data_05A # _chem_comp.id 05A _chem_comp.name "[(1R,3R,4R,7S)-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-[2-[[(1S,3R,4R,7S)-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-1-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 "C24 H30 N5 O14 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 643.494 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 05A _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 7OOO _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 05A C4 C1 C 0 1 N N N -1.279 -17.045 -3.306 -2.906 1.202 2.083 C4 05A 1 05A "C1'" C2 C 0 1 N N R 0.786 -23.179 -3.402 5.456 1.233 -0.697 "C1'" 05A 2 05A C7 C3 C 0 1 N N N -0.806 -23.125 -1.204 3.466 1.271 -2.568 C7 05A 3 05A C2 C4 C 0 1 N N N 2.223 -24.081 -5.228 7.649 1.203 0.352 C2 05A 4 05A "C2'" C5 C 0 1 N N R 0.789 -24.296 -2.371 5.663 0.638 -2.125 "C2'" 05A 5 05A C21 C6 C 0 1 N N N 0.778 -20.241 -6.613 -4.022 -3.690 1.150 C21 05A 6 05A C11 C7 C 0 1 N N N 0.755 -17.954 -1.635 -1.168 0.791 -0.180 C11 05A 7 05A "C3'" C8 C 0 1 N N S 1.456 -23.624 -1.211 4.762 -0.643 -1.991 "C3'" 05A 8 05A C41 C9 C 0 1 N N N 2.781 -20.212 -7.721 -4.841 -4.625 -0.828 C41 05A 9 05A "C4'" C10 C 0 1 N N S 0.543 -22.455 -1.261 3.529 0.173 -1.460 "C4'" 05A 10 05A C8 C11 C 0 1 N N N 4.188 -23.080 -5.883 8.253 -0.380 1.961 C8 05A 11 05A C51 C12 C 0 1 N N N 3.039 -18.868 -7.204 -5.053 -3.324 -1.342 C51 05A 12 05A "C5'" C13 C 0 1 N N N 0.859 -21.422 -0.202 2.241 -0.614 -1.208 "C5'" 05A 13 05A C5 C14 C 0 1 N N N 3.976 -22.044 -4.865 6.969 -0.964 1.852 C5 05A 14 05A C6 C15 C 0 1 N N N 2.847 -22.112 -4.077 6.076 -0.433 0.990 C6 05A 15 05A C61 C16 C 0 1 N N N 2.093 -18.283 -6.395 -4.731 -2.256 -0.581 C61 05A 16 05A C5A C17 C 0 1 N N N 4.310 -18.161 -7.558 -5.625 -3.132 -2.723 C5A 05A 17 05A C5M C18 C 0 1 N N N 4.975 -20.940 -4.697 6.602 -2.164 2.688 C5M 05A 18 05A C1 C19 C 0 1 N N N 1.318 -19.273 -1.192 -0.065 -0.161 -0.564 C1 05A 19 05A N1 N1 N 0 1 N N N 1.987 -23.115 -4.236 6.425 0.656 0.239 N1 05A 20 05A N11 N2 N 0 1 N N N 0.986 -18.956 -6.097 -4.213 -2.447 0.671 N11 05A 21 05A "N5'" N3 N 0 1 N N N 0.453 -20.120 -0.661 1.168 0.311 -0.835 "N5'" 05A 22 05A N3 N4 N 0 1 N N N 3.296 -24.042 -6.006 8.558 0.693 1.204 N3 05A 23 05A N31 N5 N 0 1 N N N 1.666 -20.824 -7.397 -4.329 -4.772 0.411 N31 05A 24 05A O2 O1 O 0 1 N N N 1.429 -25.014 -5.403 7.940 2.168 -0.329 O2 05A 25 05A O21 O2 O 0 1 N N N -0.256 -20.867 -6.346 -3.560 -3.837 2.266 O21 05A 26 05A "O2'" O3 O 0 1 N N N -1.268 -18.471 -3.330 -2.108 0.040 2.387 "O2'" 05A 27 05A "O3'" O4 O 0 1 N N N 1.331 -24.347 0.034 4.506 -1.267 -3.251 "O3'" 05A 28 05A O31 O5 O 0 1 N N N -0.555 -24.340 -1.913 4.833 1.479 -2.976 O31 05A 29 05A O41 O6 O 0 1 N N N 3.606 -20.770 -8.448 -5.120 -5.604 -1.497 O41 05A 30 05A "O4'" O7 O 0 1 N N N 0.716 -22.011 -2.594 4.115 0.862 -0.320 "O4'" 05A 31 05A O4 O8 O 0 1 N N N 5.189 -23.057 -6.613 9.075 -0.842 2.731 O4 05A 32 05A O1 O9 O 0 1 N N N 2.496 -19.526 -1.336 -0.286 -1.352 -0.628 O1 05A 33 05A "O5'" O10 O 0 1 N N N 1.951 -15.283 -3.896 -4.955 2.881 0.689 "O5'" 05A 34 05A OP1 O11 O 0 1 N N N 2.442 -13.132 -2.672 -4.608 5.163 -0.332 OP1 05A 35 05A OP2 O12 O 0 1 N N N 4.160 -13.999 -4.241 -6.648 3.869 -1.063 OP2 05A 36 05A P P1 P 0 1 N N N 2.693 -13.872 -3.944 -5.650 4.229 0.148 P 05A 37 05A "C1'1" C20 C 0 0 N N R -0.030 -18.351 -5.248 -3.864 -1.289 1.496 "C1'1" 05A 38 05A "C2'1" C21 C 0 0 N N R 0.003 -18.867 -3.824 -2.353 -0.932 1.332 "C2'1" 05A 39 05A "C3'1" C22 C 0 0 N N S 0.889 -17.878 -3.133 -2.456 0.004 0.073 "C3'1" 05A 40 05A "C4'1" C23 C 0 0 N N R 0.140 -16.725 -3.702 -3.587 0.890 0.713 "C4'1" 05A 41 05A "C5'1" C24 C 0 0 N N N 0.673 -15.373 -3.302 -4.062 2.094 -0.101 "C5'1" 05A 42 05A "O4'1" O13 O 0 0 N N N 0.229 -16.965 -5.089 -4.597 -0.105 1.046 "O4'1" 05A 43 05A HC31 H1 H 0 0 N N N -1.512 -16.662 -2.301 -3.661 1.354 2.854 HC31 05A 44 05A HC32 H2 H 0 0 N N N -2.000 -16.637 -4.030 -2.272 2.084 1.997 HC32 05A 45 05A "H1'" H3 H 0 1 N N N -0.109 -23.269 -4.034 5.555 2.319 -0.723 "H1'" 05A 46 05A H71 H4 H 0 1 N N N -1.576 -22.520 -1.705 2.869 0.923 -3.411 H71 05A 47 05A H72 H5 H 0 1 N N N -1.112 -23.322 -0.166 3.047 2.192 -2.163 H72 05A 48 05A "H2'1" H6 H 0 0 N N N 1.241 -25.243 -2.702 6.694 0.494 -2.446 "H2'1" 05A 49 05A H2 H7 H 0 1 N N N 1.315 -17.131 -1.167 -0.887 1.327 0.726 H2 05A 50 05A H3 H8 H 0 1 N N N -0.305 -17.885 -1.350 -1.331 1.503 -0.988 H3 05A 51 05A "H3'" H9 H 0 1 N N N 2.496 -23.347 -1.439 5.147 -1.349 -1.254 "H3'" 05A 52 05A "H5'1" H10 H 0 0 N N N 0.318 -21.669 0.723 1.960 -1.151 -2.114 "H5'1" 05A 53 05A "H5'2" H11 H 0 0 N N N 1.941 -21.419 -0.004 2.404 -1.327 -0.399 "H5'2" 05A 54 05A H6 H12 H 0 1 N N N 2.661 -21.353 -3.332 5.091 -0.865 0.893 H6 05A 55 05A H61 H13 H 0 1 N N N 2.248 -17.287 -6.006 -4.886 -1.255 -0.957 H61 05A 56 05A H5A1 H14 