data_A1IXL
# 
_chem_comp.id                                    A1IXL 
_chem_comp.name                                  "~{N}-[4-[4-[2,3-bis(chloranyl)phenyl]piperazin-1-yl]butyl]-2-oxidanylidene-6-pyridin-3-yl-3~{H}-benzimidazole-1-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H28 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                        539.456 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1IXL 
_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        9HUK 
_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 
A1IXL C12  C1  C  0 1 N N N N N N -1.358 -3.063  34.317 1.040   0.782  0.674  C12  A1IXL 1  
A1IXL C13  C2  C  0 1 N N N N N N -1.066 -2.924  35.839 -0.238  1.602  0.484  C13  A1IXL 2  
A1IXL C14  C3  C  0 1 N N N N N N 0.426  -3.202  36.201 -1.443  0.660  0.418  C14  A1IXL 3  
A1IXL C16  C4  C  0 1 N N N N N N 1.498  -5.515  35.960 -3.859  0.824  0.151  C16  A1IXL 4  
A1IXL C19  C5  C  0 1 N N N N N N 1.127  -7.454  37.648 -5.054  2.887  -0.113 C19  A1IXL 5  
A1IXL C24  C6  C  0 1 Y N N N N N 3.970  -10.277 35.097 -9.016  0.643  -0.389 C24  A1IXL 6  
A1IXL C25  C7  C  0 1 Y N N N N N 4.052  -9.122  34.299 -8.166  -0.451 -0.222 C25  A1IXL 7  
A1IXL C27  C8  C  0 1 Y N N N N N 2.553  -7.952  35.830 -6.279  1.031  -0.120 C27  A1IXL 8  
A1IXL C29  C9  C  0 1 Y N N N N N 5.360  -7.923  32.667 -10.099 -2.037 -0.321 C29  A1IXL 9  
A1IXL C30  C10 C  0 1 Y N N N N N 6.127  -7.964  31.512 -10.568 -3.339 -0.290 C30  A1IXL 10 
A1IXL C31  C11 C  0 1 Y N N N N N 6.336  -9.178  30.878 -9.670  -4.379 -0.131 C31  A1IXL 11 
A1IXL C33  C12 C  0 1 Y N N N N N 5.085  -10.301 32.451 -7.885  -2.926 -0.027 C33  A1IXL 12 
A1IXL C34  C13 C  0 1 N N N N N N 1.252  -1.442  32.411 4.615   1.807  1.226  C34  A1IXL 13 
A1IXL C35  C14 C  0 1 N N N N N N 2.632  -2.007  32.012 5.853   0.946  1.486  C35  A1IXL 14 
A1IXL C36  C15 C  0 1 Y N N N N N 3.725  -4.793  29.625 8.361   -0.472 -0.396 C36  A1IXL 15 
A1IXL C02  C16 C  0 1 Y N N N N N 4.885  -5.289  29.038 9.515   -1.215 -0.221 C02  A1IXL 16 
A1IXL C03  C17 C  0 1 Y N N N N N 6.130  -4.843  29.449 9.606   -2.117 0.825  C03  A1IXL 17 
A1IXL C04  C18 C  0 1 Y N N N N N 6.208  -3.892  30.462 8.545   -2.279 1.696  C04  A1IXL 18 
A1IXL C05  C19 C  0 1 Y N N N N N 5.045  -3.395  31.054 7.390   -1.540 1.527  C05  A1IXL 19 
A1IXL C06  C20 C  0 1 Y N N N N N 3.801  -3.832  30.638 7.294   -0.633 0.479  C06  A1IXL 20 
A1IXL C08  C21 C  0 1 N N N N N N 1.763  -4.172  32.091 4.983   -0.756 0.001  C08  A1IXL 21 
A1IXL C09  C22 C  0 1 N N N N N N 0.387  -3.572  32.359 3.745   0.105  -0.259 C09  A1IXL 22 
