data_PKH
# 
_chem_comp.id                                    PKH 
_chem_comp.name                                  "~{N}-[(1~{R},2~{R},4~{S},7~{E})-7-[azanyl(sulfanyl)methylidene]-7$l^{4}-azabicyclo[2.2.1]heptan-2-yl]-2-chloranyl-4-(6-cyclopropylpyrazin-2-yl)benzamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H23 Cl N5 O S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2022-05-26 
_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                        428.958 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     PKH 
_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        8D0A 
_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 
PKH C15  C1  C  0 1 N N S N N N 7.313  -10.205 -8.369 5.310  -1.520 -0.472 C15  PKH 1  
PKH C17  C2  C  0 1 N N N N N N 8.065  -8.418  -6.973 3.706  -1.208 1.339  C17  PKH 2  
PKH C20  C3  C  0 1 N N N N N N 8.294  -11.213 -7.719 4.259  -1.051 -1.523 C20  PKH 3  
PKH C22  C4  C  0 1 N N N N N N 9.560  -10.422 -4.250 1.126  0.645  -0.491 C22  PKH 4  
PKH C24  C5  C  0 1 Y N N N N N 10.826 -10.023 -3.661 -0.298 0.274  -0.363 C24  PKH 5  
PKH C26  C6  C  0 1 Y N N N N N 12.678 -8.465  -3.548 -2.004 -1.415 -0.282 C26  PKH 6  
PKH C28  C7  C  0 1 Y N N N N N 12.504 -10.230 -1.913 -2.597 0.919  -0.080 C28  PKH 7  
PKH C12  C8  C  0 1 N N N N N N 5.184  -9.299  -7.486 6.690  0.388  0.515  C12  PKH 8  
PKH C16  C9  C  0 1 N N N N N N 8.044  -8.854  -8.450 4.492  -2.313 0.592  C16  PKH 9  
PKH C18  C10 C  0 1 N N R N N N 7.297  -9.571  -6.273 4.155  0.102  0.624  C18  PKH 10 
PKH C19  C11 C  0 1 N N R N N N 8.166  -10.847 -6.230 3.473  0.054  -0.776 C19  PKH 11 
PKH C25  C12 C  0 1 Y N N N N N 11.526 -8.920  -4.171 -0.677 -1.070 -0.401 C25  PKH 12 
PKH C27  C13 C  0 1 Y N N N N N 13.170 -9.100  -2.397 -2.973 -0.423 -0.124 C27  PKH 13 
PKH C29  C14 C  0 1 Y N N N N N 11.346 -10.692 -2.539 -1.268 1.267  -0.199 C29  PKH 14 
PKH C31  C15 C  0 1 Y N N N N N 14.322 -8.543  -1.694 -4.402 -0.796 -0.002 C31  PKH 15 
PKH C32  C16 C  0 1 Y N N N N N 15.355 -9.348  -1.184 -4.772 -2.140 0.064  C32  PKH 16 
PKH C34  C17 C  0 1 Y N N N N N 16.382 -7.515  -0.329 -6.971 -1.523 0.218  C34  PKH 17 
PKH C35  C18 C  0 1 Y N N N N N 15.367 -6.699  -0.845 -6.608 -0.188 0.157  C35  PKH 18 
PKH C37  C19 C  0 1 N N N N N N 15.308 -5.195  -0.654 -7.667 0.882  0.215  C37  PKH 19 
PKH C38  C20 C  0 1 N N N N N N 16.007 -4.398  -1.718 -8.903 0.607  1.074  C38  PKH 20 
PKH C39  C21 C  0 1 N N N N N N 16.551 -4.420  -0.309 -9.011 0.583  -0.452 C39  PKH 21 
PKH N13  N1  N  0 1 N N N N N N 4.611  -8.816  -6.462 6.674  1.569  1.221  N13  PKH 22 
PKH N14  N2  N  1 1 N N N N N N 6.369  -9.980  -7.303 5.574  -0.238 0.265  N14  PKH 23 
PKH N21  N3  N  0 1 N N N N N N 9.477  -10.619 -5.603 2.060  -0.314 -0.649 N21  PKH 24 
PKH N33  N4  N  0 1 Y N N N N N 16.381 -8.841  -0.503 -6.046 -2.467 0.173  N33  PKH 25 
PKH N36  N5  N  0 1 Y N N N N N 14.351 -7.216  -1.524 -5.336 0.148  0.049  N36  PKH 26 
PKH O23  O1  O  0 1 N N N N N N 8.531  -10.551 -3.602 1.455  1.814  -0.453 O23  PKH 27 
PKH CL30 CL1 CL 0 0 N N N N N N 10.578 -12.112 -1.895 -0.800 2.938  -0.144 CL30 PKH 28 
