data_DAU # _chem_comp.id DAU _chem_comp.name "2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H26 N2 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-11-16 _chem_comp.pdbx_modified_date 2012-05-16 _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 564.329 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DAU _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 1G1L _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 DAU O6 O6 O 0 1 N N N 47.805 16.783 19.152 -3.106 2.914 2.683 O6 DAU 1 DAU C6 C6 C 0 1 N N N 48.107 16.991 20.534 -3.867 3.428 1.588 C6 DAU 2 DAU C5 C5 C 0 1 N N R 47.813 18.385 21.062 -4.089 2.321 0.556 C5 DAU 3 DAU O5 O5 O 0 1 N N N 46.425 18.650 20.987 -4.898 1.291 1.128 O5 DAU 4 DAU C4 C4 C 0 1 N N S 48.326 18.480 22.512 -4.796 2.901 -0.672 C4 DAU 5 DAU O4 O4 O 0 1 N N N 49.769 18.450 22.548 -3.963 3.890 -1.280 O4 DAU 6 DAU C3 C3 C 0 1 N N S 47.837 19.754 23.161 -5.068 1.775 -1.674 C3 DAU 7 DAU O3 O3 O 0 1 N N N 48.179 19.731 24.529 -5.793 2.294 -2.791 O3 DAU 8 DAU C2 C2 C 0 1 N N R 46.362 19.912 23.036 -5.896 0.684 -0.988 C2 DAU 9 DAU O2 O2 O 0 1 N N N 45.956 21.146 23.573 -6.094 -0.405 -1.892 O2 DAU 10 DAU C1 C1 C 0 1 N N R 45.928 19.796 21.581 -5.146 0.190 0.252 C1 DAU 11 DAU O1 O1 O 0 1 N N N 46.500 20.867 20.851 -3.904 -0.394 -0.144 O1 DAU 12 DAU P2 P2 P 0 1 N N N 45.813 21.446 19.521 -3.194 -1.584 0.675 P2 DAU 13 DAU O3P O3P O 0 1 N N N 44.286 21.602 19.953 -3.015 -1.174 2.086 O3P DAU 14 DAU O4P O4P O 0 1 N N N 46.622 22.673 18.957 -4.115 -2.903 0.613 O4P DAU 15 DAU OPP OPP O 0 1 N N N 45.566 20.364 18.427 -1.757 -1.902 0.023 OPP DAU 16 DAU P P P 0 1 N N N 44.235 20.603 17.491 -0.461 -2.721 0.515 P DAU 17 DAU O1P O1P O 0 1 N N N 43.798 22.126 17.528 -0.227 -2.456 1.952 O1P DAU 18 DAU O2P O2P O 0 1 N N N 44.786 19.749 16.252 -0.705 -4.297 0.293 O2P DAU 19 DAU "O5'" "O5'" O 0 1 N N N 42.924 19.924 18.176 0.825 -2.253 -0.333 "O5'" DAU 20 DAU "C5'" "C5'" C 0 1 N N N 42.973 18.560 18.544 2.148 -2.719 -0.062 "C5'" DAU 21 DAU "C4'" "C4'" C 0 1 N N R 41.748 17.844 18.033 3.126 -2.079 -1.050 "C4'" DAU 22 DAU "O4'" "O4'" O 0 1 N N N 40.585 18.231 18.751 3.216 -0.655 -0.826 "O4'" DAU 23 DAU "C3'" "C3'" C 0 1 N N S 41.472 18.145 16.576 4.570 -2.578 -0.788 "C3'" DAU 24 DAU "O3'" "O3'" O 0 1 N N N 40.918 16.932 16.011 4.822 -3.800 -1.484 "O3'" DAU 25 DAU "C2'" "C2'" C 0 1 N N N 40.530 19.310 16.744 5.422 -1.424 -1.371 "C2'" DAU 26 DAU "C1'" "C1'" C 0 1 N N R 39.634 18.880 17.893 4.462 -0.219 -1.393 "C1'" DAU 27 DAU N11 N11 N 0 1 N N N 38.990 19.885 18.768 5.018 0.875 -0.593 N11 DAU 28 DAU C61 C61 C 0 1 N N N 39.700 20.926 19.249 5.361 2.052 -1.200 C61 DAU 29 