data_XKN
# 
_chem_comp.id                                    XKN 
_chem_comp.name                                  "3-ethynyl-5-{[(3R)-4-{1-[(2-methoxyphenyl)methyl]-1H-benzimidazole-5-carbonyl}-3-methylpiperazin-1-yl]methyl}benzene-1-sulfonyl fluoride" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C30 H29 F N4 O4 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-11-23 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        560.639 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XKN 
_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        8F93 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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 
XKN C1  C1  C 0 1 N N N N N N 32.144 7.753  26.855 -4.074 3.256  -3.870 C1  XKN 1  
XKN C10 C2  C 0 1 N N R N N N 25.753 3.650  25.530 -1.456 -3.414 1.122  C10 XKN 2  
XKN C11 C3  C 0 1 N N N N N N 26.506 4.762  24.827 -0.932 -4.843 1.280  C11 XKN 3  
XKN C12 C4  C 0 1 N N N N N N 24.067 2.315  24.473 0.876  -2.995 0.490  C12 XKN 4  
XKN C13 C5  C 0 1 Y N N N N N 23.557 1.318  23.471 1.954  -2.071 0.085  C13 XKN 5  
XKN C14 C6  C 0 1 Y N N N N N 23.028 0.096  23.886 3.079  -2.562 -0.571 C14 XKN 6  
XKN C15 C7  C 0 1 Y N N N N N 22.481 -0.762 22.934 4.091  -1.682 -0.951 C15 XKN 7  
XKN C16 C8  C 0 1 Y N N N N N 21.548 -2.358 21.867 5.870  -0.690 -1.706 C16 XKN 8  
XKN C17 C9  C 0 1 N N N N N N 21.476 -1.500 19.483 5.426  1.716  -1.093 C17 XKN 9  
XKN C18 C10 C 0 1 Y N N N N N 22.574 -1.973 18.559 6.071  2.027  0.233  C18 XKN 10 
XKN C19 C11 C 0 1 Y N N N N N 22.836 -3.340 18.465 7.437  1.845  0.401  C19 XKN 11 
XKN C2  C12 C 0 1 N N N N N N 31.504 6.819  27.182 -4.423 2.519  -3.025 C2  XKN 12 
XKN C20 C13 C 0 1 N N N N N N 22.143 -5.524 19.108 9.592  1.223  -0.385 C20 XKN 13 
XKN C21 C14 C 0 1 Y N N N N N 23.836 -3.818 17.635 8.027  2.133  1.623  C21 XKN 14 
XKN C22 C15 C 0 1 Y N N N N N 24.575 -2.933 16.878 7.255  2.600  2.669  C22 XKN 15 
XKN C23 C16 C 0 1 Y N N N N N 24.318 -1.584 16.937 5.895  2.780  2.499  C23 XKN 16 
XKN C24 C17 C 0 1 Y N N N N N 23.316 -1.104 17.763 5.305  2.499  1.280  C24 XKN 17 
XKN C25 C18 C 0 1 Y N N N N N 22.418 -0.371 21.594 3.961  -0.311 -0.665 C25 XKN 18 
XKN C26 C19 C 0 1 Y N N N N N 22.902 0.859  21.161 2.831  0.162  -0.008 C26 XKN 19 
XKN C27 C20 C 0 1 Y N N N N N 23.451 1.690  22.123 1.839  -0.701 0.356  C27 XKN 20 
XKN C28 C21 C 0 1 N N N N N N 26.498 1.884  24.001 -0.747 -1.183 0.177  C28 XKN 21 
XKN C29 C22 C 0 1 N N N N N N 27.247 1.218  25.136 -1.947 -1.259 -0.772 C29 XKN 22 
XKN C3  C23 C 0 1 Y N N N N N 30.741 5.669  27.574 -4.847 1.620  -1.994 C3  XKN 23 
XKN C30 C24 C 0 1 Y N N N N N 30.187 4.855  26.591 -4.365 0.311  -1.963 C30 XKN 24 
XKN C4  C25 C 0 1 Y N N N N N 30.558 5.331  28.911 -5.741 2.051  -1.013 C4  XKN 25 
