data_L5R # _chem_comp.id L5R _chem_comp.name "[(2R,3S,5R)-5-[(1R,6R)-3,5-bis(oxidanylidene)-8-phenyl-6-(2-phenylethynyl)-2,4-diazabicyclo[4.2.0]oct-7-en-2-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C25 H23 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-08-16 _chem_comp.pdbx_modified_date 2024-05-24 _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 510.432 _chem_comp.one_letter_code ? _chem_comp.three_letter_code L5R _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 8REV _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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 L5R C5 C1 C 0 1 N N R N N N 202.746 155.656 175.606 -2.544 -0.307 -1.061 C5 L5R 1 L5R C6 C2 C 0 1 N N R N N N 202.488 154.103 175.494 -1.387 -0.669 -0.096 C6 L5R 2 L5R N1 N1 N 0 1 N N N N N N 203.622 153.307 175.122 -0.032 -0.628 -0.668 N1 L5R 3 L5R C2 C3 C 0 1 N N N N N N 204.315 153.738 174.034 0.147 -0.293 -1.954 C2 L5R 4 L5R N3 N2 N 0 1 N N N N N N 204.465 155.120 173.957 -0.832 0.021 -2.804 N3 L5R 5 L5R C4 C4 C 0 1 N N N N N N 203.959 156.059 174.816 -2.136 0.043 -2.477 C4 L5R 6 L5R "C1'" C5 C 0 1 N N R N N N 203.968 152.102 175.915 1.125 -0.954 0.170 "C1'" L5R 7 L5R O4 O1 O 0 1 N N N N N N 204.470 157.166 174.931 -2.972 0.338 -3.304 O4 L5R 8 L5R O2 O2 O 0 1 N N N N N N 204.790 153.011 173.167 1.286 -0.274 -2.376 O2 L5R 9 L5R C7 C6 C 0 1 N N N N N N 201.371 155.731 174.937 -2.946 -1.765 -0.955 C7 L5R 10 L5R C8 C7 C 0 1 N N N N N N 201.613 154.522 174.315 -1.947 -2.077 -0.122 C8 L5R 11 L5R C21 C8 C 0 1 Y N N N N N 201.261 153.809 173.074 -1.538 -3.337 0.533 C21 L5R 12 L5R C10 C9 C 0 1 N N N N N N 202.841 156.183 176.957 -3.528 0.629 -0.493 C10 L5R 13 L5R C11 C10 C 0 1 N N N N N N 202.973 156.658 178.038 -4.312 1.376 -0.039 C11 L5R 14 L5R C12 C11 C 0 1 Y N N N N N 203.158 157.286 179.317 -5.269 2.287 0.513 C12 L5R 15 L5R C13 C12 C 0 1 Y N N N N N 202.092 157.932 179.942 -6.364 2.699 -0.247 C13 L5R 16 L5R C14 C13 C 0 1 Y N N N N N 202.270 158.537 181.173 -7.283 3.576 0.292 C14 L5R 17 L5R C15 C14 C 0 1 Y N N N N N 203.501 158.506 181.792 -7.120 4.047 1.582 C15 L5R 18 L5R C16 C15 C 0 1 Y N N N N N 204.562 157.871 181.184 -6.036 3.643 2.341 C16 L5R 19 L5R C17 C16 C 0 1 Y N N N N N 204.399 157.261 179.951 -5.113 2.762 1.816 C17 L5R 20 L5R "O4'" O3 O 0 1 N N N N N N 204.119 152.493 177.278 2.100 0.111 0.117 "O4'" L5R 21 L5R "C4'" C17 C 0 1 N N R N N N 205.506 152.826 177.473 3.345 -0.493 0.533 "C4'" L5R 22 L5R "C3'" C18 C 0 1 N N S N N N 206.128 152.702 176.078 3.355 -1.882 -0.143 "C3'" L5R 23 L5R "C2'" C19 C 0 1 N N N N N N 205.325 151.526 175.551 1.861 -2.192 -0.387 "C2'" L5R 24 L5R "O3'" O4 O 0 1 N Y N N N N 207.516 152.428 175.900 3.937 -2.856 0.725 "O3'" L5R 25 L5R "C5'" C20 C 0 1 N N N N N N 205.638 154.213 178.049 4.530 0.345 0.048 "C5'" L5R 26 L5R "O5'" O5 O 0 1 N N N N N N 205.872 