN 38 
DUN H3A    H3A  H 0 1 N N N 60.565 64.787 15.561 -0.326 -1.144 -2.408 H3A    DUN 39 
# 
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 
DUN N1    C2     SING Y N 1  
DUN N1    C6     SING Y N 2  
DUN N1    "C1'"  SING N N 3  
DUN C2    N3     SING Y N 4  
DUN C2    O2     DOUB N N 5  
DUN N3    C4     SING Y N 6  
DUN N3    H3     SING N N 7  
DUN C4    C5     SING Y N 8  
DUN C4    O4     DOUB N N 9  
DUN C5    C6     DOUB Y N 10 
DUN C5    H5     SING N N 11 
DUN C6    H6     SING N N 12 
DUN "C1'" "C2'"  SING N N 13 
DUN "C1'" "O4'"  SING N N 14 
DUN "C1'" "H1'"  SING N N 15 
DUN "C2'" "C3'"  SING N N 16 
DUN "C2'" "H2'1" SING N N 17 
DUN "C2'" "H2'2" SING N N 18 
DUN "C3'" "C4'"  SING N N 19 
DUN "C3'" "O3'"  SING N N 20 
DUN "C3'" "H3'"  SING N N 21 
DUN "C4'" "O4'"  SING N N 22 
DUN "C4'" "C5'"  SING N N 23 
DUN "C4'" "H4'"  SING N N 24 
DUN "O3'" HA     SING N N 25 
DUN "C5'" "O5'"  SING N N 26 
DUN "C5'" "H5'1" SING N N 27 
DUN "C5'" "H5'2" SING N N 28 
DUN "O5'" PA     SING N N 29 
DUN PA    O1A    SING N N 30 
DUN PA    O2A    DOUB N N 31 
DUN PA    N3A    SING N N 32 
DUN O1A   H1A    SING N N 33 
DUN PB    O1B    SING N N 34 
DUN PB    O2B    DOUB N N 35 
DUN PB    O3B    SING N N 36 
DUN PB    N3A    SING N N 37 
DUN O1B   H1B    SING N N 38 
DUN O3B   H3B    SING N N 39 
DUN N3A   H3A    SING N N 40 
# 
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 
DUN SMILES           ACDLabs              10.04 "O=P(O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O"                                                                                                                    
DUN SMILES_CANONICAL CACTVS               3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P@@](O)(=O)N[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                  
DUN SMILES           CACTVS               3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(=O)N[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                         
DUN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@@](=O)(NP(=O)(O)O)O)O"                                                                                                   
DUN SMILES           "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)O)O)O"                                                                                                                    
DUN InChI            InChI                1.03  "InChI=1S/C9H15N3O10P2/c13-5-3-8(12-2-1-7(14)10-9(12)15)22-6(5)4-21-24(19,20)11-23(16,17)18/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H4,11,16,17,18,19,20)/t5-,6+,8+/m0/s1" 
DUN InChIKey         InChI                1.03  COFNIXBQVWFHTR-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 
DUN "SYSTEMATIC NAME" ACDLabs              10.04 "2'-deoxy-5'-O-[(R)-hydroxy(phosphonoamino)phosphoryl]uridine"                                                     
DUN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[[(2R,3S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]amino]phosphonic 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 
DUN "Create component"  2004-07-09 EBI  
DUN "Modify descriptor" 2011-06-04 RCSB 
DUN "Modify synonyms"   2019-12-17 PDBE 
DUN "Modify synonyms"   2020-01-26 RCSB 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 DUN "1-[2-DEOXY-5-O-[HYDROXY(PHOSPHONOAMINO)PHOSPHINYL]-BETA-D-ERYTHRO-PENTOFURANOSYL]-" ? ? 
2 DUN "2,4(1H,3H)-PYRIMIDINEDIONE"                                                         ? ? 
# 
