data_LST # _chem_comp.id LST _chem_comp.name "[(1R,5R,7R,8S)-2-methyl-7-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-8-oxidanyl-3,3-bis(oxidanylidene)-6-oxa-3$l^{6}-thia-2-azabicyclo[3.2.1]octan-5-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H18 N3 O10 P S" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-08-07 _chem_comp.pdbx_modified_date 2016-07-15 _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 427.324 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _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 5AXF _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 LST C2 C1 C 0 1 N N N 1.265 41.718 18.077 3.502 -0.450 0.590 C2 LST 1 LST C4 C2 C 0 1 N N N 0.683 43.018 16.109 3.908 -2.688 0.058 C4 LST 2 LST C5 C3 C 0 1 N N N -0.438 42.146 15.883 2.535 -2.854 -0.244 C5 LST 3 LST C6 C4 C 0 1 N N N -0.640 41.112 16.721 1.702 -1.798 -0.118 C6 LST 4 LST "C1'" C5 C 0 1 N N R 0.054 39.733 18.714 1.292 0.553 0.437 "C1'" LST 5 LST "C2'" C6 C 0 1 N N R -0.722 40.101 19.972 1.314 1.395 -0.861 "C2'" LST 6 LST "C3'" C7 C 0 1 N N S -2.173 39.928 19.435 0.060 0.866 -1.610 "C3'" LST 7 LST "O3'" O1 O 0 1 N N N -3.170 39.857 20.468 -0.486 1.870 -2.468 "O3'" LST 8 LST "C4'" C8 C 0 1 N N R -2.020 38.567 18.742 -0.894 0.563 -0.430 "C4'" LST 9 LST "C5'" C9 C 0 1 N N N -3.118 38.187 17.803 -1.953 -0.470 -0.820 "C5'" LST 10 LST "O5'" O2 O 0 1 N N N -3.245 39.299 16.898 -2.879 -0.633 0.257 "O5'" LST 11 LST "C6'" C10 C 0 1 N N N -1.900 37.473 19.791 -1.539 1.891 -0.001 "C6'" LST 12 LST P P1 P 0 1 N N N -4.328 39.123 15.693 -4.129 -1.645 0.193 P LST 13 LST OP1 O3 O 0 1 N N N -5.549 38.467 16.146 -4.949 -1.341 -1.001 OP1 LST 14 LST OP2 O4 O 0 1 N N N -4.392 40.500 15.036 -3.589 -3.159 0.102 OP2 LST 15 LST "N2'" N1 N 0 1 N N N -0.392 39.244 21.152 1.000 2.787 -0.461 "N2'" LST 16 LST "C7'" C11 C 0 1 N N N 0.772 39.654 21.944 1.734 3.931 -1.008 "C7'" LST 17 LST S S1 S 0 1 N N N -0.507 37.634 20.870 -0.233 2.983 0.643 S LST 18 LST "O7'" O5 O 0 1 N N N -0.831 37.038 22.158 -0.610 4.347 0.518 "O7'" LST 19 LST "O8'" O6 O 0 1 N N N 0.654 37.179 20.182 0.295 2.472 1.860 "O8'" LST 20 LST "O4'" O7 O 0 1 N N N -0.747 38.740 18.054 -0.050 0.095 0.632 "O4'" LST 21 LST N1 N2 N 0 1 N N N 0.196 40.874 17.796 2.195 -0.593 0.301 N1 LST 22 LST C7 C12 C 0 1 N N N -1.329 42.441 14.729 2.010 -4.190 -0.705 C7 LST 23 LST N3 N3 N 0 1 N N N 1.451 42.721 17.204 4.354 -1.484 0.468 N3 LST 24 LST O2 O8 O 0 1 N N N 1.989 41.537 19.055 3.918 0.631 0.961 O2 LST 25 LST O4 O9 O 0 1 N N N 0.959 43.985 15.404 4.679 -3.625 -0.052 O4 LST 26 LST H1 H1 H 0 1 N N N -1.477 40.451 16.549 0.652 -1.906 -0.344 H1 LST 27 LST H2 H2 H 0 1 N N N 1.040 39.330 18.987 1.600 1.168 1.282 H2 LST 28 LST H3 H3 H 0 1 N N N -0.550 41.160 20.216 2.244 1.306 -1.422 H3 LST 29 LST H4 H4 H 0 1 N N N -2.401 40.712 18.698 0.292 -0.040 -2.170 H4 LST 30 LST H5 H5 H 0 1 N N N -3.253 40.705 20.887 0.118 2.165 -3.163 H5 LST 31 LST H6 H6 H 0 1 N N N -4.057 38.028 18.353 -2.485 -0.128 -1.708 H6 LST 32 LST H7 H7 H 0 1 N N N -2.855 37.271 17.254 -1.470 -1.424 -1.031 H7 LST 33 LST H8 H8 H 0 1 N N N -2.813 37.485 20.405 -2.020 2.361 -0.859 H8 LST 34 LST H9 H9 H 0 1 N N