data_05H # _chem_comp.id 05H _chem_comp.name "[(1R,3R,4R,7S)-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-[2-[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylamino]-2-oxidanylidene-ethyl]-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C23 H30 N5 O13 P" _chem_comp.mon_nstd_parent_comp_id "DT, DT" _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-05-28 _chem_comp.pdbx_modified_date 2023-03-09 _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 615.484 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 05H _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 7OOQ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 05H C1 C1 C 0 1 N N N 10.014 16.377 5.858 0.110 -0.472 -0.849 C1 05H 1 05H "C1'" C2 C 0 1 N N R 8.011 19.341 2.849 5.673 0.135 -1.378 "C1'" 05H 2 05H C5A C3 C 0 1 N N N 14.800 20.918 5.875 -5.825 -3.225 -2.036 C5A 05H 3 05H C2 C4 C 0 1 N N N 9.450 20.771 1.340 6.448 -0.489 0.840 C2 05H 4 05H "C2'" C5 C 0 1 N N N 7.196 18.623 1.783 5.983 -1.230 -2.030 "C2'" 05H 5 05H C21 C6 C 0 1 N N N 10.648 21.722 5.783 -3.935 -3.276 1.747 C21 05H 6 05H C3 C7 C 0 1 N N N 9.198 18.389 9.389 -2.359 1.575 1.732 C3 05H 7 05H "C3'" C8 C 0 1 N N S 7.446 17.165 2.071 4.602 -1.748 -2.491 "C3'" 05H 8 05H C4 C9 C 0 1 N N N 11.762 20.611 1.378 8.097 0.710 1.981 C4 05H 9 05H "C4'" C10 C 0 1 N N R 7.639 17.116 3.562 3.621 -0.634 -2.062 "C4'" 05H 10 05H C41 C11 C 0 1 N N N 12.726 22.093 4.837 -5.000 -4.447 0.029 C41 05H 11 05H C5 C12 C 0 1 N N N 11.659 19.575 2.417 8.192 1.601 0.885 C5 05H 12 05H "C5'" C13 C 0 1 N N N 8.571 15.975 3.906 2.303 -1.243 -1.579 "C5'" 05H 13 05H C51 C14 C 0 1 N N N 13.328 21.207 5.851 -5.150 -3.236 -0.689 C51 05H 14 05H C6 C15 C 0 1 N N N 10.409 19.211 2.858 7.403 1.403 -0.193 C6 05H 15 05H C61 C16 C 0 1 N N N 12.504 20.636 6.791 -4.681 -2.091 -0.149 C61 05H 16 05H C5M C17 C 0 1 N N N 12.885 18.926 2.987 9.161 2.755 0.920 C5M 05H 17 05H C11 C18 C 0 1 N N N 10.026 16.563 7.346 -0.873 0.631 -0.552 C11 05H 18 05H N1 N1 N 0 1 N N N 9.317 19.777 2.339 6.529 0.350 -0.208 N1 05H 19 05H N11 N2 N 0 1 N N N 11.191 20.872 6.763 -4.071 -2.118 1.075 N11 05H 20 05H N3 N3 N 0 1 N N N 10.649 21.147 0.903 7.223 -0.315 1.927 N3 05H 21 05H N31 N4 N 0 1 N N N 11.417 22.297 4.862 -4.393 -4.432 1.233 N31 05H 22 05H "N5'" N5 N 0 1 N N N 8.830 16.170 5.313 1.347 -0.171 -1.291 "N5'" 05H 23 05H O2 O1 O 0 1 N N N 8.463 21.337 0.832 5.661 -1.415 0.807 O2 05H 24 05H "O2'" O2 O 0 1 N N N 8.570 18.780 8.163 -1.632 0.410 2.171 "O2'" 05H 25 05H O21 O3 O 0 1 N N N 9.425 21.952 5.765 -3.386 -3.279 2.832 O21 05H 26 05H O1 O4 O 0 1 N N N 11.044 16.436 5.215 -0.210 -1.630 -0.684 O1 05H 27 05H "O3'" O5 O 0 1 N N N 6.389 16.276 1.647 4.579 -1.917 -3.910 "O3'" 05H 28 05H O4 O6 O 0 1 N N N 12.871 20.976 0.950 8.798 0.869 2.964 O4 05H 29 05H "O4'" O7 O 0 1 N N N 8.221 18.380 3.891 4.288 0.047 -0.978 "O4'" 05H 30 05H O41 O8 O 0 1 N N N 13.426 22.637 3.964 -5.415 -5.493 -0.437 O41 05H 31 05H "O5'" O9 O 0 1 N N N 12.889 17.632 9.246 -4.435 3.155 0.213 "O5'" 05H 32 05H OP1 O10 O 0 1 N N N 14.023 16.203 11.000 -5.892 4.008 -1.663 OP1 05H 33 05H OP2 O11 O 0 1 N N N 15.561 17.326 9.311 -6.018 5.227 0.543 OP2 05H 34 