A1IXL C11  C23 C  0 1 N N N N N N -0.680 -1.976  33.441 2.244   1.723  0.739  C11  A1IXL 23 
A1IXL C22  C24 C  0 1 Y N N N N N 2.471  -9.109  36.627 -7.134  2.122  -0.290 C22  A1IXL 24 
A1IXL C23  C25 C  0 1 Y N N N N N 3.180  -10.270 36.259 -8.501  1.921  -0.423 C23  A1IXL 25 
A1IXL C26  C26 C  0 1 Y N N N N N 3.344  -7.960  34.667 -6.794  -0.253 -0.089 C26  A1IXL 26 
A1IXL C28  C27 C  0 1 Y N N N N N 4.837  -9.116  33.133 -8.723  -1.826 -0.189 C28  A1IXL 27 
A1IXL N07  N1  N  0 1 N N N N N N 2.587  -3.279  31.298 6.127   0.115  0.305  N07  A1IXL 28 
A1IXL N10  N2  N  0 1 N N N N N N 0.488  -2.390  33.049 3.471   0.936  0.922  N10  A1IXL 29 
A1IXL N15  N3  N  0 1 N N N N N N 0.634  -4.581  36.695 -2.666  1.445  0.236  N15  A1IXL 30 
A1IXL N18  N4  N  0 1 N N N N N N 1.709  -6.899  36.463 -4.985  1.546  -0.017 N18  A1IXL 31 
A1IXL N21  N5  N  0 1 N N N N N N 1.580  -8.820  37.776 -6.336  3.264  -0.275 N21  A1IXL 32 
A1IXL N32  N6  N  0 1 Y N N N N N 5.821  -10.299 31.354 -8.377  -4.148 -0.008 N32  A1IXL 33 
A1IXL O17  O1  O  0 1 N N N N N N 2.041  -5.172  34.967 -3.920  -0.388 0.224  O17  A1IXL 34 
A1IXL O20  O2  O  0 1 N N N N N N 0.406  -6.886  38.384 -4.103  3.643  -0.058 O20  A1IXL 35 
A1IXL CL01 CL1 CL 0 0 N N N N N N 4.715  -6.511  27.740 10.849  -1.016 -1.314 CL01 A1IXL 36 
A1IXL CL37 CL2 CL 0 0 N N N N N N 2.172  -5.430  29.020 8.249   0.664  -1.704 CL37 A1IXL 37 
A1IXL H1   H1  H  0 1 N N N N N N -2.446 -2.999  34.167 0.972   0.213  1.601  H1   A1IXL 38 
A1IXL H2   H2  H  0 1 N N N N N N -0.999 -4.048  33.985 1.160   0.096  -0.165 H2   A1IXL 39 
A1IXL H3   H3  H  0 1 N N N N N N -1.318 -1.900  36.152 -0.358  2.287  1.322  H3   A1IXL 40 
A1IXL H4   H4  H  0 1 N N N N N N -1.698 -3.640  36.384 -0.170  2.170  -0.444 H4   A1IXL 41 
A1IXL H5   H5  H  0 1 N N N N N N 1.043  -3.051  35.303 -1.323  -0.025 -0.421 H5   A1IXL 42 
A1IXL H6   H6  H  0 1 N N N N N N 0.738  -2.495  36.983 -1.510  0.092  1.345  H6   A1IXL 43 
A1IXL H7   H7  H  0 1 N N N N N N 4.513  -11.168 34.817 -10.079 0.487  -0.493 H7   A1IXL 44 
A1IXL H8   H8  H  0 1 N N N N N N 5.178  -6.993  33.184 -10.777 -1.207 -0.449 H8   A1IXL 45 
A1IXL H9   H9  H  0 1 N N N N N N 6.557  -7.058  31.111 -11.625 -3.541 -0.389 H9   A1IXL 46 
A1IXL H10  H10 H  0 1 N N N N N N 6.931  -9.209  29.977 -10.033 -5.396 -0.105 H10  A1IXL 47 
A1IXL H11  H11 H  0 1 N N N N N N 4.674  -11.229 32.820 -6.820  -2.777 0.076  H11  A1IXL 48 
A1IXL H12  H12 H  0 1 N N N N N N 1.397  -0.586  33.086 4.394   2.403  2.111  H12  A1IXL 49 
A1IXL H13  H13 H  0 1 N N N N N N 0.726  -1.109  31.504 4.803   2.468  0.380  H13  A1IXL 50 
