data_A1AY9
# 
_chem_comp.id                                    A1AY9 
_chem_comp.name                                  "4-{5-[5-(4-carbamimidoylphenyl)-1-methyl-1H-1,3-benzimidazol-2-yl]thiophen-2-yl}benzene-1-carboximidamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H22 N6 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-07-11 
_chem_comp.pdbx_modified_date                    2025-08-01 
_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                        450.558 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1AY9 
_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        9CKM 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
A1AY9 C10 C1  C 0 1 Y N N N N N 3.635  5.469  73.127 -8.342  0.279  0.129  C10 A1AY9 1  
A1AY9 C13 C2  C 0 1 Y N N N N N 1.464  6.089  72.261 -6.385  1.621  -0.218 C13 A1AY9 2  
A1AY9 C14 C3  C 0 1 Y N N N N N 1.186  12.653 67.304 1.971   0.049  -0.078 C14 A1AY9 3  
A1AY9 C17 C4  C 0 1 Y N N N N N 2.280  15.521 65.174 5.729   -0.186 0.020  C17 A1AY9 4  
A1AY9 C18 C5  C 0 1 Y N N N N N 3.476  15.033 64.656 6.716   -1.171 -0.009 C18 A1AY9 5  
A1AY9 C20 C6  C 0 1 Y N N N N N 3.993  17.148 63.670 8.405   0.530  0.132  C20 A1AY9 6  
A1AY9 C21 C7  C 0 1 N N N N N N 4.937  17.958 62.865 9.833   0.912  0.192  C21 A1AY9 7  
A1AY9 C22 C8  C 0 1 Y N N N N N 2.819  17.665 64.197 7.417   1.515  0.162  C22 A1AY9 8  
A1AY9 C23 C9  C 0 1 Y N N N N N 1.973  16.859 64.939 6.088   1.159  0.106  C23 A1AY9 9  
A1AY9 C24 C10 C 0 1 Y N N N N N 0.058  14.956 66.257 3.941   -1.918 -0.137 C24 A1AY9 10 
A1AY9 C25 C11 C 0 1 Y N N N N N -0.745 14.132 67.018 2.615   -2.284 -0.198 C25 A1AY9 11 
A1AY9 C1  C12 C 0 1 N N N N N N -1.997 11.924 68.842 -0.585  -2.561 -0.311 C1  A1AY9 12 
A1AY9 C11 C13 C 0 1 N N N N N N 4.515  4.619  73.979 -9.814  0.167  0.215  C11 A1AY9 13 
A1AY9 C12 C14 C 0 1 Y N N N N N 2.258  5.268  73.051 -7.750  1.516  -0.138 C12 A1AY9 14 
A1AY9 C15 C15 C 0 1 Y N N N N N 1.971  13.467 66.537 3.317   0.414  -0.016 C15 A1AY9 15 
A1AY9 C16 C16 C 0 1 Y N N N N N 1.416  14.639 66.000 4.298   -0.568 -0.046 C16 A1AY9 16 
A1AY9 C19 C17 C 0 1 Y N N N N N 4.318  15.830 63.923 8.045   -0.816 0.047  C19 A1AY9 17 
A1AY9 C2  C18 C 0 1 Y N N N N N 0.406  11.111 68.566 -0.207  -0.062 -0.151 C2  A1AY9 18 
A1AY9 C26 C19 C 0 1 Y N N N N N -0.147 12.977 67.527 1.624   -1.312 -0.170 C26 A1AY9 19 
A1AY9 C3  C20 C 0 1 Y N N N N N 0.351  9.881  69.327 -1.619  0.345  -0.172 C3  A1AY9 20 
A1AY9 C4  C21 C 0 1 Y N N N N N -0.622 8.944  69.566 -2.068  1.612  -0.407 C4  A1AY9 21 
A1AY9 C5  C22 C 0 1 Y N N N N N -0.134 7.871  70.330 -3.431  1.751  -0.377 C5  A1AY9 22 
A1AY9 C6  C23 C 0 1 Y N N N N N 1.192  7.993  70.671 -4.117  0.602  -0.117 C6  A1AY9 23 
A1AY9 C7  C24 C 0 1 Y N N N N N 2.029  7.105  71.486 -5.586  0.490  -0.032 C7  A1AY9 24 
A1AY9 C8  C25 C 0 1 Y N N N N N 3.403  7.313  71.583 -6.178  -0.747 0.241  C8  A1AY9 25 
A1AY9 C9  C26 C 0 1 Y N N N N N 4.188  6.511  72.395 -7.543  -0.850 0.320  C9  A1AY9 26 
A1AY9 N1  N1  N 0 1 Y N N N N N -0.639 11.959 68.315 0.243   -1.356 -0.214 N1  A1AY9 27 