H 0 0 N N N 4.325 -17.170 -7.080 -5.813 -4.106 -3.177 H5A1 05A 57 05A H5A2 H15 H 0 0 N N N 5.168 -18.751 -7.205 -6.560 -2.576 -2.656 H5A2 05A 58 05A H5A3 H16 H 0 0 N N N 4.371 -18.042 -8.650 -4.915 -2.577 -3.337 H5A3 05A 59 05A H51 H17 H 0 1 N N N 4.646 -20.266 -3.892 7.449 -2.441 3.315 H51 05A 60 05A H52 H18 H 0 1 N N N 5.955 -21.368 -4.439 5.747 -1.920 3.318 H52 05A 61 05A H53 H19 H 0 1 N N N 5.058 -20.375 -5.637 6.346 -2.997 2.034 H53 05A 62 05A "HN5'" H20 H 0 0 N N N -0.506 -19.850 -0.576 1.345 1.263 -0.783 "HN5'" 05A 63 05A HN3 H21 H 0 1 N N N 3.430 -24.753 -6.696 9.437 1.099 1.272 HN3 05A 64 05A H31 H22 H 0 1 N N N 1.487 -21.743 -7.748 -4.180 -5.660 0.770 H31 05A 65 05A "HO3'" H23 H 0 0 N Y N 1.774 -23.868 0.725 5.301 -1.580 -3.704 "HO3'" 05A 66 05A HOP2 H25 H 0 0 N N N 4.661 -13.578 -3.552 -7.358 3.259 -0.820 HOP2 05A 67 05A H1 H26 H 0 1 N N N -1.031 -18.516 -5.674 -4.083 -1.493 2.544 H1 05A 68 05A HC21 H27 H 0 0 N N N 0.283 -19.924 -3.709 -1.659 -1.771 1.277 HC21 05A 69 05A "H3'1" H28 H 0 0 N N N 1.934 -17.926 -3.472 -2.793 -0.528 -0.817 "H3'1" 05A 70 05A HC51 H29 H 0 0 N N N 0.751 -15.299 -2.207 -4.580 1.746 -0.996 HC51 05A 71 05A HC52 H30 H 0 0 N N N 0.017 -14.574 -3.678 -3.204 2.699 -0.391 HC52 05A 72 05A OP3 OP3 O 0 1 N Y N ? ? ? -6.482 4.920 1.341 OP3 05A 73 05A HOP3 H31 H 0 0 N Y N ? ? ? -6.928 5.739 1.086 HOP3 05A 74 # 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 05A O41 C41 DOUB N N 1 05A C41 N31 SING N N 2 05A C41 C51 SING N N 3 05A C5A C51 SING N N 4 05A N31 C21 SING N N 5 05A C51 C61 DOUB N N 6 05A C21 O21 DOUB N N 7 05A C21 N11 SING N N 8 05A O4 C8 DOUB N N 9 05A C61 N11 SING N N 10 05A N11 "C1'1" SING N N 11 05A N3 C8 SING N N 12 05A N3 C2 SING N N 13 05A C8 C5 SING N N 14 05A O2 C2 DOUB N N 15 05A "C1'1" "O4'1" SING N N 16 05A "C1'1" "C2'1" SING N N 17 05A C2 N1 SING N N 18 05A "O4'1" "C4'1" SING N N 19 05A C5 C5M SING N N 20 05A C5 C6 DOUB N N 21 05A OP2 P SING N N 22 05A N1 C6 SING N N 23 05A N1 "C1'" SING N N 24 05A P "O5'" SING N N 25 05A P OP1 DOUB N N 26 05A "O5'" "C5'1" SING N N 27 05A "C2'1" "O2'" SING N N 28 05A "C2'1" "C3'1" SING N N 29 05A "C4'1" C4 SING N N 30 05A "C4'1" "C5'1" SING N N 31 05A "C4'1" "C3'1" SING N N 32 05A "C1'" "O4'" SING N N 33 05A "C1'" "C2'" SING N N 34 05A "O2'" C4 SING N N 35 05A "C3'1" C11 SING N N 36 05A "O4'" "C4'" SING N N 37 05A "C2'" O31 SING N N 38 05A "C2'" "C3'" SING N N 39 