data_YK5 # _chem_comp.id YK5 _chem_comp.name "7-[(1~{S})-1-[5-(carbamimidamidomethyl)-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-carboxylic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C24 H26 F N5 O6 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-19 _chem_comp.pdbx_modified_date 2024-07-05 _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 531.557 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YK5 _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 8PGL _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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 YK5 C13 C1 C 0 1 Y N N N N N -21.047 -13.148 6.493 3.747 0.160 1.595 C13 YK5 1 YK5 C14 C2 C 0 1 Y N N N N N -20.194 -12.154 6.004 4.748 0.500 0.704 C14 YK5 2 YK5 C15 C3 C 0 1 N N N N N N -19.585 -12.251 4.594 6.192 0.288 1.080 C15 YK5 3 YK5 O18 O1 O 0 1 N N N N N N -20.217 -11.641 2.012 6.681 -1.436 -0.855 O18 YK5 4 YK5 C20 C4 C 0 1 Y N N N N N -19.887 -11.073 6.827 4.429 1.036 -0.534 C20 YK5 5 YK5 C22 C5 C 0 1 Y N N N N N -20.425 -10.973 8.092 3.107 1.233 -0.883 C22 YK5 6 YK5 C23 C6 C 0 1 Y N N N N N -21.995 -12.813 10.957 -0.273 2.017 0.287 C23 YK5 7 YK5 C24 C7 C 0 1 Y N N N N N -21.702 -14.188 10.988 -0.171 2.918 1.350 C24 YK5 8 YK5 C25 C8 C 0 1 Y N N N N N -21.985 -14.898 12.171 -1.259 3.658 1.719 C25 YK5 9 YK5 C26 C9 C 0 1 Y N N N N N -22.562 -14.246 13.286 -2.466 3.520 1.046 C26 YK5 10 YK5 C28 C10 C 0 1 N N N N N N -25.545 -13.087 15.392 -4.962 0.162 -1.207 C28 YK5 11 YK5 C01 C11 C 0 1 N N N N N N -22.737 -12.488 15.777 -4.804 3.689 -0.378 C01 YK5 12 YK5 C02 C12 C 0 1 N N S N N N -23.397 -12.079 14.491 -3.905 2.500 -0.724 C02 YK5 13 YK5 C03 C13 C 0 1 Y N N N N N -22.834 -12.893 13.268 -2.589 2.638 -0.004 C03 YK5 14 YK5 C04 C14 C 0 1 Y N N N N N -22.549 -12.183 12.066 -1.493 1.873 -0.399 C04 YK5 15 YK5 C06 C15 C 0 1 Y N N N N N -22.332 -10.649 10.550 -0.020 0.462 -1.367 C06 YK5 16 YK5 C07 C16 C 0 1 N N N N N N -22.570 -9.311 9.969 0.532 -0.547 -2.274 C07 YK5 17 YK5 C10 C17 C 0 1 Y N N N N N -21.862 -11.824 9.969 0.676 1.099 -0.354 C10 YK5 18 YK5 C11 C18 C 0 1 Y N N N N N -21.296 -11.950 8.563 2.094 0.891 0.013 C11 YK5 19 YK5 C12 C19 C 0 1 Y N N N N N -21.573 -13.055 7.780 2.423 0.352 1.257 C12 YK5 20 YK5 C17 C20 C 0 1 N N N N N N -20.876 -9.759 3.737 8.444 -1.406 1.106 C17 YK5 21 YK5 C29 C21 C 0 1 N N N N N N -26.892 -12.821 15.029 -5.595 -0.878 -0.262 C29 YK5 22 YK5 C30 C22 C 0 1 N N N N N N -28.082 -13.390 15.725 -4.815 -2.194 -0.312 C30 YK5 23 YK5 C32 C23 C 0 1 N N N N N N -30.135 -14.647 15.157 -4.985 -4.469 0.607 C32 YK5 24 YK5 C36 C24 C 0 1 N N N N N N -25.689 -11.501 13.687 -4.891 0.931 0.947 C36 YK5 25 YK5 F21 F1 F 0 1 N N N N N N -19.092 -10.090 6.416 5.412 1.366 -1.400 F21 YK5 26 YK5 N05 N1 N 0 1 Y N N N N N -22.701 -10.884 11.783 -1.317 0.933 -1.386 N05 YK5 27 YK5 N27 N2 N 0 1 N N N N N N -24.818 -12.238 14.580 -4.560 1.256 -0.310 N27 YK5 28 YK5 N31 N3 N 0 1 N N N N N N -28.767 -14.334 14.784 -5.503 -3.200 0.500 N31 YK5 29 YK5 N33 N4 N 0 1 N N N N N N -30.719 -14.103 16.153 -3.821 -4.794 -0.050 N33 YK5 30 YK5 N34 N5 N 0 1 N N N N N N -30.724 -15.596 14.252 -5.597 -5.365 1.329 N34 YK5 31 YK5 O08 O2 O 0 1 N N N N N N -22.547 -8.288 10.706 -0.248 -1.097 -3.227 O08 YK5 32 YK5 O09 O3 O 0 1 N N N N N N -23.042 -9.313 8.768 1.694 -0.890 -2.168 O09 YK5 33 YK5 O19 O4 O 0 1 N N N N N N -22.056 -12.158 3.511 5.984 -2.330 1.319 O19 YK5 34 YK5 O35 O5 O 0 1 N N N N N N -27.005 -11.893 14.039 -5.484 -0.269 1.058 O35 YK5 35 YK5 O37 O6 O 0 1 N N N N N N -25.441 -10.675 12.873 -4.674 1.653 1.900 O37 YK5 36 YK5 S16 S1 S 0 1 N N N N N N -20.749 -11.519 3.355 6.713 -1.372 0.564 S16 YK5 37 YK5 H131 H1 H 0 0 N N N N N N -21.300 -13.993 5.870 4.002 -0.261 2.557 H131 YK5 38 YK5 H151 H2 H 0 0 N N N N N N -19.405 -13.307 4.346 6.811 1.034 0.581 H151 YK5 39 YK5 H152 H3 H 0 0 N N N N N N -18.633 -11.701 4.569 6.304 0.385 2.160 H152 YK5 40 YK5 H221 H4 H 0 0 N N N N N N -20.169 -10.133 8.720 2.858 1.651 -1.848 H221 YK5 41 YK5 H241 H5 H 0 0 N N N N N N -21.273 -14.685 10.130 0.764 3.030 1.878 H241 YK5 42 YK5 H251 H6 H 0 0 N N N N N N -21.759 -15.953 12.228 -1.180 4.354 2.541 H251 YK5 43 YK5 H261 H7 H 0 0 N N N N N N -22.795 -14.820 14.171 -3.317 4.111 1.350 H261 YK5 44 YK5 H281 H8 H 0 0 N N N N N N -25.285 -14.138 15.195 -4.092 -0.259 -1.711 H281 YK5 45 YK5 H1 H9 H 0 1 N N N N N N -25.372 -12.859 16.454 -5.693 0.512 -1.935 H1 YK5 46 YK5 H011 H10 H 0 0 N N N N N N -23.155 -11.900 16.607 -4.316 4.614 -0.686 H011 YK5 47 YK5 H012 H11 H 0 0 N N N N N N -22.918 -13.558 15.958 -5.756 3.589 -0.899 H012 YK5 48 YK5 H013 H12 H 0 0 N N N N N N -21.654 -12.306 15.707 -4.978 3.711 0.698 H013 YK5 49 YK5 H021 H13 H 0 0 N N N N N N -23.166 -11.019 14.311 -3.730 2.477 -1.800 H021 YK5 50 YK5 H121 H14 H 0 0 N N N N N N -22.198 -13.847 8.166 1.643 0.081 1.953 H121 YK5 51 YK5 H173 H15 H 0 0 N N N N N N -21.278 -9.632 4.753 8.997 -0.610 0.607 H173 YK5 52 YK5 H171 H16 H 0 0 N N N N N N -19.879 -9.298 3.677 8.490 -1.259 2.185 H171 YK5 53 YK5 H172 H17 H 0 0 N N N N N N -21.548 -9.274 3.014 8.885 -2.370 0.851 H172 YK5 54 YK5 H2 H18 H 0 1 N N N N N N -26.889 -13.644 14.300 -6.640 -1.044 -0.521 H2 YK5 55 YK5 H302 H19 H 0 0 N N N N N N -28.771 -12.580 16.007 -4.753 -2.540 -1.344 H302 YK5 56 YK5 H301 H20 H 0 0 N N N N N N -27.762 -13.931 16.628 -3.810 -2.036 0.079 H301 YK5 57 YK5 H051 H21 H 0 0 N N N N N N -23.046 -10.195 12.420 -2.004 0.643 -2.006 H051 YK5 58 YK5 H311 H22 H 0 0 N N N N N N -28.322 -14.714 13.973 -6.324 -2.971 0.964 H311 YK5 59 YK5 H331 H23 H 0 0 N N N N N N -30.233 -13.432 16.712 -3.366 -4.127 -0.588 H331 YK5 60 YK5 H3 H24 H 0 1 N N N N N N -31.663 -14.348 16.374 -3.455 -5.689 0.025 H3 YK5 61 YK5 H341 H25 H 0 0 N N N N N N -31.675 -15.798 14.487 -5.231 -6.260 1.404 H341 