05H P P1 P 0 1 N N N 14.189 17.399 10.157 -5.080 4.443 -0.504 P 05H 35 05H "C1'1" C19 C 0 0 N N R 10.304 20.266 7.758 -3.562 -0.876 1.661 "C1'1" 05H 36 05H "C2'1" C20 C 0 0 N N R 9.610 19.030 7.233 -2.049 -0.697 1.321 "C2'1" 05H 37 05H "C3'1" C21 C 0 0 N N S 10.587 17.947 7.560 -2.191 0.023 -0.069 "C3'1" 05H 38 05H "C4'1" C22 C 0 0 N N R 10.659 18.381 8.990 -3.184 1.106 0.493 "C4'1" 05H 39 05H "C5'1" C23 C 0 0 N N N 11.601 17.555 9.841 -3.636 2.195 -0.482 "C5'1" 05H 40 05H "O4'1" O12 O 0 0 N N N 11.047 19.745 8.859 -4.224 0.264 1.069 "O4'1" 05H 41 05H "H1'" H1 H 0 1 N N N 7.443 20.205 3.225 5.809 0.941 -2.100 "H1'" 05H 42 05H H5A1 H2 H 0 0 N N N 15.027 20.238 6.709 -6.131 -4.238 -2.297 H5A1 05H 43 05H H5A2 H3 H 0 0 N N N 15.096 20.446 4.927 -6.701 -2.579 -1.999 H5A2 05H 44 05H H5A3 H4 H 0 0 N N N 15.356 21.858 6.006 -5.129 -2.851 -2.788 H5A3 05H 45 05H "H2'1" H5 H 0 0 N N N 7.545 18.890 0.775 6.648 -1.103 -2.885 "H2'1" 05H 46 05H "H2'2" H6 H 0 0 N N N 6.127 18.864 1.876 6.423 -1.911 -1.301 "H2'2" 05H 47 05H HC31 H7 H 0 0 N N N 9.004 19.117 10.190 -3.026 1.923 2.520 HC31 05H 48 05H HC32 H8 H 0 0 N N N 8.864 17.392 9.712 -1.666 2.367 1.446 HC32 05H 49 05H "H3'" H9 H 0 1 N N N 8.388 16.869 1.586 4.359 -2.685 -1.990 "H3'" 05H 50 05H "H4'" H10 H 0 1 N N N 6.671 16.978 4.066 3.442 0.053 -2.889 "H4'" 05H 51 05H "H5'1" H11 H 0 0 N N N 8.088 15.003 3.725 1.897 -1.893 -2.354 "H5'1" 05H 52 05H "H5'2" H12 H 0 0 N N N 9.501 16.036 3.322 2.481 -1.824 -0.674 "H5'2" 05H 53 05H H6 H13 H 0 1 N N N 10.310 18.462 3.630 7.462 2.072 -1.038 H6 05H 54 05H H61 H14 H 0 1 N N N 12.920 19.995 7.554 -4.787 -1.157 -0.682 H61 05H 55 05H H52 H16 H 0 1 N N N 12.590 18.185 3.744 9.703 2.745 1.866 H52 05H 56 05H H53 H17 H 0 1 N N N 13.443 18.425 2.182 9.868 2.661 0.096 H53 05H 57 05H HN3 H22 H 0 1 N N N 10.711 21.853 0.197 7.152 -0.929 2.674 HN3 05H 58 05H H31 H23 H 0 1 N N N 11.000 22.894 4.177 -4.287 -5.258 1.730 H31 05H 59 05H "HN5'" H24 H 0 0 N N N 8.043 16.146 5.929 1.605 0.756 -1.419 "HN5'" 05H 60 05H "HO3'" H25 H 0 0 N Y N 6.622 15.381 1.863 5.219 -2.562 -4.240 "HO3'" 05H 61 05H HOP2 H26 H 0 0 N N N 16.016 16.517 9.513 -6.441 6.017 0.178 HOP2 05H 62 05H H1 H27 H 0 1 N N N 9.555 20.996 8.099 -3.710 -0.879 2.741 H1 05H 63 05H HC21 H28 H 0 0 N N N 9.316 19.085 6.174 -1.436 -1.597 1.346 HC21 05H 64 05H OP3 OP3 O 0 1 N Y N ? ? ? -3.905 5.421 -1.010 OP3 05H 65 05H HOP3 H29 H 0 0 N Y N ? ? ? -3.333 5.746 -0.302 HOP3 05H 66 05H H2 H30 H 0 1 N N N 9.007 16.491 7.753 -0.467 1.281 0.223 H2 05H 67 05H H3 H31 H 0 1 N N N 10.666 15.808 7.825 -1.051 1.212 -1.457 H3 05H 68 05H "H3'1" H32 H 0 0 N N N 11.546 18.085 7.039 -2.650 -0.615 -0.825 "H3'1" 05H 69 05H HC52 H33 H 0 0 N N N 11.635 17.958 10.864 -4.222 1.746 -1.283 HC52 05H 70 05H H51 H34 H 0 1 N N N 13.522 19.692 3.453 8.613 3.692 0.825 H51 05H 71 05H HC51 H35 H 0 0 N N N 11.262 16.509 9.870 -2.761 2.689 -0.905 HC51 05H 72 # 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 05H O2 C2 DOUB N N 1 05H N3 C2 SING N N 2 05H N3 C4 SING N N 3 05H O4 C4 DOUB N N 4 05H C2 N1 SING N N 5 05H C4 C5 SING N N 6 05H "O3'" "C3'" SING N N 7 05H "C2'" "C3'" SING N N 8 05H "C2'" "C1'" SING N N 9 05H "C3'" "C4'" SING