data_5X4
# 
_chem_comp.id                                    5X4 
_chem_comp.name                                  "~{N}-[7-methyl-1-[(3~{R})-1-propanoylazepan-3-yl]benzimidazol-2-yl]-3-(trifluoromethyl)benzamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H27 F3 N4 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2015-12-17 
_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                        472.503 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     5X4 
_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        5FEE 
_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 
5X4 C11 C1  C 0 1 N N N N N N -53.006 1.531  -21.084 -1.730 -0.925 -0.032 C11 5X4 1  
5X4 C12 C2  C 0 1 Y N N N N N -53.274 1.232  -22.526 -2.837 0.051  0.044  C12 5X4 2  
5X4 C13 C3  C 0 1 Y N N N N N -54.389 1.684  -23.232 -2.571 1.393  0.321  C13 5X4 3  
5X4 C14 C4  C 0 1 Y N N N N N -54.597 1.354  -24.571 -3.609 2.299  0.390  C14 5X4 4  
5X4 C15 C5  C 0 1 Y N N N N N -53.706 0.539  -25.249 -4.912 1.879  0.186  C15 5X4 5  
5X4 C16 C6  C 0 1 Y N N N N N -52.594 0.060  -24.554 -5.182 0.550  -0.089 C16 5X4 6  
5X4 C17 C7  C 0 1 N N N N N N -51.599 -0.846 -25.260 -6.604 0.103  -0.310 C17 5X4 7  
5X4 C21 C8  C 0 1 Y N N N N N -52.398 0.399  -23.222 -4.153 -0.364 -0.167 C21 5X4 8  
5X4 C24 C9  C 0 1 N N R N N N -49.939 -0.741 -18.915 2.456  0.178  0.601  C24 5X4 9  
5X4 C25 C10 C 0 1 N N N N N N -49.054 -0.175 -20.015 1.997  0.607  1.931  C25 5X4 10 
5X4 C26 C11 C 0 1 N N N N N N -48.085 -1.221 -20.533 2.575  1.941  2.395  C26 5X4 11 
5X4 C27 C12 C 0 1 N N N N N N -48.718 -2.213 -21.508 1.736  3.068  1.845  C27 5X4 12 
5X4 C28 C13 C 0 1 N N N N N N -49.319 -3.479 -20.824 2.306  3.542  0.496  C28 5X4 13 
5X4 C30 C14 C 0 1 N N N N N N -49.980 -4.109 -18.522 3.917  2.534  -1.017 C30 5X4 14 
5X4 C01 C15 C 0 1 N N N N N N -48.966 -0.696 -15.811 4.974  -1.581 0.510  C01 5X4 15 
5X4 C02 C16 C 0 1 Y N N N N N -50.097 0.294  -15.790 3.951  -2.647 0.213  C02 5X4 16 
5X4 C03 C17 C 0 1 Y N N N N N -50.422 0.912  -14.580 4.351  -3.952 0.010  C03 5X4 17 
5X4 C04 C18 C 0 1 Y N N N N N -51.466 1.851  -14.480 3.416  -4.939 -0.264 C04 5X4 18 
5X4 C05 C19 C 0 1 Y N N N N N -52.205 2.194  -15.593 2.076  -4.631 -0.337 C05 5X4 19 
5X4 C06 C20 C 0 1 Y N N N N N -51.905 1.585  -16.830 1.654  -3.315 -0.134 C06 5X4 20 
5X4 C07 C21 C 0 1 Y N N N N N -50.861 0.642  -16.938 2.605  -2.320 0.149  C07 5X4 21 
5X4 N08 N1  N 0 1 Y N N N N N -50.845 0.256  -18.332 1.895  -1.141 0.297  N08 5X4 22 
5X4 C09 C22 C 0 1 Y N N N N N -51.863 0.974  -18.975 0.576  -1.436 0.108  C09 5X4 23 
5X4 N10 N2  N 0 1 N N N N N N -52.134 0.810  -20.317 -0.460 -0.521 0.173  N10 5X4 24 
5X4 F18 F1  F 0 1 N N N N N N -50.493 -0.218 -25.707 -6.943 -0.863 0.644  F18 5X4 25 
5X4 F19 F2  F 0 1 N N N N N N -51.136 -1.805 -24.452 -7.463 1.201  -0.188 F19 5X4 26 
5X4 F20 F3  F 0 1 N N N N N N -52.066 -1.563 -26.328 -6.727 -0.445 -1.592 F20 5X4 27 
5X4 O22 O1  O 0 1 N N N N N N -53.615 2.443  -20.537 -1.964 -2.093 -0.273 O22 5X4 28 
5X4 N23 N3  N 0 1 Y N N N N N -52.517 1.767  -18.107 0.436  -2.713 -0.140 N23 5X4 29 
5X4 N29 N4  N 0 1 N N N N N N -50.041 -3.180 -19.571 2.755  2.416  -0.345 N29 5X4 30 