DAU C51 C51 C 0 1 N N N 39.096 21.833 20.102 5.873 3.061 -0.462 C51 DAU 30 DAU C5A C5A C 0 1 N N N 39.892 23.008 20.676 6.256 4.365 -1.113 C5A DAU 31 DAU C21 C21 C 0 1 N N N 37.690 19.754 19.133 5.181 0.715 0.733 C21 DAU 32 DAU O21 O21 O 0 1 N N N 36.971 18.766 18.681 4.865 -0.338 1.253 O21 DAU 33 DAU N31 N31 N 0 1 N N N 37.090 20.611 19.985 5.688 1.704 1.492 N31 DAU 34 DAU C41 C41 C 0 1 N N N 37.783 21.635 20.467 6.044 2.877 0.931 C41 DAU 35 DAU O41 O41 O 0 1 N N N 37.219 22.468 21.295 6.503 3.772 1.617 O41 DAU 36 DAU HO6 HO6 H 0 1 N N N 48.020 15.889 18.912 -2.928 3.563 3.377 HO6 DAU 37 DAU HC61 HC61 H 0 0 N N N 47.516 16.274 21.122 -4.831 3.785 1.951 HC61 DAU 38 DAU HC62 HC62 H 0 0 N N N 49.179 16.791 20.681 -3.326 4.253 1.125 HC62 DAU 39 DAU HC5 HC5 H 0 1 N N N 48.367 19.114 20.452 -3.127 1.903 0.258 HC5 DAU 40 DAU HC4 HC4 H 0 1 N N N 47.927 17.624 23.075 -5.739 3.355 -0.368 HC4 DAU 41 DAU HO4 HO4 H 0 1 N N N 50.065 18.510 23.449 -4.349 4.301 -2.065 HO4 DAU 42 DAU HC3 HC3 H 0 1 N N N 48.327 20.607 22.668 -4.122 1.355 -2.017 HC3 DAU 43 DAU HO3 HO3 H 0 1 N N N 47.875 20.529 24.945 -6.000 1.634 -3.467 HO3 DAU 44 DAU HC2 HC2 H 0 1 N N N 45.881 19.096 23.596 -6.862 1.092 -0.692 HC2 DAU 45 DAU HO2 HO2 H 0 1 N N N 45.014 21.235 23.487 -6.612 -1.133 -1.522 HO2 DAU 46 DAU HC1 HC1 H 0 1 N N N 44.830 19.830 21.526 -5.750 -0.556 0.768 HC1 DAU 47 DAU H4PO H4PO H 0 0 N N N 46.061 23.439 18.934 -4.275 -3.229 -0.284 H4PO DAU 48 DAU H2PO H2PO H 0 0 N N N 44.825 20.300 15.479 -0.866 -4.544 -0.628 H2PO DAU 49 DAU HC51 HC51 H 0 0 N N N 43.872 18.098 18.111 2.428 -2.446 0.955 HC51 DAU 50 DAU HC52 HC52 H 0 0 N N N 43.011 18.480 19.640 2.180 -3.803 -0.170 HC52 DAU 51 DAU "H4'C" "H4'C" H 0 0 N N N 41.907 16.761 18.140 2.826 -2.288 -2.076 "H4'C" DAU 52 DAU "H3'C" "H3'C" H 0 0 N N N 42.392 18.455 16.059 4.753 -2.695 0.280 "H3'C" DAU 53 DAU "H3'O" "H3'O" H 0 0 N N N 40.726 17.070 15.091 5.713 -4.152 -1.351 "H3'O" DAU 54 DAU HC21 HC21 H 0 0 N N N 41.081 20.228 16.998 6.278 -1.219 -0.728 HC21 DAU 55 DAU HC22 HC22 H 0 0 N N N 39.943 19.476 15.829 5.753 -1.667 -2.381 HC22 DAU 56 DAU "H1'C" "H1'C" H 0 0 N N N 38.885 18.162 17.527 4.307 0.112 -2.420 "H1'C" DAU 57 DAU H61C H61C H 0 0 N N N 40.736 21.051 18.970 5.224 2.174 -2.264 H61C DAU 58 DAU H5A1 H5A1 H 0 0 N N N 39.240 23.610 21.326 5.401 5.040 -1.106 H5A1 DAU 59 DAU H5A2 H5A2 H 0 0 N N N 40.741 22.625 21.261 7.081 4.817 -0.562 H5A2 DAU 60 DAU H5A3 H5A3 H 0 0 N N N 40.267 23.634 19.853 6.565 4.180 -2.142 H5A3 DAU 61 DAU H31N H31N H 0 0 N N N 36.135 20.476 20.250 5.799 1.571 2.447 H31N DAU 62 # 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 DAU O6 C6 SING N