154.146 179.470 4.526 1.608 0.716 "O5'" L5R 27 L5R C22 C21 C 0 1 Y N N N N N 200.771 154.491 171.966 -1.094 -4.414 -0.235 C22 L5R 28 L5R C23 C22 C 0 1 Y N N N N N 200.443 153.815 170.806 -0.714 -5.588 0.384 C23 L5R 29 L5R C24 C23 C 0 1 Y N N N N N 200.598 152.449 170.733 -0.773 -5.698 1.761 C24 L5R 30 L5R C25 C24 C 0 1 Y N N N N N 201.082 151.757 171.820 -1.212 -4.634 2.528 C25 L5R 31 L5R C26 C25 C 0 1 Y N N N N N 201.411 152.431 172.982 -1.589 -3.453 1.923 C26 L5R 32 L5R P P1 P 0 1 N N N N N N 207.302 153.873 180.136 5.634 2.745 0.450 P L5R 33 L5R OP1 O6 O 0 1 N N N N N N 208.058 152.873 179.328 6.984 2.178 0.668 OP1 L5R 34 L5R OP2 O7 O 0 1 N N N N N N 207.949 155.187 180.420 5.511 3.269 -1.067 OP2 L5R 35 L5R H6 H1 H 0 1 N N N N N N 201.910 153.712 176.344 -1.455 -0.184 0.878 H6 L5R 36 L5R H3 H2 H 0 1 N N N N N N 205.003 155.466 173.188 -0.587 0.247 -3.715 "H1'" L5R 37 L5R "H1'" H3 H 0 1 N N N N N N 203.191 151.332 175.803 0.810 -1.129 1.199 H1 L5R 38 L5R H71 H4 H 0 1 N N N N N N 200.553 156.436 174.947 -3.747 -2.341 -1.393 H71 L5R 39 L5R H7 H7 H 0 1 N N N N N N 201.124 157.960 179.463 -6.492 2.332 -1.254 H7 L5R 40 L5R H8 H8 H 0 1 N N N N N N 201.440 159.036 181.651 -8.131 3.896 -0.295 H8 L5R 41 L5R H9 H9 H 0 1 N N N N N N 203.634 158.979 182.754 -7.841 4.734 1.999 H9 L5R 42 L5R H10 H10 H 0 1 N N N N N N 205.526 157.849 181.671 -5.913 4.015 3.348 H10 L5R 43 L5R H11 H11 H 0 1 N N N N N N 205.235 156.765 179.480 -4.269 2.443 2.411 H11 L5R 44 L5R "H4'" H12 H 0 1 N N N N N N 205.984 152.101 178.148 3.372 -0.596 1.617 "H4'" L5R 45 L5R "H3'" H13 H 0 1 N N N N N N 205.852 153.596 175.499 3.896 -1.842 -1.089 "H3'" L5R 46 L5R "H2'" H14 H 0 1 N N N N N N 205.546 150.587 176.079 1.564 -3.089 0.155 "H2'" L5R 47 L5R "H2''" H15 H 0 0 N N N N N N 205.449 151.375 174.468 1.664 -2.306 -1.453 "H2''" L5R 48 L5R "HO3'" H16 H 0 0 N Y N N N N 208.028 153.158 176.227 3.969 -3.747 0.350 "HO3'" L5R 49 L5R "H5'" H17 H 0 1 N N N N N N 206.482 154.727 177.566 5.460 -0.180 0.269 "H5'" L5R 50 L5R "H5''" H18 H 0 0 N N N N N N 204.711 154.774 177.860 4.448 0.502 -1.027 "H5''" L5R 51 L5R H19 H19 H 0 1 N N N N N N 200.645 155.563 172.012 -1.049 -4.330 -1.310 H19 L5R 52 L5R H20 H20 H 0 1 N N N N N N 200.064 154.360 169.954 -0.370 -6.422 -0.210 H20 L5R 53 L5R H21 H21 H 0 1 N N N N N N 200.341 151.922 169.826 -0.474 -6.619 2.240 H21 L5R 54 L5R H22 H22 H 0 1 N N N N N N 201.205 150.685 171.765 -1.256 -4.726 3.603 H22 L5R 55 L5R H23 H23 H 0 1 N N N N N N 201.790 151.879 173.829 -1.932 -2.622 2.523 H23 L5R 56 L5R HOP2 H25 H 0 0 N N N N N N 208.811 155.209 180.021 4.650 3.654 -1.282 HOP2 L5R 57 L5R OP3 O8 O 0 1 N Y N N N N 206.795 153.208 181.513 5.398 3.973 1.463 OP3 L5R 58 L5R HOP3 H27 H 0 0 N Y N N N N 207.075 152.301 181.549 6.031 4.697 1.359 HOP3 L5R 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 L5R C24 C23 DOUB Y N 