XKN C5  C26 C 0 1 Y N N N N N 29.820 4.206  29.246 -6.147 1.180  -0.023 C5  XKN 26 
XKN C6  C27 C 0 1 Y N N N N N 29.269 3.412  28.249 -5.669 -0.118 -0.001 C6  XKN 27 
XKN C7  C28 C 0 1 Y N N N N N 29.445 3.734  26.911 -4.778 -0.550 -0.967 C7  XKN 28 
XKN C8  C29 C 0 1 N N N N N N 28.849 2.912  25.795 -4.258 -1.964 -0.932 C8  XKN 29 
XKN C9  C30 C 0 1 N N N N N N 26.550 3.016  26.646 -2.629 -3.402 0.135  C9  XKN 30 
XKN N1  N1  N 0 1 N N N N N N 27.656 2.159  26.190 -3.030 -2.014 -0.127 N1  XKN 31 
XKN N2  N2  N 0 1 N N N N N N 25.367 2.579  24.597 -0.391 -2.549 0.592  N2  XKN 32 
XKN N3  N3  N 0 1 Y N N N N N 21.920 -2.026 23.079 5.281  -1.843 -1.587 N3  XKN 33 
XKN N4  N4  N 0 1 Y N N N N N 21.816 -1.422 20.914 5.102  0.288  -1.155 N4  XKN 34 
XKN O1  O1  O 0 1 N N N N N N 30.407 4.712  31.699 -6.848 3.021  1.607  O1  XKN 35 
XKN O2  O2  O 0 1 N N N N N N 29.991 2.448  31.097 -8.578 1.449  0.721  O2  XKN 36 
XKN O3  O3  O 0 1 N N N N N N 22.058 -4.111 19.274 8.194  1.386  -0.630 O3  XKN 37 
XKN O4  O4  O 0 1 N N N N N N 23.245 2.938  25.148 1.132  -4.159 0.732  O4  XKN 38 
XKN S1  S1  S 0 1 N N N N N N 29.553 3.817  30.947 -7.275 1.723  1.217  S1  XKN 39 
XKN F1  F1  F 0 1 N Y N N N N 28.015 4.115  31.250 -7.067 0.772  2.500  F1  XKN 40 
XKN H1  H1  H 0 1 N N N N N N 32.720 8.593  26.561 -3.763 3.914  -4.626 H1  XKN 41 
XKN H2  H2  H 0 1 N N N N N N 24.839 4.081  25.966 -1.788 -3.037 2.089  H2  XKN 42 
XKN H3  H3  H 0 1 N N N N N N 26.776 5.540  25.556 -0.512 -5.183 0.333  H3  XKN 43 
XKN H4  H4  H 0 1 N N N N N N 27.420 4.354  24.371 -0.159 -4.863 2.048  H4  XKN 44 
XKN H5  H5  H 0 1 N N N N N N 25.869 5.198  24.044 -1.751 -5.501 1.571  H5  XKN 45 
XKN H6  H6  H 0 1 N N N N N N 23.042 -0.181 24.930 3.167  -3.617 -0.785 H6  XKN 46 
XKN H7  H7  H 0 1 N N N N N N 21.067 -3.299 21.642 6.831  -0.532 -2.173 H7  XKN 47 
XKN H8  H8  H 0 1 N N N N N N 21.172 -0.495 19.155 4.513  2.301  -1.200 H8  XKN 48 
XKN H9  H9  H 0 1 N N N N N N 20.628 -2.192 19.377 6.115  1.967  -1.900 H9  XKN 49 
XKN H10 H10 H 0 1 N N N N N N 21.467 -6.019 19.820 10.027 2.183  -0.108 H10 XKN 50 
XKN H11 H11 H 0 1 N N N N N N 21.852 -5.791 18.081 9.738  0.510  0.427  H11 XKN 51 
XKN H12 H12 H 0 1 N N N N N N 23.176 -5.853 19.294 10.078 0.851  -1.287 H12 XKN 52 
XKN H13 H13 H 0 1 N N N N N N 24.036 -4.878 17.581 9.089  1.992  1.756  H13 XKN 53 
XKN H14 H14 H 0 1 N N N N N N 25.360 -3.302 16.235 7.713  2.820  3.622  H14 XKN 54 
XKN H15 H15 H 0 1 N N N N N N 24.898 -0.898 16.338 5.293  3.145  3.318  H15 XKN 55 
XKN H16 H16 H 0 1 N N N N N N 23.108 -0.045 17.790 4.242  2.641  1.150  H16 XKN 56 
XKN H17 H17 H 0 1 N N N N N N 22.852 1.152  20.123 2.735  1.215  0.209  H17 XKN 57 
XKN H18 H18 H 0 1 N N N N N N 23.812 2.663  21.823 0.963  -0.328 0.866  H18 XKN 58 
