data_05K # _chem_comp.id 05K _chem_comp.name "[(2S,3R,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-[2-[[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylamino]-2-oxidanylidene-ethyl]oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C22 H30 N5 O12 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 587.474 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 05K _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 7OOS _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 05K C1 C1 C 0 1 N N N -18.818 0.515 -9.147 0.251 0.635 -0.911 C1 05K 1 05K "C1'" C2 C 0 1 N N R -20.409 3.242 -5.766 5.822 1.383 -0.489 "C1'" 05K 2 05K C5A C3 C 0 1 N N N -25.594 -1.838 -8.702 -4.927 -5.955 1.368 C5A 05K 3 05K C2 C4 C 0 1 N N N -22.481 2.531 -4.554 6.453 -0.880 0.138 C2 05K 4 05K "C2'" C5 C 0 1 N N N -19.441 3.344 -4.604 6.205 1.255 -1.976 "C2'" 05K 5 05K C21 C6 C 0 1 N N N -24.346 2.198 -8.474 -4.406 -2.362 -0.802 C21 05K 6 05K "C3'" C7 C 0 1 N N S -18.244 2.542 -5.043 4.876 0.885 -2.679 "C3'" 05K 7 05K C4 C8 C 0 1 N N N -23.430 0.443 -4.879 8.063 -1.332 1.770 C4 05K 8 05K "C4'" C9 C 0 1 N N R -18.249 2.690 -6.540 3.820 1.368 -1.653 "C4'" 05K 9 05K C41 C10 C 0 1 N N N -25.697 0.519 -7.636 -5.222 -4.550 -0.724 C41 05K 10 05K C5 C11 C 0 1 N N N -22.368 0.127 -5.849 8.245 0.060 1.959 C5 05K 11 05K "C5'" C12 C 0 1 N N N -17.642 1.467 -7.195 2.508 0.601 -1.828 "C5'" 05K 12 05K C51 C13 C 0 1 N N N -25.145 -0.407 -8.638 -4.738 -4.672 0.601 C51 05K 13 05K C6 C14 C 0 1 N N N -21.412 1.081 -6.100 7.508 0.924 1.229 C6 05K 14 05K C61 C15 C 0 1 N N N -24.194 0.072 -9.510 -4.109 -3.621 1.169 C61 05K 15 05K C5M C16 C 0 1 N N N -22.310 -1.197 -6.550 9.240 0.569 2.970 C5M 05K 16 05K C11 C17 C 0 1 N N N -19.281 0.784 -10.552 -0.791 1.203 0.018 C11 05K 17 05K N1 N1 N 0 1 N N N -21.450 2.256 -5.473 6.613 0.445 0.312 N1 05K 18 05K N11 N2 N 0 1 N N N -23.805 1.345 -9.442 -3.946 -2.463 0.459 N11 05K 19 05K N3 N3 N 0 1 N N N -23.424 1.631 -4.287 7.167 -1.764 0.860 N3 05K 20 05K N31 N4 N 0 1 N N N -25.265 1.773 -7.613 -5.041 -3.392 -1.391 N31 05K 21 05K "N5'" N5 N 0 1 N N N -18.172 1.499 -8.541 1.494 1.157 -0.929 "N5'" 05K 22 05K O2 O1 O 0 1 N N N -22.529 3.616 -3.951 5.649 -1.284 -0.680 O2 05K 23 05K O21 O2 O 0 1 N N N -23.962 3.378 -8.431 -4.250 -1.324 -1.415 O21 05K 24 05K O1 O3 O 0 1 N N N -19.043 -0.555 -8.611 -0.027 -0.294 -1.639 O1 05K 25 05K "O3'" O4 O 0 1 N N N -17.011 3.011 -4.456 4.742 1.587 -3.917 "O3'" 05K 26 05K O4 O5 O 0 1 N N N -24.316 -0.389 -4.618 8.709 -2.130 2.424 O4 05K 27 05K "O4'" O6 O 0 1 N N N -19.629 2.803 -6.881 4.425 1.062 -0.378 "O4'" 05K 28 05K O41 O7 O 0 1 N N N -26.554 0.130 -6.824 -5.797 -5.483 -1.256 O41 05K 29 05K "O5'" O8 O 0 1 N N N -22.102 -1.548 -11.790 -4.917 2.647 1.074 "O5'" 05K 30 05K OP1 O9 O 0 1 N N N -23.604 -3.680 -11.337 -6.594 3.626 -0.539 OP1 05K 31 05K OP2 O10 O 0 1 N N N -21.859 -3.689 -13.345 -6.953 4.080 1.918 OP2 05K 32 05K P P1 P 0 1 N N N -22.841 -2.806 -12.441 -5.882 3.890 0.731 P 05K 33 05K "C1'1" C18 C 0 0 N N R -22.794 