PKH H1   H1  H  0 1 N N N N N N 6.888  -10.546 -9.325 6.187  -2.025 -0.877 H1   PKH 29 
PKH H2   H2  H  0 1 N N N N N N 9.095  -8.340  -6.596 2.632  -1.358 1.226  H2   PKH 30 
PKH H3   H3  H  0 1 N N N N N N 7.550  -7.456  -6.835 3.980  -1.184 2.393  H3   PKH 31 
PKH H4   H4  H  0 1 N N N N N N 7.985  -12.252 -7.906 4.754  -0.642 -2.404 H4   PKH 32 
PKH H5   H5  H  0 1 N N N N N N 9.322  -11.065 -8.082 3.599  -1.873 -1.798 H5   PKH 33 
PKH H6   H6  H  0 1 N N N N N N 13.203 -7.612  -3.953 -2.297 -2.454 -0.316 H6   PKH 34 
PKH H7   H7  H  0 1 N N N N N N 12.889 -10.749 -1.048 -3.347 1.686  0.043  H7   PKH 35 
PKH H9   H9  H  0 1 N N N N N N 9.063  -8.973  -8.847 3.809  -3.012 0.109  H9   PKH 36 
PKH H10  H10 H  0 1 N N N N N N 7.490  -8.135  -9.072 5.160  -2.838 1.276  H10  PKH 37 
PKH H11  H11 H  0 1 N N N N N N 6.853  -9.294  -5.306 4.004  1.022  1.190  H11  PKH 38 
PKH H12  H12 H  0 1 N N N N N N 7.621  -11.643 -5.702 3.577  1.011  -1.287 H12  PKH 39 
PKH H13  H13 H  0 1 N N N N N N 11.164 -8.420  -5.057 0.072  -1.839 -0.524 H13  PKH 40 
PKH H14  H14 H  0 1 N N N N N N 15.315 -10.414 -1.350 -4.017 -2.911 0.027  H14  PKH 41 
PKH H15  H15 H  0 1 N N N N N N 17.189 -7.060  0.226  -8.012 -1.794 0.308  H15  PKH 42 
PKH H16  H16 H  0 1 N N N N N N 14.357 -4.789  -0.280 -7.301 1.908  0.173  H16  PKH 43 
PKH H17  H17 H  0 1 N N N N N N 16.549 -4.913  -2.525 -8.950 -0.348 1.597  H17  PKH 44 
PKH H18  H18 H  0 1 N N N N N N 15.543 -3.483  -2.114 -9.351 1.452  1.597  H18  PKH 45 
PKH H19  H19 H  0 1 N N N N N N 17.488 -4.952  -0.089 -9.530 1.413  -0.933 H19  PKH 46 
PKH H20  H20 H  0 1 N N N N N N 16.482 -3.522  0.322  -9.129 -0.387 -0.933 H20  PKH 47 
PKH H21  H21 H  0 1 N N N N N N 3.793  -8.250  -6.567 5.832  1.936  1.533  H21  PKH 48 
PKH H22  H22 H  0 1 N N N N N N 10.305 -10.608 -6.163 1.797  -1.247 -0.680 H22  PKH 49 
PKH S1   S1  S  0 1 N Y N N N N 4.477  -8.910  -8.847 8.220  -0.278 -0.052 S1   PKH 50 
PKH H8   H8  H  0 1 N N N N N N 4.977  -9.001  -5.550 7.504  2.034  1.407  H8   PKH 51 
PKH H23  H23 H  0 1 N N N N N N 3.413  -8.290  -8.431 9.109  0.702  0.435  H23  PKH 52 
# 
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 
PKH C16 C15  SING N N 1  
PKH C16 C17  SING N N 2  
PKH C15 C20  SING N N 3  
PKH C15 N14  SING N N 4  
PKH C20 C19  SING N N 5  
PKH C12 N14  DOUB N E 6  
PKH C12 N13  SING N N 7  
PKH N14 C18  SING N N 8  
PKH C17 C18  SING N N 9  
PKH C18 C19  SING N N 10 
PKH C19 N21  SING N N 11 
PKH N21 C22  SING N N 12 
PKH C22 C24  SING N N 13 
PKH C22 O23  DOUB N N 14 
PKH C25 C24  DOUB Y N 15 
PKH C25 C26  SING Y N 16 
PKH C24 C29  SING Y N 17 
PKH C26 C27  DOUB Y N 18 
PKH C29 C28  DOUB Y N 19 
PKH C29 CL30 SING N N 20 
PKH C27 C28  SING Y N 21 
PKH C27 C31  SING N N 22 
PKH C38 C37  SING N N 23 
PKH C38 C39  SING N N 24 
PKH C31 N36  DOUB Y N 25 
PKH C31 C32  SING Y N 26 
PKH N36 C35  SING Y N 27 
PKH C32 N33  DOUB Y N 28 
PKH C35 C37  SING N N 29 
PKH C35 C34  DOUB Y N 30 
PKH C37 C39  SING N N 31 
PKH N33 C34  SING Y N 32 
PKH C15 H1   SING N N 33 
PKH C17 H2   SING N N 34 
PKH C17 H3   SING N N 35 
PKH C20 H4   SING N N 36 
