data_A1IXN
# 
_chem_comp.id                                    A1IXN 
_chem_comp.name                                  "2-oxidanylidene-~{N}-[3-(4-phenylpiperazin-1-yl)propyl]-6-pyridin-3-yl-3~{H}-benzimidazole-1-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H28 N6 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-12-26 
_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                        456.540 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1IXN 
_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        9HV3 
_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 
A1IXN C02 C1  C 0 1 N N N N N N 1.699  -5.877  36.102 -1.891  -0.162 -0.172 C02 A1IXN 1  
A1IXN C04 C2  C 0 1 N N N N N N 0.754  -3.571  36.130 0.361   0.766  -0.243 C04 A1IXN 2  
A1IXN C05 C3  C 0 1 N N N N N N -0.517 -2.829  36.596 1.800   0.255  -0.334 C05 A1IXN 3  
A1IXN C06 C4  C 0 1 N N N N N N -0.478 -1.347  36.080 2.764   1.444  -0.333 C06 A1IXN 4  
A1IXN C08 C5  C 0 1 N N N N N N -1.798 -1.873  34.424 5.083   2.060  -0.659 C08 A1IXN 5  
A1IXN C09 C6  C 0 1 N N N N N N -3.254 -1.954  34.006 6.498   1.501  -0.822 C09 A1IXN 6  
A1IXN C11 C7  C 0 1 N N N N N N -3.943 -0.393  35.641 5.932   -0.354 0.627  C11 A1IXN 7  
A1IXN C12 C8  C 0 1 N N N N N N -2.612 -0.670  36.342 4.517   0.206  0.790  C12 A1IXN 8  
A1IXN C13 C9  C 0 1 Y N N N N N -3.727 0.393   33.140 8.183   0.287  0.305  C13 A1IXN 9  
A1IXN C14 C10 C 0 1 Y N N N N N -2.829 0.153   32.111 8.949   0.561  -0.821 C14 A1IXN 10 
A1IXN C15 C11 C 0 1 Y N N N N N -2.652 1.103   31.117 10.250  0.103  -0.897 C15 A1IXN 11 
A1IXN C16 C12 C 0 1 Y N N N N N -3.405 2.309   31.157 10.790  -0.627 0.146  C16 A1IXN 12 
A1IXN C17 C13 C 0 1 Y N N N N N -4.315 2.539   32.193 10.030  -0.901 1.269  C17 A1IXN 13 
A1IXN C18 C14 C 0 1 Y N N N N N -4.498 1.611   33.183 8.728   -0.447 1.351  C18 A1IXN 14 
A1IXN C20 C15 C 0 1 N N N N N N 1.241  -7.728  37.905 -2.391  -2.507 -0.242 C20 A1IXN 15 
A1IXN C23 C16 C 0 1 Y N N N N N 2.547  -9.410  36.959 -4.609  -2.446 -0.126 C23 A1IXN 16 
A1IXN C24 C17 C 0 1 Y N N N N N 3.255  -10.606 36.624 -5.974  -2.691 -0.068 C24 A1IXN 17 
A1IXN C25 C18 C 0 1 Y N N N N N 4.039  -10.644 35.474 -6.860  -1.639 0.022  C25 A1IXN 18 
A1IXN C26 C19 C 0 1 Y N N N N N 4.119  -9.485  34.606 -6.389  -0.327 0.055  C26 A1IXN 19 
A1IXN C27 C20 C 0 1 Y N N N N N 3.430  -8.311  34.935 -5.020  -0.076 -0.003 C27 A1IXN 20 
A1IXN C28 C21 C 0 1 Y N N N N N 2.645  -8.269  36.101 -4.133  -1.133 -0.102 C28 A1IXN 21 
A1IXN C29 C22 C 0 1 Y N N N N N 4.924  -9.516  33.466 -7.346  0.803  0.161  C29 A1IXN 22 
A1IXN C30 C23 C 0 1 Y N N N N N 5.342  -8.287  32.910 -8.722  0.564  0.220  C30 A1IXN 23 
A1IXN C31 C24 C 0 1 Y N N N N N 6.152  -8.350  31.831 -9.573  1.652  0.319  C31 A1IXN 24 
A1IXN C32 C25 C 0 1 Y N N N N N 6.556  -9.616  31.327 -9.039  2.927  0.357  C32 A1IXN 25 
A1IXN C34 C26 C 0 1 Y N N N N N 5.376  -10.729 32.943 -6.887  2.117  0.210  C34 A1IXN 26 
A1IXN N03 N1  N 0 1 N N N N N N 0.877  -4.901  36.758 -0.562  -0.372 -0.245 N03 A1IXN 27 
A1IXN N07 N2  N 0 1 N N N N N N -1.568 -1.023  35.485 4.146   0.954  -0.419 N07 A1IXN 28 
A1IXN N10 N3  N 0 1 N N N N N N -3.903 -0.666  34.208 6.869   0.753  0.388  N10 A1IXN 29 