1.886 -10.346 -3.264 -1.323 1.076 "C1'1" 05K 34 05K "C2'1" C19 C 0 0 N N N -21.445 1.647 -9.705 -1.949 -1.032 0.327 "C2'1" 05K 35 05K "C3'1" C20 C 0 0 N N R -20.783 0.586 -10.551 -2.101 0.432 -0.154 "C3'1" 05K 36 05K "C4'1" C21 C 0 0 N N S -21.443 0.751 -11.902 -3.192 0.976 0.803 "C4'1" 05K 37 05K "C5'1" C22 C 0 0 N N N -21.504 -0.577 -12.636 -3.927 2.158 0.167 "C5'1" 05K 38 05K "O4'1" O11 O 0 0 N N N -22.764 1.206 -11.600 -4.084 -0.147 0.970 "O4'1" 05K 39 05K "H1'" H1 H 0 1 N N N -20.857 4.227 -5.963 5.999 2.402 -0.147 "H1'" 05K 40 05K H5A1 H2 H 0 0 N N N -26.353 -2.020 -7.927 -5.456 -6.676 0.745 H5A1 05K 41 05K H5A2 H3 H 0 0 N N N -26.026 -2.043 -9.693 -3.953 -6.359 1.645 H5A2 05K 42 05K H5A3 H4 H 0 0 N N N -24.732 -2.500 -8.534 -5.508 -5.757 2.269 H5A3 05K 43 05K "H2'1" H5 H 0 0 N N N -19.162 4.392 -4.421 6.587 2.203 -2.354 "H2'1" 05K 44 05K "H2'2" H6 H 0 0 N N N -19.882 2.917 -3.691 6.944 0.465 -2.113 "H2'2" 05K 45 05K "H3'" H7 H 0 1 N N N -18.405 1.485 -4.785 4.805 -0.191 -2.835 "H3'" 05K 46 05K "H4'" H8 H 0 1 N N N -17.690 3.591 -6.833 3.652 2.441 -1.750 "H4'" 05K 47 05K "H5'1" H9 H 0 0 N N N -17.951 0.549 -6.674 2.169 0.693 -2.860 "H5'1" 05K 48 05K "H5'2" H10 H 0 0 N N N -16.544 1.532 -7.204 2.668 -0.451 -1.590 "H5'2" 05K 49 05K H6 H11 H 0 1 N N N -20.624 0.877 -6.810 7.634 1.989 1.360 H6 05K 50 05K H61 H12 H 0 1 N N N -23.762 -0.585 -10.251 -3.736 -3.694 2.180 H61 05K 51 05K H52 H13 H 0 1 N N N -23.153 -1.823 -6.222 9.725 -0.275 3.460 H52 05K 52 05K H53 H14 H 0 1 N N N -22.372 -1.039 -7.637 9.992 1.177 2.466 H53 05K 53 05K H51 H15 H 0 1 N N N -21.363 -1.700 -6.306 8.724 1.174 3.715 H51 05K 54 05K H2 H16 H 0 1 N N N -18.805 0.081 -11.251 -0.448 1.111 1.048 H2 05K 55 05K H3 H17 H 0 1 N N N -19.033 1.815 -10.844 -0.954 2.254 -0.218 H3 05K 56 05K HN3 H18 H 0 1 N N N -24.142 1.854 -3.628 7.036 -2.715 0.725 HN3 05K 57 05K H31 H19 H 0 1 N N N -25.637 2.409 -6.937 -5.371 -3.301 -2.299 H31 05K 58 05K "HN5'" H20 H 0 0 N N N -18.038 2.342 -9.062 1.716 1.900 -0.347 "HN5'" 05K 59 05K "HO3'" H21 H 0 0 N Y N -17.047 2.901 -3.513 5.435 1.385 -4.561 "HO3'" 05K 60 05K HOP2 H23 H 0 0 N N N -21.900 -4.596 -13.065 -7.569 4.813 1.778 HOP2 05K 61 05K H1 H24 H 0 1 N N N -22.948 2.966 -10.490 -3.054 -1.539 2.123 H1 05K 62 05K HC22 H25 H 0 0 N N N -21.567 1.294 -8.670 -1.097 -1.125 1.002 HC22 05K 63 05K HC21 H26 H 0 0 N N N -20.848 2.571 -9.709 -1.836 -1.705 -0.523 HC21 05K 64 05K "H3'1" H27 H 0 0 N N N -21.021 -0.409 -10.146 -2.439 0.468 -1.189 "H3'1" 05K 65 05K HC41 H28 H 0 0 N N N -20.893 1.489 -12.504 -2.755 1.264 1.759 HC41 05K 66 05K HC51 H29 H 0 0 N N N -22.105 -0.465 -13.551 -4.408 1.832 -0.755 HC51 05K 67 05K HC52 H30 H 0 0 N N N -20.486 -0.898 -12.903 -3.214 2.951 -0.055 HC52 05K 68 05K OP3 OP3 O 0 1 N Y N ? ? ? -5.000 5.229 0.584 OP3 05K 69 05K HOP3 H22 H 0 0 N Y N ? ? ? -4.505 5.463 1.381 HOP3 05K 70 # 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 05K OP2 P SING N N 1 05K "C5'1" "C4'1" SING N N 2 05K "C5'1" "O5'" SING N N 3 05K P "O5'" SING N N 4 05K P OP1 DOUB N N 