N N 10 05H N1 "C1'" SING N N 11 05H N1 C6 SING N N 12 05H C5 C6 DOUB N N 13 05H C5 C5M SING N N 14 05H "C1'" "O4'" SING N N 15 05H "C4'" "O4'" SING N N 16 05H "C4'" "C5'" SING N N 17 05H "C5'" "N5'" SING N N 18 05H O41 C41 DOUB N N 19 05H C41 N31 SING N N 20 05H C41 C51 SING N N 21 05H N31 C21 SING N N 22 05H O1 C1 DOUB N N 23 05H "N5'" C1 SING N N 24 05H O21 C21 DOUB N N 25 05H C21 N11 SING N N 26 05H C51 C5A SING N N 27 05H C51 C61 DOUB N N 28 05H C1 C11 SING N N 29 05H N11 C61 SING N N 30 05H N11 "C1'1" SING N N 31 05H "C2'1" "C3'1" SING N N 32 05H "C2'1" "C1'1" SING N N 33 05H "C2'1" "O2'" SING N N 34 05H C11 "C3'1" SING N N 35 05H "C3'1" "C4'1" SING N N 36 05H "C1'1" "O4'1" SING N N 37 05H "O2'" C3 SING N N 38 05H "O4'1" "C4'1" SING N N 39 05H "C4'1" C3 SING N N 40 05H "C4'1" "C5'1" SING N N 41 05H "O5'" "C5'1" SING N N 42 05H "O5'" P SING N N 43 05H OP2 P SING N N 44 05H P OP1 DOUB N N 45 05H "C1'" "H1'" SING N N 46 05H C5A H5A1 SING N N 47 05H C5A H5A2 SING N N 48 05H C5A H5A3 SING N N 49 05H "C2'" "H2'1" SING N N 50 05H "C2'" "H2'2" SING N N 51 05H C3 HC31 SING N N 52 05H C3 HC32 SING N N 53 05H "C3'" "H3'" SING N N 54 05H "C4'" "H4'" SING N N 55 05H "C5'" "H5'1" SING N N 56 05H "C5'" "H5'2" SING N N 57 05H C6 H6 SING N N 58 05H C61 H61 SING N N 59 05H C5M H52 SING N N 60 05H C5M H53 SING N N 61 05H N3 HN3 SING N N 62 05H N31 H31 SING N N 63 05H "N5'" "HN5'" SING N N 64 05H "O3'" "HO3'" SING N N 65 05H OP2 HOP2 SING N N 66 05H "C1'1" H1 SING N N 67 05H "C2'1" HC21 SING N N 68 05H P OP3 SING N N 69 05H OP3 HOP3 SING N N 70 05H C11 H2 SING N N 71 05H C11 H3 SING N N 72 05H "C3'1" "H3'1" SING N N 73 05H "C5'1" HC52 SING N N 74 05H C5M H51 SING N N 75 05H "C5'1" HC51 SING N N 76 # 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 05H InChI InChI 1.06 "InChI=1S/C23H30N5O13P/c1-10-6-27(21(33)25-18(10)31)16-4-13(29)14(40-16)5-24-15(30)3-12-17-20(28-7-11(2)19(32)26-22(28)34)41-23(12,8-38-17)9-39-42(35,36)37/h6-7,12-14,16-17,20,29H,3-5,8-9H2,1-2H3,(H,24,30)(H,25,31,33)(H,26,32,34)(H2,35,36,37)/t12-,13-,14+,16+,17+,20+,23+/m0/s1" 05H InChIKey InChI 1.06 ITNKNYJNRRELEH-CDWNFYEKSA-N 05H SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CNC(=O)C[C@H]3[C@H]4OC[C@]3(CO[P](O)(O)=O)O[C@H]4N5C=C(C)C(=O)NC5=O)O2)C(=O)NC1=O" 05H SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CNC(=O)C[CH]3[CH]4OC[C]3(CO[P](O)(O)=O)O[CH]4N5C=C(C)C(=O)NC5=O)O2)C(=O)NC1=O" 05H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CNC(=O)C[C@H]3[C@@H]4[C@@H](O[C@]3(CO4)COP(=O)(O)O)N5C=C(C(=O)NC5=O)C)O" 05H SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CNC(=O)CC3C4C(OC3(CO4)COP(=O)(O)O)N5C=C(C(=O)NC5=O)C)O" # _pdbx_chem_comp_identifier.comp_id 05H _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(1~{R},3~{R},4~{R},7~{S})-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-[2-[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylamino]-2-oxidanylidene-ethyl]-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methyl dihydrogen 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 05H "Create component" 2021-05-28 PDBE 05H "Initial release" 2022-08-03 RCSB 05H "Modify leaving atom flag" 2023-03-09 PDBE #