A1IXL H14  H14 H  0 1 N N N N N N 3.222  -2.150  32.929 6.710   1.591  1.684  H14  A1IXL 51 
A1IXL H15  H15 H  0 1 N N N N N N 3.131  -1.269  31.366 5.675   0.304  2.349  H15  A1IXL 52 
A1IXL H16  H16 H  0 1 N N N N N N 7.028  -5.228  28.990 10.507  -2.695 0.960  H16  A1IXL 53 
A1IXL H17  H17 H  0 1 N N N N N N 7.173  -3.537  30.792 8.619   -2.984 2.511  H17  A1IXL 54 
A1IXL H18  H18 H  0 1 N N N N N N 5.118  -2.662  31.844 6.562   -1.668 2.208  H18  A1IXL 55 
A1IXL H19  H19 H  0 1 N N N N N N 1.640  -5.121  31.548 4.794   -1.417 0.847  H19  A1IXL 56 
A1IXL H20  H20 H  0 1 N N N N N N 2.264  -4.361  33.052 5.204   -1.352 -0.884 H20  A1IXL 57 
A1IXL H21  H21 H  0 1 N N N N N N -0.116 -3.385  31.399 3.923   0.747  -1.122 H21  A1IXL 58 
A1IXL H22  H22 H  0 1 N N N N N N -0.206 -4.284  32.952 2.888   -0.539 -0.456 H22  A1IXL 59 
A1IXL H23  H23 H  0 1 N N N N N N -0.562 -1.054  34.030 2.312   2.292  -0.188 H23  A1IXL 60 
A1IXL H24  H24 H  0 1 N N N N N N -1.309 -1.771  32.562 2.124   2.409  1.578  H24  A1IXL 61 
A1IXL H25  H25 H  0 1 N N N N N N 3.116  -11.157 36.872 -9.161  2.766  -0.554 H25  A1IXL 62 
A1IXL H26  H26 H  0 1 N N N N N N 3.409  -7.073  34.054 -6.134  -1.099 0.040  H26  A1IXL 63 
A1IXL H28  H28 H  0 1 N N N N N N 0.183  -4.880  37.536 -2.618  2.412  0.177  H28  A1IXL 64 
A1IXL H29  H29 H  0 1 N N N N N N 1.336  -9.456  38.508 -6.651  4.177  -0.365 H29  A1IXL 65 
# 
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 
A1IXL CL01 C02 SING N N 1  
A1IXL CL37 C36 SING N N 2  
A1IXL C02  C03 DOUB Y N 3  
A1IXL C02  C36 SING Y N 4  
A1IXL C03  C04 SING Y N 5  
A1IXL C36  C06 DOUB Y N 6  
A1IXL C04  C05 DOUB Y N 7  
A1IXL C06  C05 SING Y N 8  
A1IXL C06  N07 SING N N 9  
A1IXL C31  N32 DOUB Y N 10 
A1IXL C31  C30 SING Y N 11 
A1IXL N07  C35 SING N N 12 
A1IXL N07  C08 SING N N 13 
A1IXL N32  C33 SING Y N 14 
A1IXL C30  C29 DOUB Y N 15 
A1IXL C35  C34 SING N N 16 
A1IXL C08  C09 SING N N 17 
A1IXL C09  N10 SING N N 18 
A1IXL C34  N10 SING N N 19 
A1IXL C33  C28 DOUB Y N 20 
A1IXL C29  C28 SING Y N 21 
A1IXL N10  C11 SING N N 22 
A1IXL C28  C25 SING N N 23 
A1IXL C11  C12 SING N N 24 
A1IXL C25  C26 DOUB Y N 25 
A1IXL C25  C24 SING Y N 26 
A1IXL C12  C13 SING N N 27 
A1IXL C26  C27 SING Y N 28 
A1IXL O17  C16 DOUB N N 29 
A1IXL C24  C23 DOUB Y N 30 
A1IXL C27  N18 SING N N 31 
A1IXL C27  C22 DOUB Y N 32 
A1IXL C13  C14 SING N N 33 
A1IXL C16  N18 SING N N 34 
A1IXL C16  N15 SING N N 35 
A1IXL C14  N15 SING N N 36 
A1IXL C23  C22 SING Y N 37 
A1IXL N18  C19 SING N N 38 
A1IXL C22  N21 SING N N 39 