5X4 C31 C23 C 0 1 N N N N N N -49.210 -5.384 -18.683 4.730  3.798  -0.901 C31 5X4 31 
5X4 C32 C24 C 0 1 N N N N N N -50.047 -6.628 -18.952 5.992  3.673  -1.756 C32 5X4 32 
5X4 O33 O2  O 0 1 N N N N N N -50.575 -3.846 -17.469 4.309  1.623  -1.716 O33 5X4 33 
5X4 C34 C25 C 0 1 N N N N N N -50.789 -1.948 -19.393 1.995  1.191  -0.476 C34 5X4 34 
5X4 H1  H1  H 0 1 N N N N N N -55.112 2.307  -22.727 -1.555 1.721  0.481  H1  5X4 35 
5X4 H2  H2  H 0 1 N N N N N N -55.465 1.739  -25.086 -3.405 3.337  0.605  H2  5X4 36 
5X4 H3  H3  H 0 1 N N N N N N -53.867 0.281  -26.285 -5.721 2.592  0.241  H3  5X4 37 
5X4 H4  H4  H 0 1 N N N N N N -51.536 0.003  -22.706 -4.366 -1.401 -0.382 H4  5X4 38 
5X4 H5  H5  H 0 1 N N N N N N -49.277 -1.108 -18.117 3.544  0.117  0.597  H5  5X4 39 
5X4 H6  H6  H 0 1 N N N N N N -48.483 0.676  -19.614 0.910  0.689  1.912  H6  5X4 40 
5X4 H7  H7  H 0 1 N N N N N N -49.689 0.168  -20.845 2.273  -0.158 2.656  H7  5X4 41 
5X4 H8  H8  H 0 1 N N N N N N -47.688 -1.783 -19.674 2.568  1.981  3.484  H8  5X4 42 
5X4 H9  H9  H 0 1 N N N N N N -47.260 -0.706 -21.047 3.598  2.039  2.034  H9  5X4 43 
5X4 H10 H10 H 0 1 N N N N N N -47.946 -2.539 -22.220 0.712  2.721  1.703  H10 5X4 44 
5X4 H11 H11 H 0 1 N N N N N N -49.524 -1.698 -22.051 1.739  3.898  2.551  H11 5X4 45 
5X4 H12 H12 H 0 1 N N N N N N -50.020 -3.955 -21.525 1.536  4.098  -0.038 H12 5X4 46 
5X4 H13 H13 H 0 1 N N N N N N -48.498 -4.175 -20.596 3.152  4.204  0.683  H13 5X4 47 
5X4 H14 H14 H 0 1 N N N N N N -48.023 -0.172 -16.028 5.226  -1.053 -0.410 H14 5X4 48 
5X4 H15 H15 H 0 1 N N N N N N -48.893 -1.190 -14.831 4.565  -0.876 1.233  H15 5X4 49 
5X4 H16 H16 H 0 1 N N N N N N -49.154 -1.450 -16.589 5.872  -2.043 0.920  H16 5X4 50 
5X4 H17 H17 H 0 1 N N N N N N -49.856 0.662  -13.695 5.399  -4.206 0.064  H17 5X4 51 
5X4 H18 H18 H 0 1 N N N N N N -51.690 2.306  -13.526 3.741  -5.957 -0.421 H18 5X4 52 
5X4 H19 H19 H 0 1 N N N N N N -53.002 2.919  -15.519 1.354  -5.405 -0.551 H19 5X4 53 
5X4 H20 H20 H 0 1 N N N N N N -51.635 0.079  -20.783 -0.273 0.411  0.366  H20 5X4 54 
5X4 H21 H21 H 0 1 N N N N N N -48.639 -5.554 -17.758 4.137  4.644  -1.248 H21 5X4 55 
5X4 H22 H22 H 0 1 N N N N N N -48.514 -5.255 -19.525 5.011  3.954  0.141  H22 5X4 56 
5X4 H23 H23 H 0 1 N N N N N N -49.385 -7.501 -19.053 6.584  2.827  -1.408 H23 5X4 57 
5X4 H24 H24 H 0 1 N N N N N N -50.742 -6.790 -18.115 5.711  3.516  -2.798 H24 5X4 58 
5X4 H25 H25 H 0 1 N N N N N N -50.618 -6.492 -19.882 6.580  4.587  -1.672 H25 5X4 59 
5X4 H26 H26 H 0 1 N N N N N N -51.249 -1.684 -20.356 2.161  0.765  -1.465 H26 5X4 60 
5X4 H27 H27 H 0 1 N N N N N N -51.577 -2.130 -18.647 0.935  1.407  -0.347 H27 5X4 61 
# 
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 
5X4 F20 C17 SING N N 1  
5X4 F18 C17 SING N N 2  
5X4 C17 C16 SING N N 3  
5X4 C17 F19 SING N N 4  
5X4 C15 C14 DOUB Y N 5  
5X4 C15 C16 SING Y N 6  
5X4 C14 C13 SING Y N 7  
5X4 C16 C21 DOUB Y N 8  
5X4 C13 C12 DOUB Y N 9  
5X4 C21 C12 SING Y N 10 
5X4 C12 C11 SING N N 11 
5X4 C27 C28 SING N N 12 
5X4 C27 C26 SING N N 13 
5X4 C11 O22 DOUB N N 14 
5X4 C11 N10 SING N N 15 
5X4 C28 N29 SING N N 16 
5X4 C26 C25 SING N N 17 