5 05K "C4'1" "O4'1" SING N N 6 05K "C4'1" "C3'1" SING N N 7 05K "O4'1" "C1'1" SING N N 8 05K C11 "C3'1" SING N N 9 05K C11 C1 SING N N 10 05K "C3'1" "C2'1" SING N N 11 05K "C1'1" "C2'1" SING N N 12 05K "C1'1" N11 SING N N 13 05K C61 N11 SING N N 14 05K C61 C51 DOUB N N 15 05K N11 C21 SING N N 16 05K C1 O1 DOUB N N 17 05K C1 "N5'" SING N N 18 05K C5A C51 SING N N 19 05K C51 C41 SING N N 20 05K "N5'" "C5'" SING N N 21 05K C21 O21 DOUB N N 22 05K C21 N31 SING N N 23 05K C41 N31 SING N N 24 05K C41 O41 DOUB N N 25 05K "C5'" "C4'" SING N N 26 05K "O4'" "C4'" SING N N 27 05K "O4'" "C1'" SING N N 28 05K C5M C5 SING N N 29 05K "C4'" "C3'" SING N N 30 05K C6 C5 DOUB N N 31 05K C6 N1 SING N N 32 05K C5 C4 SING N N 33 05K "C1'" N1 SING N N 34 05K "C1'" "C2'" SING N N 35 05K N1 C2 SING N N 36 05K "C3'" "C2'" SING N N 37 05K "C3'" "O3'" SING N N 38 05K C4 O4 DOUB N N 39 05K C4 N3 SING N N 40 05K C2 N3 SING N N 41 05K C2 O2 DOUB N N 42 05K "C1'" "H1'" SING N N 43 05K C5A H5A1 SING N N 44 05K C5A H5A2 SING N N 45 05K C5A H5A3 SING N N 46 05K "C2'" "H2'1" SING N N 47 05K "C2'" "H2'2" SING N N 48 05K "C3'" "H3'" SING N N 49 05K "C4'" "H4'" SING N N 50 05K "C5'" "H5'1" SING N N 51 05K "C5'" "H5'2" SING N N 52 05K C6 H6 SING N N 53 05K C61 H61 SING N N 54 05K C5M H52 SING N N 55 05K C5M H53 SING N N 56 05K C5M H51 SING N N 57 05K C11 H2 SING N N 58 05K C11 H3 SING N N 59 05K N3 HN3 SING N N 60 05K N31 H31 SING N N 61 05K "N5'" "HN5'" SING N N 62 05K "O3'" "HO3'" SING N N 63 05K OP2 HOP2 SING N N 64 05K "C1'1" H1 SING N N 65 05K "C2'1" HC22 SING N N 66 05K "C2'1" HC21 SING N N 67 05K "C3'1" "H3'1" SING N N 68 05K "C4'1" HC41 SING N N 69 05K "C5'1" HC51 SING N N 70 05K "C5'1" HC52 SING N N 71 05K P OP3 SING N N 72 05K OP3 HOP3 SING N N 73 # 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 05K InChI InChI 1.06 "InChI=1S/C22H30N5O12P/c1-10-7-26(21(32)24-19(10)30)17-4-12(15(39-17)9-37-40(34,35)36)3-16(29)23-6-14-13(28)5-18(38-14)27-8-11(2)20(31)25-22(27)33/h7-8,12-15,17-18,28H,3-6,9H2,1-2H3,(H,23,29)(H,24,30,32)(H,25,31,33)(H2,34,35,36)/t12-,13-,14+,15+,17+,18+/m0/s1" 05K InChIKey InChI 1.06 LKZCDFBGSPSCDT-LVBQRNIJSA-N 05K SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CNC(=O)C[C@H]3C[C@@H](O[C@@H]3CO[P](O)(O)=O)N4C=C(C)C(=O)NC4=O)O2)C(=O)NC1=O" 05K SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CNC(=O)C[CH]3C[CH](O[CH]3CO[P](O)(O)=O)N4C=C(C)C(=O)NC4=O)O2)C(=O)NC1=O" 05K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)CC(=O)NC[C@@H]3[C@H](C[C@@H](O3)N4C=C(C(=O)NC4=O)C)O" 05K SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)CC(=O)NCC3C(CC(O3)N4C=C(C(=O)NC4=O)C)O" # _pdbx_chem_comp_identifier.comp_id 05K _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 "[(2~{S},3~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-[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]oxolan-2-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 05K "Create component" 2021-05-28 PDBE 05K "Initial release" 2022-08-03 RCSB 05K "Modify leaving atom flag" 2023-03-09 PDBE #