A1IXL C19  N21 SING N N 40 
A1IXL C19  O20 DOUB N N 41 
A1IXL C12  H1  SING N N 42 
A1IXL C12  H2  SING N N 43 
A1IXL C13  H3  SING N N 44 
A1IXL C13  H4  SING N N 45 
A1IXL C14  H5  SING N N 46 
A1IXL C14  H6  SING N N 47 
A1IXL C24  H7  SING N N 48 
A1IXL C29  H8  SING N N 49 
A1IXL C30  H9  SING N N 50 
A1IXL C31  H10 SING N N 51 
A1IXL C33  H11 SING N N 52 
A1IXL C34  H12 SING N N 53 
A1IXL C34  H13 SING N N 54 
A1IXL C35  H14 SING N N 55 
A1IXL C35  H15 SING N N 56 
A1IXL C03  H16 SING N N 57 
A1IXL C04  H17 SING N N 58 
A1IXL C05  H18 SING N N 59 
A1IXL C08  H19 SING N N 60 
A1IXL C08  H20 SING N N 61 
A1IXL C09  H21 SING N N 62 
A1IXL C09  H22 SING N N 63 
A1IXL C11  H23 SING N N 64 
A1IXL C11  H24 SING N N 65 
A1IXL C23  H25 SING N N 66 
A1IXL C26  H26 SING N N 67 
A1IXL N15  H28 SING N N 68 
A1IXL N21  H29 SING N N 69 
# 
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 
A1IXL InChI            InChI                1.06  "InChI=1S/C27H28Cl2N6O2/c28-21-6-3-7-23(25(21)29)34-15-13-33(14-16-34)12-2-1-11-31-26(36)35-24-17-19(20-5-4-10-30-18-20)8-9-22(24)32-27(35)37/h3-10,17-18H,1-2,11-16H2,(H,31,36)(H,32,37)" 
A1IXL InChIKey         InChI                1.06  VELXFGYVMVTLMF-UHFFFAOYSA-N                                                                                                                                                                
A1IXL SMILES_CANONICAL CACTVS               3.385 "Clc1cccc(N2CCN(CCCCNC(=O)N3C(=O)Nc4ccc(cc34)c5cccnc5)CC2)c1Cl"                                                                                                                            
A1IXL SMILES           CACTVS               3.385 "Clc1cccc(N2CCN(CCCCNC(=O)N3C(=O)Nc4ccc(cc34)c5cccnc5)CC2)c1Cl"                                                                                                                            
A1IXL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(c(c1)Cl)Cl)N2CCN(CC2)CCCCNC(=O)N3c4cc(ccc4NC3=O)c5cccnc5"                                                                                                                          
A1IXL SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c(c(c1)Cl)Cl)N2CCN(CC2)CCCCNC(=O)N3c4cc(ccc4NC3=O)c5cccnc5"                                                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           A1IXL 
_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}-[4-[4-[2,3-bis(chloranyl)phenyl]piperazin-1-yl]butyl]-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 
A1IXL "Create component" 2024-12-23 PDBE 
A1IXL "Initial release"  2025-07-23 RCSB 
# 