N 1 DAU O6 HO6 SING N N 2 DAU C6 C5 SING N N 3 DAU C6 HC61 SING N N 4 DAU C6 HC62 SING N N 5 DAU C5 O5 SING N N 6 DAU C5 C4 SING N N 7 DAU C5 HC5 SING N N 8 DAU O5 C1 SING N N 9 DAU C4 O4 SING N N 10 DAU C4 C3 SING N N 11 DAU C4 HC4 SING N N 12 DAU O4 HO4 SING N N 13 DAU C3 O3 SING N N 14 DAU C3 C2 SING N N 15 DAU C3 HC3 SING N N 16 DAU O3 HO3 SING N N 17 DAU C2 O2 SING N N 18 DAU C2 C1 SING N N 19 DAU C2 HC2 SING N N 20 DAU O2 HO2 SING N N 21 DAU C1 O1 SING N N 22 DAU C1 HC1 SING N N 23 DAU O1 P2 SING N N 24 DAU P2 O3P DOUB N N 25 DAU P2 O4P SING N N 26 DAU P2 OPP SING N N 27 DAU O4P H4PO SING N N 28 DAU OPP P SING N N 29 DAU P O1P DOUB N N 30 DAU P O2P SING N N 31 DAU P "O5'" SING N N 32 DAU O2P H2PO SING N N 33 DAU "O5'" "C5'" SING N N 34 DAU "C5'" "C4'" SING N N 35 DAU "C5'" HC51 SING N N 36 DAU "C5'" HC52 SING N N 37 DAU "C4'" "O4'" SING N N 38 DAU "C4'" "C3'" SING N N 39 DAU "C4'" "H4'C" SING N N 40 DAU "O4'" "C1'" SING N N 41 DAU "C3'" "O3'" SING N N 42 DAU "C3'" "C2'" SING N N 43 DAU "C3'" "H3'C" SING N N 44 DAU "O3'" "H3'O" SING N N 45 DAU "C2'" "C1'" SING N N 46 DAU "C2'" HC21 SING N N 47 DAU "C2'" HC22 SING N N 48 DAU "C1'" N11 SING N N 49 DAU "C1'" "H1'C" SING N N 50 DAU N11 C61 SING N N 51 DAU N11 C21 SING N N 52 DAU C61 C51 DOUB N N 53 DAU C61 H61C SING N N 54 DAU C51 C5A SING N N 55 DAU C51 C41 SING N N 56 DAU C5A H5A1 SING N N 57 DAU C5A H5A2 SING N N 58 DAU C5A H5A3 SING N N 59 DAU C21 O21 DOUB N N 60 DAU C21 N31 SING N N 61 DAU N31 C41 SING N N 62 DAU N31 H31N SING N N 63 DAU C41 O41 DOUB N N 64 # 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 DAU SMILES ACDLabs 12.01 "O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)CO)O)O)C" DAU InChI InChI 1.03 "InChI=1S/C16H26N2O16P2/c1-6-3-18(16(25)17-14(6)24)10-2-7(20)9(31-10)5-30-35(26,27)34-36(28,29)33-15-13(23)12(22)11(21)8(4-19)32-15/h3,7-13,15,19-23H,2,4-5H2,1H3,(H,26,27)(H,28,29)(H,17,24,25)/t7-,8+,9+,10+,11+,12-,13+,15+/m0/s1" DAU InChIKey InChI 1.03 YSYKRGRSMLTJNL-URARBOGNSA-N DAU SMILES_CANONICAL CACTVS 3.370 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=O" DAU SMILES CACTVS 3.370 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)O2)C(=O)NC1=O" DAU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O" DAU SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)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 DAU "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" DAU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen 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 DAU "Create component" 2000-11-16 RCSB DAU "Modify descriptor" 2011-06-04 RCSB DAU "Modify atom id" 2012-05-16 RCSB #