data_Y5U # _chem_comp.id Y5U _chem_comp.name "(2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide)" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H16 N8 Se" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-12 _chem_comp.pdbx_modified_date 2024-06-07 _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 447.355 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y5U _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 8T4N _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 Y5U C1 C1 C 0 1 N N N N N N 14.473 26.552 0.361 8.505 1.281 -0.004 C1 Y5U 1 Y5U C2 C2 C 0 1 Y N N N N N 13.439 26.669 1.432 7.285 0.446 -0.003 C2 Y5U 2 Y5U C3 C3 C 0 1 Y N N N N N 12.699 27.857 1.544 7.395 -0.950 -0.001 C3 Y5U 3 Y5U C4 C4 C 0 1 Y N N N N N 11.733 28.023 2.505 6.280 -1.733 -0.000 C4 Y5U 4 Y5U C5 C5 C 0 1 Y N N N N N 11.512 26.985 3.411 5.008 -1.143 -0.001 C5 Y5U 5 Y5U C6 C6 C 0 1 Y N N N N N 10.818 25.657 5.027 2.882 -0.669 -0.002 C6 Y5U 6 Y5U C7 C7 C 0 1 Y N N N N N 10.071 25.141 6.164 1.428 -0.839 -0.002 C7 Y5U 7 Y5U C8 C8 C 0 1 Y N N N N N 8.843 25.566 6.689 0.694 -1.988 0.000 C8 Y5U 8 Y5U C9 C9 C 0 1 Y N N N N N 8.374 24.854 7.811 -0.685 -1.989 -0.000 C9 Y5U 9 Y5U C10 C10 C 0 1 Y N N N N N 9.205 23.840 8.269 -1.420 -0.840 -0.002 C10 Y5U 10 Y5U C11 C11 C 0 1 Y N N N N N 9.007 22.970 9.414 -2.874 -0.672 -0.002 C11 Y5U 11 Y5U C12 C12 C 0 1 Y N N N N N 8.046 21.937 11.086 -4.999 -1.148 0.000 C12 Y5U 12 Y5U C13 C13 C 0 1 Y N N N N N 7.164 21.433 12.038 -6.271 -1.739 -0.001 C13 Y5U 13 Y5U C14 C14 C 0 1 Y N N N N N 7.662 20.588 12.994 -7.386 -0.958 -0.002 C14 Y5U 14 Y5U C15 C15 C 0 1 Y N N N N N 9.018 20.251 13.042 -7.278 0.439 -0.001 C15 Y5U 15 Y5U C16 C16 C 0 1 N N N N N N 9.468 19.341 14.125 -8.498 1.274 -0.002 C16 Y5U 16 Y5U C17 C17 C 0 1 Y N N N N N 9.902 20.746 12.090 -6.023 1.043 -0.000 C17 Y5U 17 Y5U C18 C18 C 0 1 Y N N N N N 9.400 21.586 11.116 -4.884 0.256 0.001 C18 Y5U 18 Y5U C19 C19 C 0 1 Y N N N N N 12.255 25.806 3.320 4.891 0.261 -0.002 C19 Y5U 19 Y5U C20 C20 C 0 1 Y N N N N N 13.223 25.632 2.338 6.029 1.049 0.002 C20 Y5U 20 Y5U SE1 SE1 SE 0 0 Y N N N N N 10.733 23.738 7.205 0.004 0.540 0.005 SE1 Y5U 21 Y5U N1 N1 N 0 1 N N N N N N 15.175 27.554 -0.063 8.404 2.581 -0.006 N1 Y5U 22 Y5U N2 N2 N 0 1 N N N N N N 14.645 25.353 -0.246 9.748 0.686 0.003 N2 Y5U 23 Y5U N3 N3 N 0 1 Y N N N N N 10.606 26.900 4.457 3.760 -1.649 -0.001 N3 Y5U 24 Y5U N4 N4 N 0 1 Y N N N N N 7.799 22.809 10.039 -3.751 -1.653 0.001 N4 Y5U 25 Y5U N5 N5 N 0 1 N N N N N N 8.638 18.561 14.727 -8.399 2.573 -0.001 N5 Y5U 26 Y5U N6 N6 N 0 1 N N N N N N 10.745 19.439 14.529 -9.741 0.677 -0.003 N6 Y5U 27 Y5U N7 N7 N 0 1 Y N N N N N 9.977 22.267 10.074 -3.530 0.534 0.002 N7 Y5U 28 Y5U N8 N8 N 0 1 Y N N N N N 11.795 24.997 4.339 3.537 0.537 -0.003 N8 Y5U 29 Y5U H4 H1 H 0 1 N N N N N N 12.896 28.664 0.854 8.372 -1.411 -0.000 H4 Y5U 30 Y5U H5 H2 H 0 1 N N N N N N 11.158 28.935 2.559 6.376 -2.809 0.000 H5 Y5U 31 Y5U H6 H3 H 0 1 N N N N N N 8.290 26.389 6.260 1.214 -2.935 0.002 H6 Y5U 32 Y5U H7 H4 H 0 1 N N N N N N 7.430 25.082 8.284 -1.203 -2.936 0.001 H7 Y5U 33 Y5U H8 H5 H 0 1 N N N N N N 6.118 21.700 12.023 -6.366 -2.815 -0.002 H8 Y5U 34 Y5U H9 H6 H 0 1 N N N N N N 6.990 20.171 13.730 -8.363 -1.419 -0.003 H9 Y5U 35 Y5U H13 H7 H 0 1 N N N N N N 10.949 20.482 12.112 -5.939 2.120 -0.000 H13 Y5U 36 Y5U H16 H8 H 0 1 N N N N N N 13.793 24.717 2.278 5.944 2.126 0.006 H16 Y5U 37 Y5U H1 H9 H 0 1 N N N N N N 14.940 28.403 0.411 7.529 3.000 -0.006 H1 Y5U 38 Y5U H2 H10 H 0 1 N N N N N N 14.085 24.570 0.026 9.823 -0.281 0.008 H2 Y5U 39 Y5U H3 H11 H 0 1 N N N N N N 15.332 25.251 -0.966 10.548 1.234 0.002 H3 Y5U 40 Y5U H10 H14 H 0 1 N N N N N N 9.066 18.075 15.489 -9.200 3.121 -0.002 H10 Y5U 41 Y5U H12 H15 H 0 1 N N N N N N 11.065 18.901 15.309 -9.815 -0.290 -0.003 H12 Y5U 42 Y5U H11 H16 H 0 1 N N N N N N 11.376 20.050 14.050 -10.542 1.225 -0.003 H11 Y5U 43 Y5U H14 H17 H 0 1 N N N N N N 10.948 22.252 9.836 -3.121 1.413 0.005 H14 Y5U 44 Y5U H15 H18 H 0 1 N N N N N N 12.125 24.075 4.541 3.127 1.416 -0.004 H15 Y5U 45 # 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 Y5U N2 C1 SING N N 1 Y5U N1 C1 DOUB N N 2 Y5U C1 C2 SING N N 3 Y5U C2 C3 DOUB Y N 4 Y5U C2 C20 SING Y N 5 Y5U C3 C4 SING Y N 6 Y5U C20 C19 DOUB Y N 7 Y5U C4 C5 DOUB Y N 8 Y5U C19 C5 SING Y N 9 Y5U C19 N8 SING Y N 10 Y5U C5 N3 SING Y N 11 Y5U N8 C6 SING Y N 12 Y5U N3 C6 DOUB Y N 13 Y5U C6 C7 SING N N 14 Y5U C7 C8 DOUB Y N 15 Y5U C7 SE1 SING Y N 16 Y5U C8 C9 SING Y N 17 Y5U SE1 C10 SING Y N 18 Y5U C9 C10 DOUB Y N 19 Y5U C10 C11 SING N N 20 Y5U C11 N4 DOUB Y N 21 Y5U C11 N7 SING Y N 22 Y5U N4 C12 SING Y N 23 Y5U N7 C18 SING Y N 24 Y5U C12 C18 DOUB Y N 25 Y5U C12 C13 SING Y N 26 Y5U C18 C17 SING Y N 27 Y5U C13 C14 DOUB Y N 28 Y5U C17 C15 DOUB Y N 29 Y5U C14 C15 SING Y N 30 Y5U C15 C16 SING N N 31 Y5U C16 N6 SING N N 32 Y5U C16 N5 DOUB N N 33 Y5U C3 H4 SING N N 34 Y5U C4 H5 SING N N 35 Y5U C8 H6 SING N N 36 Y5U C9 H7 SING N N 37 Y5U C13 H8 SING N N 38 Y5U C14 H9 SING N N 39 Y5U C17 H13 SING N N 40 Y5U C20 H16 SING N N 41 Y5U N1 H1 SING N N 42 Y5U N2 H2 SING N N 43 Y5U N2 H3 SING N N 44 Y5U N5 H10 SING N N 45 Y5U N6 H12 SING N N 46 Y5U N6 H11 SING N N 47 Y5U N7 H14 SING N N 48 Y5U N8 H15 SING N N 49 # 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 Y5U SMILES ACDLabs 12.01 "N=C(N)c1ccc2nc([NH]c2c1)c1ccc([se]1)c1[NH]c2cc(ccc2n1)C(=N)N" Y5U InChI InChI 1.06 "InChI=1S/C20H16N8Se/c21-17(22)9-1-3-11-13(7-9)27-19(25-11)15-5-6-16(29-15)20-26-12-4-2-10(18(23)24)8-14(12)28-20/h1-8H,(H3,21,22)(H3,23,24)(H,25,27)(H,26,28)" Y5U InChIKey InChI 1.06 NXECULIQZLOKFU-UHFFFAOYSA-N Y5U SMILES_CANONICAL CACTVS 3.385 "NC(=N)c1ccc2nc([nH]c2c1)c3[se]c(cc3)c4[nH]c5cc(ccc5n4)C(N)=N" Y5U SMILES CACTVS 3.385 "NC(=N)c1ccc2nc([nH]c2c1)c3[se]c(cc3)c4[nH]c5cc(ccc5n4)C(N)=N" Y5U SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\N)/c1cc2[nH]c(nc2cc1)c3[se]c(cc3)c4nc5c([nH]4)cc(cc5)/C(=N\[H])/N" Y5U SMILES "OpenEye OEToolkits" 2.0.7 "c1cc2c(cc1C(=N)N)[nH]c(n2)c3ccc([se]3)c4[nH]c5cc(ccc5n4)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 Y5U "SYSTEMATIC NAME" ACDLabs 12.01 "(2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide)" Y5U "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[5-(6-carbamimidoyl-1~{H}-benzimidazol-2-yl)selenophen-2-yl]-3~{H}-benzimidazole-5-carboximidamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Y5U "Create component" 2023-06-12 RCSB Y5U "Initial release" 2024-06-12 RCSB #