data_A1JCQ
# 
_chem_comp.id                                    A1JCQ 
_chem_comp.name                                  "5-[6-[(4-methylpiperazin-1-yl)methyl]benzimidazol-1-yl]-3-[(1~{R})-1-[2-(trifluoromethyl)phenyl]ethoxy]thiophene-2-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H28 F3 N5 O2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-05-09 
_chem_comp.pdbx_modified_date                    2025-11-21 
_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                        543.604 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1JCQ 
_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        9R1Y 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              ? 
# 
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 
A1JCQ C5  C1  C 0 1 Y N N N N N 26.860 9.638  8.460  6.140   -0.414 0.063  C5  A1JCQ 1  
A1JCQ C6  C2  C 0 1 Y N N N N N 27.583 9.594  7.243  5.251   0.609  0.337  C6  A1JCQ 2  
A1JCQ C7  C3  C 0 1 Y N N N N N 28.791 8.886  7.206  5.684   1.921  0.328  C7  A1JCQ 3  
A1JCQ C8  C4  C 0 1 Y N N N N N 29.279 8.216  8.323  7.005   2.211  0.044  C8  A1JCQ 4  
A1JCQ C10 C5  C 0 1 Y N N N N N 27.374 8.956  9.574  7.462   -0.125 -0.215 C10 A1JCQ 5  
A1JCQ C13 C6  C 0 1 Y N N N N N 26.881 8.376  4.482  1.719   1.170  -0.064 C13 A1JCQ 6  
A1JCQ C17 C7  C 0 1 Y N N N N N 25.593 8.111  4.819  1.204   -0.101 -0.156 C17 A1JCQ 7  
A1JCQ C21 C8  C 0 1 Y N N N N N 21.972 5.779  5.114  -2.380  -2.918 -0.629 C21 A1JCQ 8  
A1JCQ C22 C9  C 0 1 Y N N N N N 23.065 6.438  5.534  -2.061  -1.615 -0.211 C22 A1JCQ 9  
A1JCQ C24 C10 C 0 1 Y N N N N N 22.016 6.798  7.652  -4.171  -1.466 0.906  C24 A1JCQ 10 
A1JCQ C26 C11 C 0 1 Y N N N N N 20.909 5.610  5.898  -3.608  -3.476 -0.264 C26 A1JCQ 11 
A1JCQ F3  F1  F 0 1 N N N N N N 24.724 9.811  7.826  6.741   -2.692 -0.225 F3  A1JCQ 12 
A1JCQ C2  C12 C 0 1 N N N N N N 25.631 10.335 8.608  5.668   -1.845 0.073  C2  A1JCQ 13 
A1JCQ F4  F2  F 0 1 N N N N N N 25.790 11.620 8.309  5.162   -2.161 1.339  F4  A1JCQ 14 
A1JCQ F1  F3  F 0 1 N N N N N N 25.182 10.261 9.861  4.662   -2.012 -0.885 F1  A1JCQ 15 
A1JCQ C9  C13 C 0 1 Y N N N N N 28.570 8.250  9.512  7.894   1.189  -0.229 C9  A1JCQ 16 
A1JCQ C11 C14 C 0 1 N N R N N N 27.165 10.255 6.056  3.810   0.292  0.646  C11 A1JCQ 17 
A1JCQ C38 C15 C 0 1 N N N N N N 27.827 11.637 5.991  3.667   -0.033 2.134  C38 A1JCQ 18 
A1JCQ O12 O1  O 0 1 N N N N N N 27.529 9.533  4.855  2.995   1.422  0.325  O12 A1JCQ 19 
A1JCQ C14 C16 C 0 1 Y N N N N N 27.445 7.407  3.735  0.835   2.164  -0.405 C14 A1JCQ 20 
A1JCQ C35 C17 C 0 1 N N N N N N 28.692 7.359  3.238  1.118   3.548  -0.395 C35 A1JCQ 21 