05A O31 C7 SING N N 40 05A C11 C1 SING N N 41 05A O1 C1 DOUB N N 42 05A "C4'" "C3'" SING N N 43 05A "C4'" C7 SING N N 44 05A "C4'" "C5'" SING N N 45 05A "C3'" "O3'" SING N N 46 05A C1 "N5'" SING N N 47 05A "N5'" "C5'" SING N N 48 05A C4 HC31 SING N N 49 05A C4 HC32 SING N N 50 05A "C1'" "H1'" SING N N 51 05A C7 H71 SING N N 52 05A C7 H72 SING N N 53 05A "C2'" "H2'1" SING N N 54 05A C11 H2 SING N N 55 05A C11 H3 SING N N 56 05A "C3'" "H3'" SING N N 57 05A "C5'" "H5'1" SING N N 58 05A "C5'" "H5'2" SING N N 59 05A C6 H6 SING N N 60 05A C61 H61 SING N N 61 05A C5A H5A1 SING N N 62 05A C5A H5A2 SING N N 63 05A C5A H5A3 SING N N 64 05A C5M H51 SING N N 65 05A C5M H52 SING N N 66 05A C5M H53 SING N N 67 05A "N5'" "HN5'" SING N N 68 05A N3 HN3 SING N N 69 05A N31 H31 SING N N 70 05A "O3'" "HO3'" SING N N 71 05A OP2 HOP2 SING N N 72 05A "C1'1" H1 SING N N 73 05A "C2'1" HC21 SING N N 74 05A "C3'1" "H3'1" SING N N 75 05A "C5'1" HC51 SING N N 76 05A "C5'1" HC52 SING N N 77 05A P OP3 SING N N 78 05A OP3 HOP3 SING N N 79 # 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 05A InChI InChI 1.06 "InChI=1S/C24H30N5O14P/c1-10-4-28(21(34)26-17(10)32)19-14-12(24(43-19,8-39-14)9-41-44(36,37)38)3-13(30)25-6-23-7-40-15(16(23)31)20(42-23)29-5-11(2)18(33)27-22(29)35/h4-5,12,14-16,19-20,31H,3,6-9H2,1-2H3,(H,25,30)(H,26,32,34)(H,27,33,35)(H2,36,37,38)/t12-,14+,15+,16-,19+,20+,23-,24+/m0/s1" 05A InChIKey InChI 1.06 ZPMMRXCRABIQDW-XVYZCTGRSA-N 05A SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@@H]2O[C@@]3(CNC(=O)C[C@H]4[C@H]5OC[C@]4(CO[P](O)(O)=O)O[C@H]5N6C=C(C)C(=O)NC6=O)CO[C@@H]2[C@@H]3O)C(=O)NC1=O" 05A SMILES CACTVS 3.385 "CC1=CN([CH]2O[C]3(CNC(=O)C[CH]4[CH]5OC[C]4(CO[P](O)(O)=O)O[CH]5N6C=C(C)C(=O)NC6=O)CO[CH]2[CH]3O)C(=O)NC1=O" 05A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2[C@H]3[C@@H]([C@@](O2)(CO3)COP(=O)(O)O)CC(=O)NC[C@]45CO[C@H]([C@@H]4O)[C@@H](O5)N6C=C(C(=O)NC6=O)C" 05A SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2C3C(C(O2)(CO3)COP(=O)(O)O)CC(=O)NCC45COC(C4O)C(O5)N6C=C(C(=O)NC6=O)C" # _pdbx_chem_comp_identifier.comp_id 05A _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-[[(1~{S},3~{R},4~{R},7~{S})-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-1-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 05A "Create component" 2021-05-28 PDBE 05A "Initial release" 2022-08-03 RCSB 05A "Modify leaving atom flag" 2023-03-09 PDBE #