A1AY9 N2  N2  N 0 1 N N N N N N 5.637  5.137  74.461 -10.398 -1.053 0.479  N2  A1AY9 28 
A1AY9 N3  N3  N 0 1 N N N N N N 4.241  3.342  74.153 -10.559 1.222  0.042  N3  A1AY9 29 
A1AY9 N4  N4  N 0 1 Y N N N N N 1.521  11.493 67.980 0.816   0.759  -0.076 N4  A1AY9 30 
A1AY9 N5  N5  N 0 1 N N N N N N 5.865  17.337 62.164 10.809  -0.062 0.163  N5  A1AY9 31 
A1AY9 N6  N6  N 0 1 N N N N N N 4.924  19.263 62.939 10.169  2.168  0.272  N6  A1AY9 32 
A1AY9 S1  S1  S 0 1 Y N N N N N 1.843  9.489  70.097 -2.986  -0.728 0.094  S1  A1AY9 33 
A1AY9 H13 H1  H 0 1 N N N N N N 0.394  5.940  72.245 -5.928  2.577  -0.425 H13 A1AY9 34 
A1AY9 H15 H2  H 0 1 N N N N N N 3.747  14.003 64.835 6.437   -2.213 -0.075 H15 A1AY9 35 
A1AY9 H21 H3  H 0 1 N N N N N N 2.564  18.701 64.028 7.694   2.557  0.229  H21 A1AY9 36 
A1AY9 H22 H4  H 0 1 N N N N N N 1.061  17.274 65.342 5.323   1.922  0.129  H22 A1AY9 37 
A1AY9 H23 H5  H 0 1 N N N N N N -0.358 15.865 65.847 4.709   -2.676 -0.159 H23 A1AY9 38 
A1AY9 H24 H6  H 0 1 N N N N N N -1.781 14.368 67.210 2.346   -3.327 -0.268 H24 A1AY9 39 
A1AY9 H2  H7  H 0 1 N N N N N N -2.574 12.763 68.426 -0.760  -2.799 -1.360 H2  A1AY9 40 
A1AY9 H3  H8  H 0 1 N N N N N N -2.475 10.974 68.560 -0.073  -3.394 0.170  H3  A1AY9 41 
A1AY9 H1  H9  H 0 1 N N N N N N -1.967 12.008 69.938 -1.540  -2.386 0.185  H1  A1AY9 42 
A1AY9 H12 H10 H 0 1 N N N N N N 1.804  4.465  73.613 -8.368  2.390  -0.282 H12 A1AY9 43 
A1AY9 H14 H11 H 0 1 N N N N N N 3.003  13.212 66.347 3.595   1.456  0.054  H14 A1AY9 44 
A1AY9 H16 H12 H 0 1 N N N N N N 5.243  15.423 63.541 8.809   -1.579 0.024  H16 A1AY9 45 
A1AY9 H4  H13 H 0 1 N N N N N N -1.639 9.022  69.210 -1.402  2.439  -0.601 H4  A1AY9 46 
A1AY9 H5  H14 H 0 1 N N N N N N -0.744 7.029  70.622 -3.924  2.697  -0.545 H5  A1AY9 47 
A1AY9 H6  H15 H 0 1 N N N N N N 3.862  8.110  71.018 -5.561  -1.620 0.390  H6  A1AY9 48 
A1AY9 H7  H16 H 0 1 N N N N N N 5.249  6.700  72.460 -8.001  -1.806 0.531  H7  A1AY9 49 
A1AY9 H8  H17 H 0 1 N N N N N N 6.281  4.557  74.960 -9.843  -1.839 0.608  H8  A1AY9 50 
A1AY9 H9  H18 H 0 1 N N N N N N 5.839  6.107  74.325 -11.363 -1.127 0.535  H9  A1AY9 51 
A1AY9 H10 H19 H 0 1 N N N N N N 4.959  2.871  74.665 -11.525 1.149  0.099  H10 A1AY9 52 
A1AY9 H17 H20 H 0 1 N N N N N N 6.566  17.865 61.684 10.559  -0.997 0.103  H17 A1AY9 53 
A1AY9 H18 H21 H 0 1 N N N N N N 5.868  16.338 62.112 11.745  0.189  0.202  H18 A1AY9 54 
A1AY9 H20 H22 H 0 1 N N N N N N 5.672  19.675 62.419 11.105  2.418  0.310  H20 A1AY9 55 
# 
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 
A1AY9 C1  N1  SING N N 1  
A1AY9 N1  C2  SING Y N 2  
A1AY9 C2  C3  SING N N 3  
A1AY9 C3  C4  DOUB Y N 4  
A1AY9 C4  C5  SING Y N 5  
A1AY9 C5  C6  DOUB Y N 6  
A1AY9 C6  C7  SING N N 7  
A1AY9 C7  C8  DOUB Y N 8  
A1AY9 C8  C9  SING Y N 9  
A1AY9 C9  C10 DOUB Y N 10 
A1AY9 C10 C11 SING N N 11 
A1AY9 C11 N2  SING N N 12 
A1AY9 C11 N3  DOUB N N 13 
A1AY9 C10 C12 SING Y N 14 
A1AY9 C12 C13 DOUB Y N 15 
A1AY9 C6  S1  SING Y N 16 
A1AY9 C2  N4  DOUB Y N 17 
A1AY9 N4  C14 SING Y N 18 
A1AY9 C14 C15 DOUB Y N 19 
A1AY9 C15 C16 SING Y N 20 
