data_LR6 # _chem_comp.id LR6 _chem_comp.name ;[(1R,3R,4R,7S)-5-(N'-tert-butyl-N-methyl-carbamimidoyl)-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-oxidanyl-2-oxa-5-azabicyclo[2.2.1]heptan-1-yl]methyl dihydrogen phosphate ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C17 H28 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-12-07 _chem_comp.pdbx_modified_date 2023-08-04 _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 461.407 _chem_comp.one_letter_code ? _chem_comp.three_letter_code LR6 _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 8HIS _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 LR6 C2 C1 C 0 1 N N N -0.777 -5.311 4.549 1.579 3.202 -0.695 C2 LR6 1 LR6 C4 C2 C 0 1 N N N -0.425 -4.025 6.465 0.457 5.203 -0.252 C4 LR6 2 LR6 C5 C3 C 0 1 N N N 0.741 -4.877 6.804 -0.731 4.471 -0.012 C5 LR6 3 LR6 C6 C4 C 0 1 N N N 1.058 -5.923 5.950 -0.708 3.126 -0.126 C6 LR6 4 LR6 N1 N1 N 0 1 N N N 0.326 -6.139 4.843 0.457 2.495 -0.469 N1 LR6 5 LR6 N3 N2 N 0 1 N N N -1.120 -4.290 5.353 1.584 4.544 -0.588 N3 LR6 6 LR6 CD C5 C 0 1 N N N 1.135 -8.037 0.743 2.497 -1.703 0.189 CD LR6 7 LR6 "C1'" C6 C 0 1 N N R 0.646 -7.247 3.927 0.482 1.035 -0.592 "C1'" LR6 8 LR6 "C2'" C7 C 0 1 N N R 1.566 -6.825 2.790 1.102 0.395 0.689 "C2'" LR6 9 LR6 "C3'" C8 C 0 1 N N S 2.913 -6.893 3.443 -0.199 0.295 1.566 "C3'" LR6 10 LR6 "C4'" C9 C 0 1 N N R 2.685 -8.284 3.972 -1.027 -0.416 0.436 "C4'" LR6 11 LR6 "C5'" C10 C 0 1 N N N 3.767 -8.779 4.915 -2.468 -0.794 0.785 "C5'" LR6 12 LR6 C5M C11 C 0 1 N N N 1.560 -4.618 8.045 -2.004 5.183 0.366 C5M LR6 13 LR6 "C6'" C12 C 0 1 N N N 2.442 -9.043 2.682 -0.055 -1.588 0.096 "C6'" LR6 14 LR6 "C7'" C13 C 0 1 N N N -1.003 -7.688 -0.439 3.658 0.335 0.930 "C7'" LR6 15 LR6 "C8'" C14 C 0 1 N N N 2.183 -9.385 -1.144 3.787 -3.623 -0.444 "C8'" LR6 16 LR6 "C9'" C15 C 0 1 N N N 2.703 -8.912 -2.495 3.523 -5.033 -0.976 "C9'" LR6 17 LR6 "N2'" N3 N 0 1 N N N 1.678 -8.024 1.958 1.301 -1.036 0.312 "N2'" LR6 18 LR6 "N3'" N4 N 0 1 N N N -0.101 -7.782 0.692 3.677 -1.056 0.469 "N3'" LR6 19 LR6 "N4'" N5 N 0 1 N N N 1.877 -8.189 -0.360 2.511 -2.950 -0.192 "N4'" LR6 20 LR6 O2 O1 O 0 1 N N N -1.446 -5.541 3.517 2.604 2.621 -0.993 O2 LR6 21 LR6 "O3'" O2 O 0 1 N N N 3.947 -6.873 2.465 -0.020 -0.535 2.716 "O3'" LR6 22 LR6 O4 O3 O 0 1 N N N -0.751 -3.073 7.206 0.461 6.417 -0.155 O4 LR6 23 LR6 "O4'" O4 O 0 1 N N N 1.425 -8.206 4.640 -0.860 0.517 -0.668 "O4'" LR6 24 LR6 "O5'" O5 O 0 1 N N N 3.880 -7.768 5.912 -3.043 -1.529 -0.298 "O5'" LR6 25 LR6 OP1 O6 O 0 1 N N N 5.866 -8.799 7.115 -4.749 -2.926 0.930 OP1 LR6 26 LR6 OP2 O7 