N -1.821 36.507 19.271 -2.279 1.705 0.778 H9 LST 35 LST H11 H11 H 0 1 N N N -5.295 40.791 14.997 -3.043 -3.428 0.853 H11 LST 36 LST H12 H12 H 0 1 N N N 1.368 38.768 22.207 1.238 4.283 -1.912 H12 LST 37 LST H13 H13 H 0 1 N N N 1.389 40.349 21.356 1.757 4.734 -0.271 H13 LST 38 LST H14 H14 H 0 1 N N N 0.432 40.153 22.863 2.753 3.628 -1.247 H14 LST 39 LST H15 H15 H 0 1 N N N -2.134 41.693 14.686 2.830 -4.907 -0.746 H15 LST 40 LST H16 H16 H 0 1 N N N -1.766 43.443 14.850 1.253 -4.543 -0.005 H16 LST 41 LST H17 H17 H 0 1 N N N -0.746 42.405 13.797 1.569 -4.084 -1.696 H17 LST 42 LST H18 H18 H 0 1 N N N 2.236 43.317 17.371 5.294 -1.362 0.677 H18 LST 43 LST OP3 OP3 O 0 1 N N N -3.630 38.056 14.712 -5.027 -1.474 1.518 OP3 LST 44 LST H10 H10 H 0 1 N N N -4.166 37.273 14.663 -5.799 -2.054 1.548 H10 LST 45 # 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 LST C7 C5 SING N N 1 LST OP2 P SING N N 2 LST O4 C4 DOUB N N 3 LST P OP1 DOUB N N 4 LST P "O5'" SING N N 5 LST C5 C4 SING N N 6 LST C5 C6 DOUB N N 7 LST C4 N3 SING N N 8 LST C6 N1 SING N N 9 LST "O5'" "C5'" SING N N 10 LST N3 C2 SING N N 11 LST N1 C2 SING N N 12 LST N1 "C1'" SING N N 13 LST "C5'" "C4'" SING N N 14 LST "O4'" "C1'" SING N N 15 LST "O4'" "C4'" SING N N 16 LST C2 O2 DOUB N N 17 LST "C1'" "C2'" SING N N 18 LST "C4'" "C3'" SING N N 19 LST "C4'" "C6'" SING N N 20 LST "C3'" "C2'" SING N N 21 LST "C3'" "O3'" SING N N 22 LST "C6'" S SING N N 23 LST "C2'" "N2'" SING N N 24 LST "O8'" S DOUB N N 25 LST S "N2'" SING N N 26 LST S "O7'" DOUB N N 27 LST "N2'" "C7'" SING N N 28 LST C6 H1 SING N N 29 LST "C1'" H2 SING N N 30 LST "C2'" H3 SING N N 31 LST "C3'" H4 SING N N 32 LST "O3'" H5 SING N N 33 LST "C5'" H6 SING N N 34 LST "C5'" H7 SING N N 35 LST "C6'" H8 SING N N 36 LST "C6'" H9 SING N N 37 LST OP2 H11 SING N N 38 LST "C7'" H12 SING N N 39 LST "C7'" H13 SING N N 40 LST "C7'" H14 SING N N 41 LST C7 H15 SING N N 42 LST C7 H16 SING N N 43 LST C7 H17 SING N N 44 LST N3 H18 SING N N 45 LST P OP3 SING N N 46 LST OP3 H10 SING N N 47 # 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 LST InChI InChI 1.03 "InChI=1S/C12H18N3O10PS/c1-6-3-15(11(18)13-9(6)17)10-7-8(16)12(25-10,4-24-26(19,20)21)5-27(22,23)14(7)2/h3,7-8,10,16H,4-5H2,1-2H3,(H,13,17,18)(H2,19,20,21)/t7-,8+,10-,12+/m1/s1" LST InChIKey InChI 1.03 GLEXYOQXMPFGCY-CCCLYZFWSA-N LST SMILES_CANONICAL CACTVS 3.385 "CN1[C@@H]2[C@H](O)[C@](CO[P](O)(O)=O)(C[S]1(=O)=O)O[C@H]2N3C=C(C)C(=O)NC3=O" LST SMILES CACTVS 3.385 "CN1[CH]2[CH](O)[C](CO[P](O)(O)=O)(C[S]1(=O)=O)O[CH]2N3C=C(C)C(=O)NC3=O" LST SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)NC1=O)[C@H]2[C@H]3[C@@H]([C@@](O2)(CS(=O)(=O)N3C)COP(=O)(O)O)O" LST SMILES "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)NC1=O)C2C3C(C(O2)(CS(=O)(=O)N3C)COP(=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 LST "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(1R,5R,7R,8S)-2-methyl-7-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-8-oxidanyl-3,3-bis(oxidanylidene)-6-oxa-3$l^{6}-thia-2-azabicyclo[3.2.1]octan-5-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 LST "Create component" 2015-08-07 PDBJ LST "Initial release" 2016-07-20 RCSB #