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 #