1 L5R C24 C25 SING Y N 2 L5R C23 C22 SING Y N 3 L5R C25 C26 DOUB Y N 4 L5R C22 C21 DOUB Y N 5 L5R C26 C21 SING Y N 6 L5R C21 C8 SING N N 7 L5R O2 C2 DOUB N N 8 L5R N3 C2 SING N N 9 L5R N3 C4 SING N N 10 L5R C2 N1 SING N N 11 L5R C8 C7 DOUB N N 12 L5R C8 C6 SING N N 13 L5R C4 O4 DOUB N N 14 L5R C4 C5 SING N N 15 L5R C7 C5 SING N N 16 L5R N1 C6 SING N N 17 L5R N1 "C1'" SING N N 18 L5R C6 C5 SING N N 19 L5R "C2'" "C1'" SING N N 20 L5R "C2'" "C3'" SING N N 21 L5R C5 C10 SING N N 22 L5R "O3'" "C3'" SING N N 23 L5R "C1'" "O4'" SING N N 24 L5R "C3'" "C4'" SING N N 25 L5R C10 C11 TRIP N N 26 L5R "O4'" "C4'" SING N N 27 L5R "C4'" "C5'" SING N N 28 L5R C11 C12 SING N N 29 L5R "C5'" "O5'" SING N N 30 L5R C12 C13 DOUB Y N 31 L5R C12 C17 SING Y N 32 L5R OP1 P DOUB N N 33 L5R "O5'" P SING N N 34 L5R C13 C14 SING Y N 35 L5R C17 C16 DOUB Y N 36 L5R P OP2 SING N N 37 L5R C14 C15 DOUB Y N 38 L5R C16 C15 SING Y N 39 L5R C6 H6 SING N N 40 L5R N3 H3 SING N N 41 L5R "C1'" "H1'" SING N N 42 L5R C7 H71 SING N N 43 L5R C13 H7 SING N N 44 L5R C14 H8 SING N N 45 L5R C15 H9 SING N N 46 L5R C16 H10 SING N N 47 L5R C17 H11 SING N N 48 L5R "C4'" "H4'" SING N N 49 L5R "C3'" "H3'" SING N N 50 L5R "C2'" "H2'" SING N N 51 L5R "C2'" "H2''" SING N N 52 L5R "O3'" "HO3'" SING N N 53 L5R "C5'" "H5'" SING N N 54 L5R "C5'" "H5''" SING N N 55 L5R C22 H19 SING N N 56 L5R C23 H20 SING N N 57 L5R C24 H21 SING N N 58 L5R C25 H22 SING N N 59 L5R C26 H23 SING N N 60 L5R OP2 HOP2 SING N N 61 L5R P OP3 SING N N 62 L5R OP3 HOP3 SING N N 63 # 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 L5R InChI InChI 1.06 "InChI=1S/C25H23N2O8P/c28-19-13-21(35-20(19)15-34-36(31,32)33)27-22-18(17-9-5-2-6-10-17)14-25(22,23(29)26-24(27)30)12-11-16-7-3-1-4-8-16/h1-10,14,19-22,28H,13,15H2,(H,26,29,30)(H2,31,32,33)/t19-,20+,21+,22+,25-/m0/s1" L5R InChIKey InChI 1.06 XLEZPOFLRQLYTH-UDCDXJBOSA-N L5R SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2[C@@H]3C(=C[C@]3(C#Cc4ccccc4)C(=O)NC2=O)c5ccccc5" L5R SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2[CH]3C(=C[C]3(C#Cc4ccccc4)C(=O)NC2=O)c5ccccc5" L5R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C#C[C@]23C=C([C@H]2N(C(=O)NC3=O)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O)c5ccccc5" L5R SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C#CC23C=C(C2N(C(=O)NC3=O)C4CC(C(O4)COP(=O)(O)O)O)c5ccccc5" # _pdbx_chem_comp_identifier.comp_id L5R _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~{R},3~{S},5~{R})-5-[(1~{R},6~{R})-3,5-bis(oxidanylidene)-8-phenyl-6-(2-phenylethynyl)-2,4-diazabicyclo[4.2.0]oct-7-en-2-yl]-3-oxidanyl-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 L5R "Create component" 2023-08-16 PDBE L5R "Modify linking type" 2023-12-16 PDBE L5R "Modify coordinates" 2023-12-19 PDBE L5R "Modify leaving atom flag" 2023-12-20 PDBE L5R "Initial release" 2024-05-29 RCSB #