A1AY9 C16 C17 SING N N 21 
A1AY9 C17 C18 DOUB Y N 22 
A1AY9 C18 C19 SING Y N 23 
A1AY9 C19 C20 DOUB Y N 24 
A1AY9 C20 C21 SING N N 25 
A1AY9 C21 N5  SING N N 26 
A1AY9 C21 N6  DOUB N N 27 
A1AY9 C20 C22 SING Y N 28 
A1AY9 C22 C23 DOUB Y N 29 
A1AY9 C16 C24 DOUB Y N 30 
A1AY9 C24 C25 SING Y N 31 
A1AY9 C25 C26 DOUB Y N 32 
A1AY9 N1  C26 SING Y N 33 
A1AY9 C3  S1  SING Y N 34 
A1AY9 C14 C26 SING Y N 35 
A1AY9 C7  C13 SING Y N 36 
A1AY9 C17 C23 SING Y N 37 
A1AY9 C13 H13 SING N N 38 
A1AY9 C18 H15 SING N N 39 
A1AY9 C22 H21 SING N N 40 
A1AY9 C23 H22 SING N N 41 
A1AY9 C24 H23 SING N N 42 
A1AY9 C25 H24 SING N N 43 
A1AY9 C1  H2  SING N N 44 
A1AY9 C1  H3  SING N N 45 
A1AY9 C1  H1  SING N N 46 
A1AY9 C12 H12 SING N N 47 
A1AY9 C15 H14 SING N N 48 
A1AY9 C19 H16 SING N N 49 
A1AY9 C4  H4  SING N N 50 
A1AY9 C5  H5  SING N N 51 
A1AY9 C8  H6  SING N N 52 
A1AY9 C9  H7  SING N N 53 
A1AY9 N2  H8  SING N N 54 
A1AY9 N2  H9  SING N N 55 
A1AY9 N3  H10 SING N N 56 
A1AY9 N5  H17 SING N N 57 
A1AY9 N5  H18 SING N N 58 
A1AY9 N6  H20 SING N N 59 
# 
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 
A1AY9 SMILES           ACDLabs              12.01 "N=C(N)c1ccc(cc1)c1cc2nc(n(C)c2cc1)c1ccc(s1)c1ccc(cc1)C(=N)N"                                                                                                  
A1AY9 InChI            InChI                1.06  "InChI=1S/C26H22N6S/c1-32-21-11-10-19(15-2-6-17(7-3-15)24(27)28)14-20(21)31-26(32)23-13-12-22(33-23)16-4-8-18(9-5-16)25(29)30/h2-14H,1H3,(H3,27,28)(H3,29,30)" 
A1AY9 InChIKey         InChI                1.06  VXKYAQDFRKKEOR-UHFFFAOYSA-N                                                                                                                                    
A1AY9 SMILES_CANONICAL CACTVS               3.385 "Cn1c2ccc(cc2nc1c3sc(cc3)c4ccc(cc4)C(N)=N)c5ccc(cc5)C(N)=N"                                                                                                    
A1AY9 SMILES           CACTVS               3.385 "Cn1c2ccc(cc2nc1c3sc(cc3)c4ccc(cc4)C(N)=N)c5ccc(cc5)C(N)=N"                                                                                                    
A1AY9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\c1ccc(cc1)c2ccc3c(c2)nc(n3C)c4ccc(s4)c5ccc(cc5)/C(=N\[H])/N)/N"                                                                                      
A1AY9 SMILES           "OpenEye OEToolkits" 2.0.7 "Cn1c2ccc(cc2nc1c3ccc(s3)c4ccc(cc4)C(=N)N)c5ccc(cc5)C(=N)N"                                                                                                    
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
A1AY9 "SYSTEMATIC NAME" ACDLabs              12.01 "4-{5-[5-(4-carbamimidoylphenyl)-1-methyl-1H-1,3-benzimidazol-2-yl]thiophen-2-yl}benzene-1-carboximidamide" 
A1AY9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "4-[2-[5-(4-carbamimidoylphenyl)thiophen-2-yl]-1-methyl-benzimidazol-5-yl]benzenecarboximidamide"           
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1AY9 "Create component" 2024-07-11 RCSB 
A1AY9 "Initial release"  2025-08-06 RCSB 
# 