A1IXN N19 N4  N 0 1 N N N N N N 1.850  -7.220  36.677 -2.740  -1.209 -0.173 N19 A1IXN 30 
A1IXN N22 N5  N 0 1 N N N N N N 1.667  -9.068  38.089 -3.495  -3.277 -0.219 N22 A1IXN 31 
A1IXN N33 N6  N 0 1 Y N N N N N 6.169  -10.740 31.898 -7.735  3.121  0.299  N33 A1IXN 32 
A1IXN O01 O1  O 0 1 N N N N N N 2.241  -5.617  35.062 -2.324  0.971  -0.100 O01 A1IXN 33 
A1IXN O21 O2  O 0 1 N N N N N N 0.529  -7.129  38.619 -1.250  -2.922 -0.319 O21 A1IXN 34 
A1IXN H1  H1  H 0 1 N N N N N N 0.712  -3.696  35.038 0.234   1.335  0.678  H1  A1IXN 35 
A1IXN H2  H2  H 0 1 N N N N N N 1.635  -2.969  36.397 0.148   1.407  -1.099 H2  A1IXN 36 
A1IXN H3  H3  H 0 1 N N N N N N -0.562 -2.833  37.695 2.013   -0.386 0.522  H3  A1IXN 37 
A1IXN H4  H4  H 0 1 N N N N N N -1.406 -3.335  36.191 1.927   -0.314 -1.255 H4  A1IXN 38 
A1IXN H5  H5  H 0 1 N N N N N N 0.359  -1.237  35.375 2.551   2.085  -1.188 H5  A1IXN 39 
A1IXN H6  H6  H 0 1 N N N N N N -0.326 -0.675  36.937 2.637   2.013  0.588  H6  A1IXN 40 
A1IXN H7  H7  H 0 1 N N N N N N -1.463 -2.881  34.709 5.059   2.747  0.187  H7  A1IXN 41 
A1IXN H8  H8  H 0 1 N N N N N N -1.210 -1.520  33.564 4.795   2.591  -1.566 H8  A1IXN 42 
A1IXN H9  H9  H 0 1 N N N N N N -3.765 -2.718  34.611 6.529   0.835  -1.684 H9  A1IXN 43 
A1IXN H10 H10 H 0 1 N N N N N N -3.313 -2.229  32.942 7.199   2.322  -0.971 H10 A1IXN 44 
A1IXN H11 H11 H 0 1 N N N N N N -4.203 0.666   35.789 6.220   -0.884 1.535  H11 A1IXN 45 
A1IXN H12 H12 H 0 1 N N N N N N -4.717 -1.027  36.097 5.956   -1.041 -0.219 H12 A1IXN 46 
A1IXN H13 H13 H 0 1 N N N N N N -2.764 -1.494  37.055 3.816   -0.615 0.939  H13 A1IXN 47 
A1IXN H14 H14 H 0 1 N N N N N N -2.316 0.238   36.888 4.486   0.871  1.653  H14 A1IXN 48 
A1IXN H15 H15 H 0 1 N N N N N N -2.270 -0.770  32.084 8.528   1.130  -1.636 H15 A1IXN 49 
A1IXN H16 H16 H 0 1 N N N N N N -1.947 0.929   30.318 10.846  0.316  -1.772 H16 A1IXN 50 
A1IXN H17 H17 H 0 1 N N N N N N -3.273 3.051   30.383 11.807  -0.984 0.084  H17 A1IXN 51 
A1IXN H18 H18 H 0 1 N N N N N N -4.880 3.459   32.213 10.455  -1.472 2.081  H18 A1IXN 52 
A1IXN H19 H19 H 0 1 N N N N N N -5.205 1.788   33.980 8.137   -0.658 2.230  H19 A1IXN 53 
A1IXN H20 H20 H 0 1 N N N N N N 3.182  -11.476 37.260 -6.342  -3.707 -0.094 H20 A1IXN 54 
A1IXN H21 H21 H 0 1 N N N N N N 4.590  -11.540 35.227 -7.922  -1.832 0.067  H21 A1IXN 55 
A1IXN H22 H22 H 0 1 N N N N N N 3.501  -7.443  34.297 -4.654  0.939  0.022  H22 A1IXN 56 
A1IXN H23 H23 H 0 1 N N N N N N 5.029  -7.342  33.328 -9.111  -0.442 0.188  H23 A1IXN 57 
A1IXN H24 H24 H 0 1 N N N N N N 6.491  -7.443  31.353 -10.642 1.506  0.366  H24 A1IXN 58 
A1IXN H25 H25 H 0 1 N N N N N N 7.194  -9.658  30.457 -9.700  3.778  0.434  H25 A1IXN 59 
A1IXN H26 H26 H 0 1 N N N N N N 5.072  -11.660 33.399 -5.826  2.316  0.170  H26 A1IXN 60 
A1IXN H27 H27 H 0 1 N N N N N N 0.403  -5.115  37.612 -0.216  -1.277 -0.298 H27 A1IXN 61 
A1IXN H29 H29 H 0 1 N N N N N N 1.416  -9.670  38.847 -3.512  -4.246 -0.261 H29 A1IXN 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 
A1IXN C15 C16 DOUB Y N 1  
A1IXN C15 C14 SING Y N 2  
A1IXN C16 C17 SING Y N 3  
A1IXN C32 C31 DOUB Y N 4  
A1IXN C32 N33 SING Y N 5  
A1IXN C31 C30 SING Y N 6  
A1IXN N33 C34 DOUB Y N 7  
A1IXN C14 C13 DOUB Y N 8  