A1JCQ O36 O2  O 0 1 N N N N N N 29.055 6.394  2.565  2.223   3.941  -0.064 O36 A1JCQ 22 
A1JCQ N37 N1  N 0 1 N N N N N N 29.493 8.397  3.472  0.167   4.434  -0.751 N37 A1JCQ 23 
A1JCQ S15 S1  S 0 1 Y N N N N N 26.371 6.222  3.498  -0.705  1.445  -0.858 S15 A1JCQ 24 
A1JCQ C16 C18 C 0 1 Y N N N N N 25.167 6.932  4.357  -0.080  -0.170 -0.559 C16 A1JCQ 25 
A1JCQ N18 N2  N 0 1 Y N N N N N 23.938 6.422  4.511  -0.803  -1.349 -0.720 N18 A1JCQ 26 
A1JCQ C23 C19 C 0 1 Y N N N N N 23.105 6.950  6.779  -2.965  -0.896 0.558  C23 A1JCQ 27 
A1JCQ C19 C20 C 0 1 Y N N N N N 23.379 5.773  3.494  -0.403  -2.455 -1.409 C19 A1JCQ 28 
A1JCQ N20 N3  N 0 1 Y N N N N N 22.174 5.375  3.866  -1.323  -3.373 -1.351 N20 A1JCQ 29 
A1JCQ C25 C21 C 0 1 Y N N N N N 20.898 6.116  7.189  -4.485  -2.753 0.494  C25 A1JCQ 30 
A1JCQ C27 C22 C 0 1 N N N N N N 21.978 7.311  8.961  -5.154  -0.687 1.742  C27 A1JCQ 31 
A1JCQ N28 N4  N 0 1 N N N N N N 23.203 7.132  9.761  -6.048  0.077  0.861  N28 A1JCQ 32 
A1JCQ C29 C23 C 0 1 N N N N N N 22.966 7.716  11.096 -6.901  -0.821 0.070  C29 A1JCQ 33 
A1JCQ C30 C24 C 0 1 N N N N N N 24.218 7.629  11.970 -7.758  0.008  -0.890 C30 A1JCQ 34 
A1JCQ N31 N5  N 0 1 N N N N N N 24.704 6.242  12.077 -8.572  0.959  -0.118 N31 A1JCQ 35 
A1JCQ C34 C25 C 0 1 N N N N N N 25.973 6.191  12.825 -9.465  1.722  -0.999 C34 A1JCQ 36 
A1JCQ C32 C26 C 0 1 N N N N N N 24.876 5.654  10.736 -7.719  1.856  0.673  C32 A1JCQ 37 
A1JCQ C33 C27 C 0 1 N N N N N N 23.575 5.720  9.951  -6.861  1.027  1.632  C33 A1JCQ 38 
A1JCQ H1  H1  H 0 1 N N N N N N 29.358 8.860  6.287  4.989   2.720  0.541  H1  A1JCQ 39 
A1JCQ H2  H2  H 0 1 N N N N N N 30.209 7.670  8.263  7.344   3.237  0.036  H2  A1JCQ 40 
A1JCQ H3  H3  H 0 1 N N N N N N 26.826 8.980  10.504 8.158   -0.924 -0.425 H3  A1JCQ 41 
A1JCQ H4  H4  H 0 1 N N N N N N 24.978 8.782  5.399  1.786   -0.981 0.077  H4  A1JCQ 42 
A1JCQ H5  H5  H 0 1 N N N N N N 20.048 5.074  5.525  -3.863  -4.477 -0.580 H5  A1JCQ 43 
A1JCQ H6  H6  H 0 1 N N N N N N 28.943 7.733  10.384 8.927   1.415  -0.450 H6  A1JCQ 44 
A1JCQ H7  H7  H 0 1 N N N N N N 26.075 10.398 6.077  3.492   -0.566 0.054  H7  A1JCQ 45 
A1JCQ H8  H8  H 0 1 N N N N N N 27.568 12.211 6.893  2.625   -0.262 2.357  H8  A1JCQ 46 
A1JCQ H9  H9  H 0 1 N N N N N N 28.919 11.518 5.933  4.288   -0.895 2.378  H9  A1JCQ 47 
A1JCQ H10 H10 H 0 1 N N N N N N 27.469 12.173 5.100  3.986   0.825  2.726  H10 A1JCQ 48 
A1JCQ H11 H11 H 0 1 N N N N N N 30.420 8.408  3.097  -0.713  4.121  -1.015 H11 A1JCQ 49 
A1JCQ H12 H12 H 0 1 N N N N N N 29.168 9.165  4.023  0.361   5.384  -0.744 H12 A1JCQ 50 