YK5 62 YK5 H4 H26 H 0 1 N N N N N N -22.923 -7.552 10.238 0.204 -1.752 -3.776 H4 YK5 63 # 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 YK5 O18 S16 DOUB N N 1 YK5 S16 O19 DOUB N N 2 YK5 S16 C17 SING N N 3 YK5 S16 C15 SING N N 4 YK5 C15 C14 SING N N 5 YK5 C14 C13 DOUB Y N 6 YK5 C14 C20 SING Y N 7 YK5 F21 C20 SING N N 8 YK5 C13 C12 SING Y N 9 YK5 C20 C22 DOUB Y N 10 YK5 C12 C11 DOUB Y N 11 YK5 C22 C11 SING Y N 12 YK5 C11 C10 SING N N 13 YK5 O09 C07 DOUB N N 14 YK5 C07 C06 SING N N 15 YK5 C07 O08 SING N N 16 YK5 C10 C06 DOUB Y N 17 YK5 C10 C23 SING Y N 18 YK5 C06 N05 SING Y N 19 YK5 C23 C24 DOUB Y N 20 YK5 C23 C04 SING Y N 21 YK5 C24 C25 SING Y N 22 YK5 N05 C04 SING Y N 23 YK5 C04 C03 DOUB Y N 24 YK5 C25 C26 DOUB Y N 25 YK5 O37 C36 DOUB N N 26 YK5 C03 C26 SING Y N 27 YK5 C03 C02 SING N N 28 YK5 C36 O35 SING N N 29 YK5 C36 N27 SING N N 30 YK5 O35 C29 SING N N 31 YK5 N34 C32 DOUB N N 32 YK5 C02 N27 SING N N 33 YK5 C02 C01 SING N N 34 YK5 N27 C28 SING N N 35 YK5 N31 C32 SING N N 36 YK5 N31 C30 SING N N 37 YK5 C29 C28 SING N N 38 YK5 C29 C30 SING N N 39 YK5 C32 N33 SING N N 40 YK5 C13 H131 SING N N 41 YK5 C15 H151 SING N N 42 YK5 C15 H152 SING N N 43 YK5 C22 H221 SING N N 44 YK5 C24 H241 SING N N 45 YK5 C25 H251 SING N N 46 YK5 C26 H261 SING N N 47 YK5 C28 H281 SING N N 48 YK5 C28 H1 SING N N 49 YK5 C01 H011 SING N N 50 YK5 C01 H012 SING N N 51 YK5 C01 H013 SING N N 52 YK5 C02 H021 SING N N 53 YK5 C12 H121 SING N N 54 YK5 C17 H173 SING N N 55 YK5 C17 H171 SING N N 56 YK5 C17 H172 SING N N 57 YK5 C29 H2 SING N N 58 YK5 C30 H302 SING N N 59 YK5 C30 H301 SING N N 60 YK5 N05 H051 SING N N 61 YK5 N31 H311 SING N N 62 YK5 N33 H331 SING N N 63 YK5 N33 H3 SING N N 64 YK5 N34 H341 SING N N 65 YK5 O08 H4 SING N N 66 # 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 YK5 InChI InChI 1.06 "InChI=1S/C24H26FN5O6S/c1-12(30-10-15(36-24(30)33)9-28-23(26)27)16-4-3-5-17-19(21(22(31)32)29-20(16)17)13-6-7-14(18(25)8-13)11-37(2,34)35/h3-8,12,15,29H,9-11H2,1-2H3,(H,31,32)(H4,26,27,28)/t12-,15+/m0/s1" YK5 InChIKey InChI 1.06 XCNBPRROAQZFCF-SWLSCSKDSA-N YK5 SMILES_CANONICAL CACTVS 3.385 "C[C@H](N1C[C@@H](CNC(N)=N)OC1=O)c2cccc3c2[nH]c(C(O)=O)c3c4ccc(C[S](C)(=O)=O)c(F)c4" YK5 SMILES CACTVS 3.385 "C[CH](N1C[CH](CNC(N)=N)OC1=O)c2cccc3c2[nH]c(C(O)=O)c3c4ccc(C[S](C)(=O)=O)c(F)c4" YK5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/N)\NCC1CN(C(=O)O1)[C@@H](C)c2cccc3c2[nH]c(c3c4ccc(c(c4)F)CS(=O)(=O)C)C(=O)O" YK5 SMILES "OpenEye OEToolkits" 2.0.7 "CC(c1cccc2c1[nH]c(c2c3ccc(c(c3)F)CS(=O)(=O)C)C(=O)O)N4CC(OC4=O)CNC(=N)N" # _pdbx_chem_comp_identifier.comp_id YK5 _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 "7-[(1~{S})-1-[5-(carbamimidamidomethyl)-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-carboxylic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YK5 "Create component" 2023-06-21 PDBE YK5 "Initial release" 2024-07-10 RCSB #