data_A1IXM
# 
_chem_comp.id                                    A1IXM 
_chem_comp.name                                  "~{N}-[3-[4-[2,3-bis(chloranyl)phenyl]piperazin-1-yl]propyl]-2-oxidanylidene-6-pyridin-3-yl-3~{H}-benzimidazole-1-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H26 Cl2 N6 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-12-23 
_chem_comp.pdbx_modified_date                    2025-07-18 
_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                        525.430 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1IXM 
_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        9HUL 
_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 
A1IXM C02  C1  C  0 1 Y N N N N N -3.116 2.002   29.921 9.127   0.161  -0.314 C02  A1IXM 1  
A1IXM C03  C2  C  0 1 Y N N N N N -1.774 1.920   29.520 9.400   1.234  0.517  C03  A1IXM 2  
A1IXM C04  C3  C  0 1 Y N N N N N -0.896 1.098   30.207 8.397   1.781  1.296  C04  A1IXM 3  
A1IXM C05  C4  C  0 1 Y N N N N N -1.336 0.365   31.278 7.119   1.258  1.248  C05  A1IXM 4  
A1IXM C06  C5  C  0 1 Y N N N N N -2.685 0.443   31.684 6.841   0.182  0.415  C06  A1IXM 5  
A1IXM C08  C6  C  0 1 N N N N N N -3.082 -1.790  32.917 5.127   -0.835 1.685  C08  A1IXM 6  
A1IXM C09  C7  C  0 1 N N N N N N -1.771 -2.307  33.589 3.743   -1.478 1.570  C09  A1IXM 7  
A1IXM C11  C8  C  0 1 N N N N N N -1.734 -2.198  35.828 1.430   -1.048 0.992  C11  A1IXM 8  
A1IXM C12  C9  C  0 1 N N N N N N -0.489 -2.565  36.734 0.432   0.070  0.684  C12  A1IXM 9  
A1IXM C13  C10 C  0 1 N N N N N N 0.558  -3.384  36.010 -0.982  -0.511 0.628  C13  A1IXM 10 
A1IXM C15  C11 C  0 1 N N N N N N 1.561  -5.761  36.002 -3.253  0.281  0.235  C15  A1IXM 11 
A1IXM C18  C12 C  0 1 N N N N N N 1.152  -7.544  37.872 -3.828  2.563  -0.231 C18  A1IXM 12 
A1IXM C21  C13 C  0 1 Y N N N N N 2.436  -9.287  36.977 -6.032  2.381  -0.451 C21  A1IXM 13 
A1IXM C22  C14 C  0 1 Y N N N N N 3.130  -10.502 36.680 -7.398  2.548  -0.636 C22  A1IXM 14 
A1IXM C23  C15 C  0 1 Y N N N N N 3.906  -10.603 35.496 -8.244  1.464  -0.544 C23  A1IXM 15 
A1IXM C24  C16 C  0 1 Y N N N N N 3.987  -9.514  34.626 -7.731  0.196  -0.266 C24  A1IXM 16 
A1IXM C25  C17 C  0 1 Y N N N N N 3.284  -8.292  34.928 -6.361  0.024  -0.082 C25  A1IXM 17 
A1IXM C26  C18 C  0 1 Y N N N N N 2.525  -8.190  36.088 -5.515  1.115  -0.165 C26  A1IXM 18 
A1IXM C27  C19 C  0 1 Y N N N N N 4.753  -9.580  33.419 -8.644  -0.970 -0.178 C27  A1IXM 19 
A1IXM C28  C20 C  0 1 Y N N N N N 4.918  -8.400  32.640 -10.020 -0.811 -0.362 C28  A1IXM 20 
A1IXM C29  C21 C  0 1 Y N N N N N 5.664  -8.504  31.468 -10.829 -1.931 -0.269 C29  A1IXM 21 
A1IXM C30  C22 C  0 1 Y N N N N N 6.213  -9.755  31.107 -10.254 -3.159 -0.001 C30  A1IXM 22 
A1IXM C32  C23 C  0 1 Y N N N N N 5.326  -10.797 33.001 -8.142  -2.244 0.084  C32  A1IXM 23 
A1IXM C33  C24 C  0 1 N N N N N N -1.576 -0.285  34.756 3.211   -0.004 -0.275 C33  A1IXM 24 
A1IXM C34  C25 C  0 1 N N N N N N -2.981 0.128   34.215 4.595   0.639  -0.160 C34  A1IXM 25 
A1IXM C35  C26 C  0 1 Y N N N N N -3.558 1.265   31.000 7.850   -0.366 -0.367 C35  A1IXM 26 
A1IXM N07  N1  N  0 1 N N N N N N -3.183 -0.352  32.861 5.549   -0.348 0.364  N07  A1IXM 27 
A1IXM N10  N2  N  0 1 N N N N N N -1.347 -1.625  34.725 2.789   -0.491 1.046  N10  A1IXM 28 
A1IXM N14  N3  N  0 1 N N N N N N 0.711  -4.710  36.665 -1.938  0.560  0.333  N14  A1IXM 29 