O 0 1 N N N 4.724 -6.789 8.105 -5.582 -0.852 -0.243 OP2 LR6 27 LR6 P P1 P 0 1 N N N 4.558 -8.077 7.333 -4.552 -2.089 -0.274 P LR6 28 LR6 "C10'" C16 C 0 0 N N N 3.261 -10.225 -0.482 4.584 -3.711 0.859 "C10'" LR6 29 LR6 "C11'" C17 C 0 0 N N N 0.969 -10.272 -1.386 4.588 -2.829 -1.479 "C11'" LR6 30 LR6 H1 H1 H 0 1 N N N 1.896 -6.566 6.175 -1.604 2.551 0.052 H1 LR6 31 LR6 H2 H2 H 0 1 N N N -1.907 -3.720 5.116 2.402 5.039 -0.754 H2 LR6 32 LR6 H3 H3 H 0 1 N N N -0.273 -7.696 3.522 1.051 0.741 -1.475 H3 LR6 33 LR6 H4 H4 H 0 1 N N N 1.311 -5.882 2.284 1.953 0.914 1.131 H4 LR6 34 LR6 H5 H5 H 0 1 N N N 3.037 -6.149 4.244 -0.603 1.273 1.826 H5 LR6 35 LR6 H6 H6 H 0 1 N N N 3.475 -9.738 5.368 -2.475 -1.408 1.685 H6 LR6 36 LR6 H7 H7 H 0 1 N N N 4.720 -8.902 4.379 -3.050 0.111 0.958 H7 LR6 37 LR6 H8 H8 H 0 1 N N N 1.148 -3.751 8.582 -1.821 6.257 0.406 H8 LR6 38 LR6 H9 H9 H 0 1 N N N 1.527 -5.503 8.697 -2.772 4.974 -0.378 H9 LR6 39 LR6 H10 H10 H 0 1 N N N 2.602 -4.412 7.760 -2.339 4.835 1.342 H10 LR6 40 LR6 H11 H11 H 0 1 N N N 1.856 -9.959 2.846 -0.231 -2.431 0.763 H11 LR6 41 LR6 H12 H12 H 0 1 N N N 3.382 -9.296 2.169 -0.180 -1.894 -0.942 H12 LR6 42 LR6 H13 H13 H 0 1 N N N -2.015 -7.446 -0.082 4.681 0.690 1.055 H13 LR6 43 LR6 H14 H14 H 0 1 N N N -0.655 -6.897 -1.120 3.145 0.954 0.194 H14 LR6 44 LR6 H15 H15 H 0 1 N N N -1.023 -8.650 -0.973 3.134 0.394 1.883 H15 LR6 45 LR6 H16 H16 H 0 1 N N N 3.582 -8.268 -2.345 2.954 -5.599 -0.239 H16 LR6 46 LR6 H17 H17 H 0 1 N N N 2.986 -9.783 -3.104 2.956 -4.971 -1.905 H17 LR6 47 LR6 H18 H18 H 0 1 N N N 1.916 -8.343 -3.012 4.473 -5.535 -1.164 H18 LR6 48 LR6 H19 H19 H 0 1 N N N -0.529 -7.617 1.581 4.522 -1.520 0.361 H19 LR6 49 LR6 "HO3'" H20 H 0 1 N Y N 4.792 -6.917 2.896 0.659 -0.218 3.328 H20 LR6 50 LR6 HOP2 H22 H 0 1 N N N 5.641 -6.663 8.318 -5.509 -0.260 -1.004 H22 LR6 51 LR6 H23 H23 H 0 1 N N N 2.903 -10.576 0.497 4.058 -4.354 1.564 H23 LR6 52 LR6 H24 H24 H 0 1 N N N 3.494 -11.091 -1.119 5.571 -4.127 0.654 H24 LR6 53 LR6 H25 H25 H 0 1 N N N 4.167 -9.616 -0.344 4.692 -2.714 1.287 H25 LR6 54 LR6 H26 H26 H 0 1 N N N 0.575 -10.626 -0.422 5.496 -3.375 -1.733 H26 LR6 55 LR6 H27 H27 H 0 1 N N N 0.192 -9.695 -1.910 3.984 -2.691 -2.376 H27 LR6 56 LR6 H28 H28 H 0 1 N N N 1.263 -11.135 -2.002 4.852 -1.856 -1.065 H28 LR6 57 LR6 OP3 OP3 O 0 1 N Y N 3.517 -9.055 8.067 -4.816 -2.975 -1.592 OP3 LR6 58 LR6 HOP3 H30 H 0 1 N N N 3.928 -9.898 8.221 -5.708 -3.345 -1.645 H30 LR6 59 # 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 LR6 "C9'" "C8'" SING N N 1 LR6 "C11'" "C8'" SING N N 2 LR6 "C8'" "C10'" SING N N 3 LR6 "C8'" "N4'" SING