XKN H19 H19 H 0 1 N N N N N N 26.144 1.128  23.285 0.099  -0.725 -0.337 H19 XKN 59 
XKN H20 H20 H 0 1 N N N N N N 27.153 2.600  23.483 -1.010 -0.591 1.054  H20 XKN 60 
XKN H21 H21 H 0 1 N N N N N N 26.596 0.453  25.584 -2.293 -0.252 -1.002 H21 XKN 61 
XKN H22 H22 H 0 1 N N N N N N 28.148 0.738  24.726 -1.651 -1.762 -1.693 H22 XKN 62 
XKN H23 H23 H 0 1 N N N N N N 30.341 5.106  25.552 -3.670 -0.027 -2.717 H23 XKN 63 
XKN H24 H24 H 0 1 N N N N N N 30.990 5.944  29.688 -6.114 3.065  -1.029 H24 XKN 64 
XKN H25 H25 H 0 1 N N N N N N 28.698 2.536  28.518 -5.990 -0.796 0.776  H25 XKN 65 
XKN H26 H26 H 0 1 N N N N N N 29.610 2.199  25.445 -5.010 -2.616 -0.489 H26 XKN 66 
XKN H27 H27 H 0 1 N N N N N N 28.575 3.589  24.973 -4.041 -2.296 -1.947 H27 XKN 67 
XKN H28 H28 H 0 1 N N N N N N 26.971 3.820  27.268 -2.323 -3.875 -0.799 H28 XKN 68 
XKN H29 H29 H 0 1 N N N N N N 25.867 2.403  27.252 -3.469 -3.950 0.562  H29 XKN 69 
# 
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 
XKN C22 C23 DOUB Y N 1  
XKN C22 C21 SING Y N 2  
XKN C23 C24 SING Y N 3  
XKN C21 C19 DOUB Y N 4  
XKN C24 C18 DOUB Y N 5  
XKN C19 C18 SING Y N 6  
XKN C19 O3  SING N N 7  
XKN C18 C17 SING N N 8  
XKN C20 O3  SING N N 9  
XKN C17 N4  SING N N 10 
XKN N4  C25 SING Y N 11 
XKN N4  C16 SING Y N 12 
XKN C26 C25 DOUB Y N 13 
XKN C26 C27 SING Y N 14 
XKN C25 C15 SING Y N 15 
XKN C16 N3  DOUB Y N 16 
XKN C27 C13 DOUB Y N 17 
XKN C15 N3  SING Y N 18 
XKN C15 C14 DOUB Y N 19 
XKN C13 C14 SING Y N 20 
XKN C13 C12 SING N N 21 
XKN C28 N2  SING N N 22 
XKN C28 C29 SING N N 23 
XKN C12 N2  SING N N 24 
XKN C12 O4  DOUB N N 25 
XKN N2  C10 SING N N 26 
XKN C11 C10 SING N N 27 
XKN C29 N1  SING N N 28 
XKN C10 C9  SING N N 29 
XKN C8  N1  SING N N 30 
XKN C8  C7  SING N N 31 
XKN N1  C9  SING N N 32 
XKN C30 C7  DOUB Y N 33 
XKN C30 C3  SING Y N 34 
XKN C1  C2  TRIP N N 35 
XKN C7  C6  SING Y N 36 
XKN C2  C3  SING N N 37 
XKN C3  C4  DOUB Y N 38 
XKN C6  C5  DOUB Y N 39 
XKN C4  C5  SING Y N 40 
XKN C5  S1  SING N N 41 
XKN S1  O2  DOUB N N 42 
XKN S1  O1  DOUB N N 43 
XKN S1  F1  SING N N 44 
XKN C1  H1  SING N N 45 
XKN C10 H2  SING N N 46 
XKN C11 H3  SING N N 47 
XKN C11 H4  SING N N 48 
XKN C11 H5  SING N N 49 
XKN C14 H6  SING N N 50 
XKN C16 H7  SING N N 51 
XKN C17 H8  SING N N 52 
XKN C17 H9  SING N N 53 
XKN C20 H10 SING N N 54 
XKN C20 H11 SING N N 55 
XKN C20 H12 SING N N 56 
XKN C21 H13 SING N N 57 
XKN C22 H14 SING N N 58 
XKN C23 H15 SING N N 59 
XKN C24 H16 SING N N 60 
XKN C26 H17 SING N N 61 
XKN C27 H18 SING N N 62 
XKN C28 H19 SING N N 63 
XKN C28 H20 SING N N 64 
XKN C29 H21 SING N N 65 
XKN C29 H22 SING N N 66 
XKN C30 H23 SING N N 67 
XKN C4  H24 SING N N 68 
XKN C6  H25 SING N N 69 
XKN C8  H26 SING N N 70 
XKN C8  H27 SING N N 71 