PKH C20 H5   SING N N 37 
PKH C26 H6   SING N N 38 
PKH C28 H7   SING N N 39 
PKH C16 H9   SING N N 40 
PKH C16 H10  SING N N 41 
PKH C18 H11  SING N N 42 
PKH C19 H12  SING N N 43 
PKH C25 H13  SING N N 44 
PKH C32 H14  SING N N 45 
PKH C34 H15  SING N N 46 
PKH C37 H16  SING N N 47 
PKH C38 H17  SING N N 48 
PKH C38 H18  SING N N 49 
PKH C39 H19  SING N N 50 
PKH C39 H20  SING N N 51 
PKH N13 H21  SING N N 52 
PKH N21 H22  SING N N 53 
PKH C12 S1   SING N N 54 
PKH N13 H8   SING N N 55 
PKH S1  H23  SING N N 56 
# 
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 
PKH SMILES           ACDLabs              12.01 "N/C(S)=[N+]1/C2CC(NC(=O)c3ccc(cc3Cl)c3cncc(n3)C3CC3)C1CC2"                                                                                                                                     
PKH InChI            InChI                1.03  "InChI=1S/C21H22ClN5OS/c22-15-7-12(18-10-24-9-17(25-18)11-1-2-11)3-5-14(15)20(28)26-16-8-13-4-6-19(16)27(13)21(23)29/h3,5,7,9-11,13,16,19H,1-2,4,6,8H2,(H3,23,26,28,29)/p+1/t13-,16+,19+/m0/s1" 
PKH InChIKey         InChI                1.03  KZSNYGBGGXEVJT-URKNILKWSA-O                                                                                                                                                                     
PKH SMILES_CANONICAL CACTVS               3.385 "N\C(S)=[N+]1\[C@H]2CC[C@@H]1[C@@H](C2)NC(=O)c3ccc(cc3Cl)c4cncc(n4)C5CC5"                                                                                                                       
PKH SMILES           CACTVS               3.385 "NC(S)=[N+]1[CH]2CC[CH]1[CH](C2)NC(=O)c3ccc(cc3Cl)c4cncc(n4)C5CC5"                                                                                                                              
PKH SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1c2cncc(n2)C3CC3)Cl)C(=O)N[C@@H]4C[C@@H]\5CC[C@H]4/[N+]5=C(\N)/S"                                                                                                                     
PKH SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1c2cncc(n2)C3CC3)Cl)C(=O)NC4CC5CCC4[N+]5=C(N)S"                                                                                                                                       
# 
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 
PKH "SYSTEMATIC NAME" ACDLabs              12.01 "(1R,2R,4S,7E)-7-[amino(sulfanyl)methylidene]-2-{[(4M)-2-chloro-4-(6-cyclopropylpyrazin-2-yl)benzene-1-carbonyl]amino}-7-azabicyclo[2.2.1]heptan-7-ium" 
PKH "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{N}-[(1~{R},2~{R},4~{S},7~{E})-7-[azanyl(sulfanyl)methylidene]-7-azoniabicyclo[2.2.1]heptan-2-yl]-2-chloranyl-4-(6-cyclopropylpyrazin-2-yl)benzamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
PKH "Create component" 2022-05-26 RCSB 
PKH "Initial release"  2023-02-01 RCSB 
PKH "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            PKH 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_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               C12 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