A1IXM N17  N4  N  0 1 N N N N N N 1.733  -7.095  36.630 -4.132  1.266  -0.037 N17  A1IXM 30 
A1IXM N20  N5  N  0 1 N N N N N N 1.577  -8.886  38.098 -4.952  3.260  -0.480 N20  A1IXM 31 
A1IXM N31  N6  N  0 1 Y N N N N N 6.030  -10.856 31.880 -8.952  -3.279 0.168  N31  A1IXM 32 
A1IXM O16  O1  O  0 1 N N N N N N 2.087  -5.519  34.983 -3.646  -0.859 0.391  O16  A1IXM 33 
A1IXM O19  O2  O  0 1 N N N N N N 0.461  -6.919  38.570 -2.708  3.034  -0.184 O19  A1IXM 34 
A1IXM CL01 CL1 CL 0 0 N N N N N N -4.251 3.062   29.037 10.388  -0.517 -1.295 CL01 A1IXM 35 
A1IXM CL36 CL2 CL 0 0 N N N N N N -5.279 1.366   31.521 7.508   -1.712 -1.410 CL36 A1IXM 36 
A1IXM H1   H1  H  0 1 N N N N N N -1.426 2.497   28.676 10.398  1.645  0.558  H1   A1IXM 37 
A1IXM H2   H2  H  0 1 N N N N N N 0.137  1.035   29.898 8.613   2.618  1.944  H2   A1IXM 38 
A1IXM H3   H3  H  0 1 N N N N N N -0.649 -0.274  31.813 6.337   1.686  1.857  H3   A1IXM 39 
A1IXM H4   H4  H  0 1 N N N N N N -3.939 -2.175  33.489 5.083   0.000  2.383  H4   A1IXM 40 
A1IXM H5   H5  H  0 1 N N N N N N -3.121 -2.180  31.889 5.842   -1.574 2.046  H5   A1IXM 41 
A1IXM H6   H6  H  0 1 N N N N N N -1.931 -3.358  33.870 3.793   -2.331 0.892  H6   A1IXM 42 
A1IXM H7   H7  H  0 1 N N N N N N -0.966 -2.246  32.842 3.415   -1.814 2.554  H7   A1IXM 43 
A1IXM H8   H8  H  0 1 N N N N N N -2.392 -1.511  36.380 1.185   -1.500 1.953  H8   A1IXM 44 
A1IXM H9   H9  H  0 1 N N N N N N -2.286 -3.117  35.583 1.380   -1.806 0.211  H9   A1IXM 45 
A1IXM H10  H10 H  0 1 N N N N N N -0.023 -1.631  37.082 0.483   0.828  1.465  H10  A1IXM 46 
A1IXM H11  H11 H  0 1 N N N N N N -0.846 -3.141  37.600 0.678   0.521  -0.277 H11  A1IXM 47 
A1IXM H12  H12 H  0 1 N N N N N N 1.520  -2.851  36.038 -1.033  -1.269 -0.154 H12  A1IXM 48 
A1IXM H13  H13 H  0 1 N N N N N N 0.248  -3.528  34.964 -1.228  -0.962 1.589  H13  A1IXM 49 
A1IXM H14  H14 H  0 1 N N N N N N 3.064  -11.342 37.356 -7.798  3.528  -0.850 H14  A1IXM 50 
A1IXM H15  H15 H  0 1 N N N N N N 4.432  -11.519 35.269 -9.306  1.595  -0.688 H15  A1IXM 51 
A1IXM H16  H16 H  0 1 N N N N N N 3.347  -7.453  34.251 -5.962  -0.956 0.134  H16  A1IXM 52 
A1IXM H17  H17 H  0 1 N N N N N N 4.482  -7.461  32.946 -10.441 0.162  -0.570 H17  A1IXM 53 
A1IXM H18  H18 H  0 1 N N N N N N 5.821  -7.638  30.842 -11.897 -1.845 -0.405 H18  A1IXM 54 
A1IXM H19  H19 H  0 1 N N N N N N 6.790  -9.837  30.198 -10.882 -4.035 0.071  H19  A1IXM 55 
A1IXM H20  H20 H  0 1 N N N N N N 5.191  -11.687 33.598 -7.080  -2.382 0.223  H20  A1IXM 56 
A1IXM H21  H21 H  0 1 N N N N N N -0.809 0.212   34.144 2.495   0.735  -0.635 H21  A1IXM 57 
A1IXM H22  H22 H  0 1 N N N N N N -1.492 0.057   35.798 3.255   -0.839 -0.974 H22  A1IXM 58 
A1IXM H23  H23 H  0 1 N N N N N N -3.060 1.225   34.222 4.923   0.975  -1.143 H23  A1IXM 59 
A1IXM H24  H24 H  0 1 N N N N N N -3.757 -0.300  34.867 4.545   1.492  0.518  H24  A1IXM 60 
A1IXM H26  H26 H  0 1 N N N N N N 0.255  -4.901  37.534 -1.624  1.469  0.208  H26  A1IXM 61 
A1IXM H27  H27 H  0 1 N N N N N N 1.333  -9.455  38.883 -5.002  4.214  -0.650 H27  A1IXM 62 
# 
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 
A1IXM CL01 C02  SING N N 1  
A1IXM C03  C02  DOUB Y N 2  
A1IXM C03  C04  SING Y N 3  
A1IXM C02  C35  SING Y N 4  
A1IXM C04  C05  DOUB Y N 5  
A1IXM C35  CL36 SING N N 6  
A1IXM C35  C06  DOUB Y N 7  
A1IXM C30  C29  DOUB Y N 8  
A1IXM C30  N31  SING Y N 9  