XKN C9  H28 SING N N 72 
XKN C9  H29 SING N N 73 
# 
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 
XKN SMILES           ACDLabs              12.01 "COc1ccccc1Cn1cnc2cc(ccc12)C(=O)N1CCN(Cc2cc(cc(C#C)c2)S(F)(=O)=O)CC1C"                                                                                                                                     
XKN InChI            InChI                1.06  "InChI=1S/C30H29FN4O4S/c1-4-22-13-23(15-26(14-22)40(31,37)38)18-33-11-12-35(21(2)17-33)30(36)24-9-10-28-27(16-24)32-20-34(28)19-25-7-5-6-8-29(25)39-3/h1,5-10,13-16,20-21H,11-12,17-19H2,2-3H3/t21-/m1/s1" 
XKN InChIKey         InChI                1.06  ADWDKRWBNOJKEH-OAQYLSRUSA-N                                                                                                                                                                                
XKN SMILES_CANONICAL CACTVS               3.385 "COc1ccccc1Cn2cnc3cc(ccc23)C(=O)N4CCN(C[C@H]4C)Cc5cc(cc(c5)[S](F)(=O)=O)C#C"                                                                                                                               
XKN SMILES           CACTVS               3.385 "COc1ccccc1Cn2cnc3cc(ccc23)C(=O)N4CCN(C[CH]4C)Cc5cc(cc(c5)[S](F)(=O)=O)C#C"                                                                                                                                
XKN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]1CN(CCN1C(=O)c2ccc3c(c2)ncn3Cc4ccccc4OC)Cc5cc(cc(c5)S(=O)(=O)F)C#C"                                                                                                                                
XKN SMILES           "OpenEye OEToolkits" 2.0.7 "CC1CN(CCN1C(=O)c2ccc3c(c2)ncn3Cc4ccccc4OC)Cc5cc(cc(c5)S(=O)(=O)F)C#C"                                                                                                                                     
# 
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 
XKN "SYSTEMATIC NAME" ACDLabs              12.01 "3-ethynyl-5-{[(3R)-4-{1-[(2-methoxyphenyl)methyl]-1H-benzimidazole-5-carbonyl}-3-methylpiperazin-1-yl]methyl}benzene-1-sulfonyl fluoride" 
XKN "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-ethynyl-5-[[(3~{R})-4-[1-[(2-methoxyphenyl)methyl]benzimidazol-5-yl]carbonyl-3-methyl-piperazin-1-yl]methyl]benzenesulfonyl fluoride"   
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
XKN "Create component" 2022-11-23 RCSB 
XKN "Initial release"  2023-05-31 RCSB 
XKN "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            XKN 
_pdbx_chem_comp_pcm.modified_residue_id                TYR 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               S1 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OH 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