A1JCQ H13 H13 H 0 1 N N N N N N 23.984 7.483  7.109  -2.725  0.106  0.882  H13 A1JCQ 51 
A1JCQ H14 H14 H 0 1 N N N N N N 23.832 5.600  2.529  0.541   -2.557 -1.923 H14 A1JCQ 52 
A1JCQ H15 H15 H 0 1 N N N N N N 20.035 5.982  7.824  -5.433  -3.188 0.775  H15 A1JCQ 53 
A1JCQ H16 H16 H 0 1 N N N N N N 21.775 8.390  8.894  -5.743  -1.376 2.347  H16 A1JCQ 54 
A1JCQ H17 H17 H 0 1 N N N N N N 21.153 6.815  9.493  -4.613  -0.001 2.393  H17 A1JCQ 55 
A1JCQ H19 H19 H 0 1 N N N N N N 22.683 8.773  10.980 -6.276  -1.507 -0.502 H19 A1JCQ 56 
A1JCQ H20 H20 H 0 1 N N N N N N 22.148 7.169  11.587 -7.548  -1.390 0.737  H20 A1JCQ 57 
A1JCQ H21 H21 H 0 1 N N N N N N 25.008 8.252  11.526 -7.111  0.555  -1.575 H21 A1JCQ 58 
A1JCQ H22 H22 H 0 1 N N N N N N 23.979 8.003  12.976 -8.413  -0.654 -1.457 H22 A1JCQ 59 
A1JCQ H24 H24 H 0 1 N N N N N N 25.829 6.633  13.822 -10.132 1.037  -1.523 H24 A1JCQ 60 
A1JCQ H25 H25 H 0 1 N N N N N N 26.295 5.144  12.930 -10.056 2.418  -0.403 H25 A1JCQ 61 
A1JCQ H26 H26 H 0 1 N N N N N N 26.743 6.758  12.280 -8.872  2.278  -1.725 H26 A1JCQ 62 
A1JCQ H27 H27 H 0 1 N N N N N N 25.183 4.603  10.839 -7.071  2.425  0.005  H27 A1JCQ 63 
A1JCQ H28 H28 H 0 1 N N N N N N 25.654 6.212  10.194 -8.344  2.543  1.244  H28 A1JCQ 64 
A1JCQ H29 H29 H 0 1 N N N N N N 22.781 5.201  10.508 -7.508  0.480  2.317  H29 A1JCQ 65 
A1JCQ H30 H30 H 0 1 N N N N N N 23.710 5.239  8.971  -6.207  1.689  2.199  H30 A1JCQ 66 
# 
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 
A1JCQ O36 C35 DOUB N N 1  
A1JCQ C35 N37 SING N N 2  
A1JCQ C35 C14 SING N N 3  
A1JCQ C19 N20 DOUB Y N 4  
A1JCQ C19 N18 SING Y N 5  
A1JCQ S15 C14 SING Y N 6  
A1JCQ S15 C16 SING Y N 7  
A1JCQ C14 C13 DOUB Y N 8  
A1JCQ N20 C21 SING Y N 9  
A1JCQ C16 N18 SING N N 10 
A1JCQ C16 C17 DOUB Y N 11 
A1JCQ C13 C17 SING Y N 12 
A1JCQ C13 O12 SING N N 13 
A1JCQ N18 C22 SING Y N 14 
A1JCQ O12 C11 SING N N 15 
A1JCQ C21 C22 DOUB Y N 16 
A1JCQ C21 C26 SING Y N 17 
A1JCQ C22 C23 SING Y N 18 
A1JCQ C26 C25 DOUB Y N 19 
A1JCQ C38 C11 SING N N 20 
A1JCQ C11 C6  SING N N 21 
A1JCQ C23 C24 DOUB Y N 22 
A1JCQ C25 C24 SING Y N 23 
A1JCQ C7  C6  DOUB Y N 24 
A1JCQ C7  C8  SING Y N 25 
A1JCQ C6  C5  SING Y N 26 
A1JCQ C24 C27 SING N N 27 
A1JCQ F3  C2  SING N N 28 
A1JCQ F4  C2  SING N N 29 
A1JCQ C8  C9  DOUB Y N 30 
A1JCQ C5  C2  SING N N 31 
A1JCQ C5  C10 DOUB Y N 32 
A1JCQ C2  F1  SING N N 33 
A1JCQ C27 N28 SING N N 34 
A1JCQ C9  C10 SING Y N 35 
A1JCQ N28 C33 SING N N 36 
A1JCQ N28 C29 SING N N 37 
A1JCQ C33 C32 SING N N 38 
A1JCQ C32 N31 SING N N 39 
A1JCQ C29 C30 SING N N 40 
A1JCQ C30 N31 SING N N 41 
A1JCQ N31 C34 SING N N 42 
