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" ? ? #