A1IXM C05  C06  SING Y N 10 
A1IXM C29  C28  SING Y N 11 
A1IXM C06  N07  SING N N 12 
A1IXM N31  C32  DOUB Y N 13 
A1IXM C28  C27  DOUB Y N 14 
A1IXM N07  C08  SING N N 15 
A1IXM N07  C34  SING N N 16 
A1IXM C08  C09  SING N N 17 
A1IXM C32  C27  SING Y N 18 
A1IXM C27  C24  SING N N 19 
A1IXM C09  N10  SING N N 20 
A1IXM C34  C33  SING N N 21 
A1IXM C24  C25  DOUB Y N 22 
A1IXM C24  C23  SING Y N 23 
A1IXM N10  C33  SING N N 24 
A1IXM N10  C11  SING N N 25 
A1IXM C25  C26  SING Y N 26 
A1IXM O16  C15  DOUB N N 27 
A1IXM C23  C22  DOUB Y N 28 
A1IXM C11  C12  SING N N 29 
A1IXM C15  N17  SING N N 30 
A1IXM C15  N14  SING N N 31 
A1IXM C13  N14  SING N N 32 
A1IXM C13  C12  SING N N 33 
A1IXM C26  N17  SING N N 34 
A1IXM C26  C21  DOUB Y N 35 
A1IXM N17  C18  SING N N 36 
A1IXM C22  C21  SING Y N 37 
A1IXM C21  N20  SING N N 38 
A1IXM C18  N20  SING N N 39 
A1IXM C18  O19  DOUB N N 40 
A1IXM C03  H1   SING N N 41 
A1IXM C04  H2   SING N N 42 
A1IXM C05  H3   SING N N 43 
A1IXM C08  H4   SING N N 44 
A1IXM C08  H5   SING N N 45 
A1IXM C09  H6   SING N N 46 
A1IXM C09  H7   SING N N 47 
A1IXM C11  H8   SING N N 48 
A1IXM C11  H9   SING N N 49 
A1IXM C12  H10  SING N N 50 
A1IXM C12  H11  SING N N 51 
A1IXM C13  H12  SING N N 52 
A1IXM C13  H13  SING N N 53 
A1IXM C22  H14  SING N N 54 
A1IXM C23  H15  SING N N 55 
A1IXM C25  H16  SING N N 56 
A1IXM C28  H17  SING N N 57 
A1IXM C29  H18  SING N N 58 
A1IXM C30  H19  SING N N 59 
A1IXM C32  H20  SING N N 60 
A1IXM C33  H21  SING N N 61 
A1IXM C33  H22  SING N N 62 
A1IXM C34  H23  SING N N 63 
A1IXM C34  H24  SING N N 64 
A1IXM N14  H26  SING N N 65 
A1IXM N20  H27  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 
A1IXM InChI            InChI                1.06  "InChI=1S/C26H26Cl2N6O2/c27-20-5-1-6-22(24(20)28)33-14-12-32(13-15-33)11-3-10-30-25(35)34-23-16-18(19-4-2-9-29-17-19)7-8-21(23)31-26(34)36/h1-2,4-9,16-17H,3,10-15H2,(H,30,35)(H,31,36)" 
A1IXM InChIKey         InChI                1.06  QSLKMFIYZMLKJC-UHFFFAOYSA-N                                                                                                                                                              
A1IXM SMILES_CANONICAL CACTVS               3.385 "Clc1cccc(N2CCN(CCCNC(=O)N3C(=O)Nc4ccc(cc34)c5cccnc5)CC2)c1Cl"                                                                                                                           
A1IXM SMILES           CACTVS               3.385 "Clc1cccc(N2CCN(CCCNC(=O)N3C(=O)Nc4ccc(cc34)c5cccnc5)CC2)c1Cl"                                                                                                                           
A1IXM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(c(c1)Cl)Cl)N2CCN(CC2)CCCNC(=O)N3c4cc(ccc4NC3=O)c5cccnc5"                                                                                                                         
A1IXM SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c(c(c1)Cl)Cl)N2CCN(CC2)CCCNC(=O)N3c4cc(ccc4NC3=O)c5cccnc5"                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           A1IXM 
_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        "~{N}-[3-[4-[2,3-bis(chloranyl)phenyl]piperazin-1-yl]propyl]-2-oxidanylidene-6-pyridin-3-yl-3~{H}-benzimidazole-1-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 
A1IXM "Create component" 2024-12-23 PDBE 
A1IXM "Initial release"  2025-07-23 RCSB 
# 