A1JCQ C7  H1  SING N N 43 
A1JCQ C8  H2  SING N N 44 
A1JCQ C10 H3  SING N N 45 
A1JCQ C17 H4  SING N N 46 
A1JCQ C26 H5  SING N N 47 
A1JCQ C9  H6  SING N N 48 
A1JCQ C11 H7  SING N N 49 
A1JCQ C38 H8  SING N N 50 
A1JCQ C38 H9  SING N N 51 
A1JCQ C38 H10 SING N N 52 
A1JCQ N37 H11 SING N N 53 
A1JCQ N37 H12 SING N N 54 
A1JCQ C23 H13 SING N N 55 
A1JCQ C19 H14 SING N N 56 
A1JCQ C25 H15 SING N N 57 
A1JCQ C27 H16 SING N N 58 
A1JCQ C27 H17 SING N N 59 
A1JCQ C29 H19 SING N N 60 
A1JCQ C29 H20 SING N N 61 
A1JCQ C30 H21 SING N N 62 
A1JCQ C30 H22 SING N N 63 
A1JCQ C34 H24 SING N N 64 
A1JCQ C34 H25 SING N N 65 
A1JCQ C34 H26 SING N N 66 
A1JCQ C32 H27 SING N N 67 
A1JCQ C32 H28 SING N N 68 
A1JCQ C33 H29 SING N N 69 
A1JCQ C33 H30 SING N N 70 
# 
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 
A1JCQ InChI            InChI                1.06  "InChI=1S/C27H28F3N5O2S/c1-17(19-5-3-4-6-20(19)27(28,29)30)37-23-14-24(38-25(23)26(31)36)35-16-32-21-8-7-18(13-22(21)35)15-34-11-9-33(2)10-12-34/h3-8,13-14,16-17H,9-12,15H2,1-2H3,(H2,31,36)/t17-/m1/s1" 
A1JCQ InChIKey         InChI                1.06  ZHJGWYRLJUCMRT-QGZVFWFLSA-N                                                                                                                                                                               
A1JCQ SMILES_CANONICAL CACTVS               3.385 "C[C@@H](Oc1cc(sc1C(N)=O)n2cnc3ccc(CN4CCN(C)CC4)cc23)c5ccccc5C(F)(F)F"                                                                                                                                    
A1JCQ SMILES           CACTVS               3.385 "C[CH](Oc1cc(sc1C(N)=O)n2cnc3ccc(CN4CCN(C)CC4)cc23)c5ccccc5C(F)(F)F"                                                                                                                                      
A1JCQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H](c1ccccc1C(F)(F)F)Oc2cc(sc2C(=O)N)n3cnc4c3cc(cc4)CN5CCN(CC5)C"                                                                                                                                     
A1JCQ SMILES           "OpenEye OEToolkits" 2.0.7 "CC(c1ccccc1C(F)(F)F)Oc2cc(sc2C(=O)N)n3cnc4c3cc(cc4)CN5CCN(CC5)C"                                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           A1JCQ 
_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        "5-[6-[(4-methylpiperazin-1-yl)methyl]benzimidazol-1-yl]-3-[(1~{R})-1-[2-(trifluoromethyl)phenyl]ethoxy]thiophene-2-carboxamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1JCQ "Create component" 2025-05-09 PDBE 
A1JCQ "Initial release"  2025-11-26 RCSB 
# 