5X4 N10 C09 SING N N 18 
5X4 C25 C24 SING N N 19 
5X4 N29 C34 SING N N 20 
5X4 N29 C30 SING N N 21 
5X4 C34 C24 SING N N 22 
5X4 C09 N08 SING Y N 23 
5X4 C09 N23 DOUB Y N 24 
5X4 C32 C31 SING N N 25 
5X4 C24 N08 SING N N 26 
5X4 C31 C30 SING N N 27 
5X4 C30 O33 DOUB N N 28 
5X4 N08 C07 SING Y N 29 
5X4 N23 C06 SING Y N 30 
5X4 C07 C06 DOUB Y N 31 
5X4 C07 C02 SING Y N 32 
5X4 C06 C05 SING Y N 33 
5X4 C01 C02 SING N N 34 
5X4 C02 C03 DOUB Y N 35 
5X4 C05 C04 DOUB Y N 36 
5X4 C03 C04 SING Y N 37 
5X4 C13 H1  SING N N 38 
5X4 C14 H2  SING N N 39 
5X4 C15 H3  SING N N 40 
5X4 C21 H4  SING N N 41 
5X4 C24 H5  SING N N 42 
5X4 C25 H6  SING N N 43 
5X4 C25 H7  SING N N 44 
5X4 C26 H8  SING N N 45 
5X4 C26 H9  SING N N 46 
5X4 C27 H10 SING N N 47 
5X4 C27 H11 SING N N 48 
5X4 C28 H12 SING N N 49 
5X4 C28 H13 SING N N 50 
5X4 C01 H14 SING N N 51 
5X4 C01 H15 SING N N 52 
5X4 C01 H16 SING N N 53 
5X4 C03 H17 SING N N 54 
5X4 C04 H18 SING N N 55 
5X4 C05 H19 SING N N 56 
5X4 N10 H20 SING N N 57 
5X4 C31 H21 SING N N 58 
5X4 C31 H22 SING N N 59 
5X4 C32 H23 SING N N 60 
5X4 C32 H24 SING N N 61 
5X4 C32 H25 SING N N 62 
5X4 C34 H26 SING N N 63 
5X4 C34 H27 SING N N 64 
# 
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 
5X4 InChI            InChI                1.03  "InChI=1S/C25H27F3N4O2/c1-3-21(33)31-13-5-4-11-19(15-31)32-22-16(2)8-6-12-20(22)29-24(32)30-23(34)17-9-7-10-18(14-17)25(26,27)28/h6-10,12,14,19H,3-5,11,13,15H2,1-2H3,(H,29,30,34)/t19-/m1/s1" 
5X4 InChIKey         InChI                1.03  DFNLNAPTJYVZSV-LJQANCHMSA-N                                                                                                                                                                    
5X4 SMILES_CANONICAL CACTVS               3.385 "CCC(=O)N1CCCC[C@H](C1)n2c(NC(=O)c3cccc(c3)C(F)(F)F)nc4cccc(C)c24"                                                                                                                             
5X4 SMILES           CACTVS               3.385 "CCC(=O)N1CCCC[CH](C1)n2c(NC(=O)c3cccc(c3)C(F)(F)F)nc4cccc(C)c24"                                                                                                                              
5X4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "CCC(=O)N1CCCC[C@H](C1)n2c3c(cccc3nc2NC(=O)c4cccc(c4)C(F)(F)F)C"                                                                                                                               
5X4 SMILES           "OpenEye OEToolkits" 2.0.4 "CCC(=O)N1CCCCC(C1)n2c3c(cccc3nc2NC(=O)c4cccc(c4)C(F)(F)F)C"                                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           5X4 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.4 
_pdbx_chem_comp_identifier.identifier        "~{N}-[7-methyl-1-[(3~{R})-1-propanoylazepan-3-yl]benzimidazol-2-yl]-3-(trifluoromethyl)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 
5X4 "Create component" 2015-12-17 RCSB 
5X4 "Initial release"  2016-07-27 RCSB 
5X4 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            5X4 
_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               C32 
_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      ? 
# 