N N 4 LR6 "C7'" "N3'" SING N N 5 LR6 "N4'" CD DOUB N N 6 LR6 "N3'" CD SING N N 7 LR6 CD "N2'" SING N N 8 LR6 "N2'" "C6'" SING N N 9 LR6 "N2'" "C2'" SING N N 10 LR6 "O3'" "C3'" SING N N 11 LR6 "C6'" "C4'" SING N N 12 LR6 "C2'" "C3'" SING N N 13 LR6 "C2'" "C1'" SING N N 14 LR6 "C3'" "C4'" SING N N 15 LR6 O2 C2 DOUB N N 16 LR6 "C1'" "O4'" SING N N 17 LR6 "C1'" N1 SING N N 18 LR6 "C4'" "O4'" SING N N 19 LR6 "C4'" "C5'" SING N N 20 LR6 C2 N1 SING N N 21 LR6 C2 N3 SING N N 22 LR6 N1 C6 SING N N 23 LR6 "C5'" "O5'" SING N N 24 LR6 N3 C4 SING N N 25 LR6 "O5'" P SING N N 26 LR6 C6 C5 DOUB N N 27 LR6 C4 C5 SING N N 28 LR6 C4 O4 DOUB N N 29 LR6 C5 C5M SING N N 30 LR6 OP1 P DOUB N N 31 LR6 P OP2 SING N N 32 LR6 C6 H1 SING N N 33 LR6 N3 H2 SING N N 34 LR6 "C1'" H3 SING N N 35 LR6 "C2'" H4 SING N N 36 LR6 "C3'" H5 SING N N 37 LR6 "C5'" H6 SING N N 38 LR6 "C5'" H7 SING N N 39 LR6 C5M H8 SING N N 40 LR6 C5M H9 SING N N 41 LR6 C5M H10 SING N N 42 LR6 "C6'" H11 SING N N 43 LR6 "C6'" H12 SING N N 44 LR6 "C7'" H13 SING N N 45 LR6 "C7'" H14 SING N N 46 LR6 "C7'" H15 SING N N 47 LR6 "C9'" H16 SING N N 48 LR6 "C9'" H17 SING N N 49 LR6 "C9'" H18 SING N N 50 LR6 "N3'" H19 SING N N 51 LR6 "O3'" "HO3'" SING N N 52 LR6 OP2 HOP2 SING N N 53 LR6 "C10'" H23 SING N N 54 LR6 "C10'" H24 SING N N 55 LR6 "C10'" H25 SING N N 56 LR6 "C11'" H26 SING N N 57 LR6 "C11'" H27 SING N N 58 LR6 "C11'" H28 SING N N 59 LR6 P OP3 SING N N 60 LR6 OP3 HOP3 SING N N 61 # 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 LR6 InChI InChI 1.06 "InChI=1S/C17H28N5O8P/c1-9-6-21(15(25)19-12(9)24)13-10-11(23)17(30-13,8-29-31(26,27)28)7-22(10)14(18-5)20-16(2,3)4/h6,10-11,13,23H,7-8H2,1-5H3,(H,18,20)(H,19,24,25)(H2,26,27,28)/t10-,11+,13-,17-/m1/s1" LR6 InChIKey InChI 1.06 VZAHOKWRQQERGL-WYFUGZQLSA-N LR6 SMILES_CANONICAL CACTVS 3.385 "CNC(=NC(C)(C)C)N1C[C@]2(CO[P](O)(O)=O)O[C@H]([C@H]1[C@@H]2O)N3C=C(C)C(=O)NC3=O" LR6 SMILES CACTVS 3.385 "CNC(=NC(C)(C)C)N1C[C]2(CO[P](O)(O)=O)O[CH]([CH]1[CH]2O)N3C=C(C)C(=O)NC3=O" LR6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2[C@H]3[C@@H]([C@@](O2)(CN3C(=NC(C)(C)C)NC)COP(=O)(O)O)O" LR6 SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2C3C(C(O2)(CN3C(=NC(C)(C)C)NC)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id LR6 _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})-5-(~{N}'-~{tert}-butyl-~{N}-methyl-carbamimidoyl)-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-oxidanyl-2-oxa-5-azabicyclo[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 LR6 "Create component" 2022-12-07 PDBJ LR6 "Initial release" 2023-08-09 RCSB #