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 
# 