A1IXN C17 C18 DOUB Y N 9  
A1IXN C30 C29 DOUB Y N 10 
A1IXN C34 C29 SING Y N 11 
A1IXN C13 C18 SING Y N 12 
A1IXN C13 N10 SING N N 13 
A1IXN C29 C26 SING N N 14 
A1IXN C09 N10 SING N N 15 
A1IXN C09 C08 SING N N 16 
A1IXN N10 C11 SING N N 17 
A1IXN C08 N07 SING N N 18 
A1IXN C26 C27 DOUB Y N 19 
A1IXN C26 C25 SING Y N 20 
A1IXN C27 C28 SING Y N 21 
A1IXN O01 C02 DOUB N N 22 
A1IXN C25 C24 DOUB Y N 23 
A1IXN N07 C06 SING N N 24 
A1IXN N07 C12 SING N N 25 
A1IXN C11 C12 SING N N 26 
A1IXN C06 C05 SING N N 27 
A1IXN C28 N19 SING N N 28 
A1IXN C28 C23 DOUB Y N 29 
A1IXN C02 N19 SING N N 30 
A1IXN C02 N03 SING N N 31 
A1IXN C04 C05 SING N N 32 
A1IXN C04 N03 SING N N 33 
A1IXN C24 C23 SING Y N 34 
A1IXN N19 C20 SING N N 35 
A1IXN C23 N22 SING N N 36 
A1IXN C20 N22 SING N N 37 
A1IXN C20 O21 DOUB N N 38 
A1IXN C04 H1  SING N N 39 
A1IXN C04 H2  SING N N 40 
A1IXN C05 H3  SING N N 41 
A1IXN C05 H4  SING N N 42 
A1IXN C06 H5  SING N N 43 
A1IXN C06 H6  SING N N 44 
A1IXN C08 H7  SING N N 45 
A1IXN C08 H8  SING N N 46 
A1IXN C09 H9  SING N N 47 
A1IXN C09 H10 SING N N 48 
A1IXN C11 H11 SING N N 49 
A1IXN C11 H12 SING N N 50 
A1IXN C12 H13 SING N N 51 
A1IXN C12 H14 SING N N 52 
A1IXN C14 H15 SING N N 53 
A1IXN C15 H16 SING N N 54 
A1IXN C16 H17 SING N N 55 
A1IXN C17 H18 SING N N 56 
A1IXN C18 H19 SING N N 57 
A1IXN C24 H20 SING N N 58 
A1IXN C25 H21 SING N N 59 
A1IXN C27 H22 SING N N 60 
A1IXN C30 H23 SING N N 61 
A1IXN C31 H24 SING N N 62 
A1IXN C32 H25 SING N N 63 
A1IXN C34 H26 SING N N 64 
A1IXN N03 H27 SING N N 65 
A1IXN N22 H29 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 
A1IXN InChI            InChI                1.06  "InChI=1S/C26H28N6O2/c33-25(28-12-5-13-30-14-16-31(17-15-30)22-7-2-1-3-8-22)32-24-18-20(21-6-4-11-27-19-21)9-10-23(24)29-26(32)34/h1-4,6-11,18-19H,5,12-17H2,(H,28,33)(H,29,34)" 
A1IXN InChIKey         InChI                1.06  YMOXHFNCFJKODZ-UHFFFAOYSA-N                                                                                                                                                      
A1IXN SMILES_CANONICAL CACTVS               3.385 "O=C(NCCCN1CCN(CC1)c2ccccc2)N3C(=O)Nc4ccc(cc34)c5cccnc5"                                                                                                                         
A1IXN SMILES           CACTVS               3.385 "O=C(NCCCN1CCN(CC1)c2ccccc2)N3C(=O)Nc4ccc(cc34)c5cccnc5"                                                                                                                         
A1IXN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)N2CCN(CC2)CCCNC(=O)N3c4cc(ccc4NC3=O)c5cccnc5"                                                                                                                         
A1IXN SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)N2CCN(CC2)CCCNC(=O)N3c4cc(ccc4NC3=O)c5cccnc5"                                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           A1IXN 
_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        "2-oxidanylidene-~{N}-[3-(4-phenylpiperazin-1-yl)propyl]-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 
A1IXN "Create component" 2024-12-26 PDBE 
A1IXN "Initial release"  2025-07-23 RCSB 
# 
