data_YU6 # _chem_comp.id YU6 _chem_comp.name "(5M)-2-[(4-benzylpiperazin-1-yl)methyl]-5-(2-chloro-4-methylphenyl)-1H-benzimidazole-7-carboxylic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H27 Cl N4 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-21 _chem_comp.pdbx_modified_date 2024-02-16 _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 474.982 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YU6 _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 7FUM _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 YU6 C10 C1 C 0 1 Y N N N N N 0.004 -23.034 -22.748 7.551 -1.720 -0.190 C10 YU6 1 YU6 C11 C2 C 0 1 Y N N N N N -0.975 -23.227 -21.781 7.767 -3.078 -0.325 C11 YU6 2 YU6 C13 C3 C 0 1 Y N N N N N 0.720 -23.386 -20.101 6.124 -3.508 1.363 C13 YU6 3 YU6 C15 C4 C 0 1 Y N N N N N 5.405 -17.150 -22.728 0.475 1.914 -1.119 C15 YU6 4 YU6 C17 C5 C 0 1 Y N N N N N 6.648 -17.199 -20.913 -1.463 1.963 -0.068 C17 YU6 5 YU6 C18 C6 C 0 1 Y N N N N N 5.636 -16.242 -20.790 -1.273 0.706 -0.665 C18 YU6 6 YU6 C20 C7 C 0 1 Y N N N N N 5.560 -15.430 -19.655 -2.253 -0.278 -0.532 C20 YU6 7 YU6 C21 C8 C 0 1 Y N N N N N 6.504 -15.577 -18.634 -3.411 -0.014 0.189 C21 YU6 8 YU6 C22 C9 C 0 1 Y N N N N N 6.457 -14.683 -17.445 -4.450 -1.065 0.327 C22 YU6 9 YU6 C23 C10 C 0 1 Y N N N N N 6.974 -13.372 -17.465 -4.916 -1.741 -0.800 C23 YU6 10 YU6 C25 C11 C 0 1 Y N N N N N 6.937 -12.560 -16.348 -5.883 -2.718 -0.665 C25 YU6 11 YU6 C26 C12 C 0 1 Y N N N N N 6.351 -13.014 -15.172 -6.389 -3.025 0.584 C26 YU6 12 YU6 C27 C13 C 0 1 N N N N N N 6.304 -12.135 -13.941 -7.443 -4.092 0.725 C27 YU6 13 YU6 C28 C14 C 0 1 Y N N N N N 5.834 -14.306 -15.142 -5.930 -2.357 1.706 C28 YU6 14 YU6 C1 C15 C 0 1 N N N N N N 4.794 -17.639 -24.003 1.811 2.336 -1.672 C1 YU6 15 YU6 C12 C16 C 0 1 Y N N N N N -0.617 -23.412 -20.459 7.053 -3.972 0.451 C12 YU6 16 YU6 C14 C17 C 0 1 Y N N N N N 1.699 -23.180 -21.066 5.917 -2.148 1.507 C14 YU6 17 YU6 C29 C18 C 0 1 Y N N N N N 5.882 -15.134 -16.254 -4.960 -1.383 1.584 C29 YU6 18 YU6 C3 C19 C 0 1 N N N N N N 3.876 -19.625 -25.100 4.166 2.510 -1.131 C3 YU6 19 YU6 C30 C20 C 0 1 Y N N N N N 7.586 -16.445 -18.820 -3.604 1.232 0.783 C30 YU6 20 YU6 C31 C21 C 0 1 Y N N N N N 7.604 -17.348 -19.887 -2.635 2.224 0.659 C31 YU6 21 YU6 C32 C22 C 0 1 N N N N N N 8.725 -18.355 -19.938 -2.838 3.542 1.288 C32 YU6 22 YU6 C4 C23 C 0 1 N N N N N N 3.561 -21.111 -24.860 5.229 2.112 -0.105 C4 YU6 23 YU6 C6 C24 C 0 1 N N N N N N 2.842 -20.497 -22.578 4.037 0.052 0.333 C6 YU6 24 YU6 C7 C25 C 0 1 N N N N N N 3.120 -19.047 -22.933 2.973 0.450 -0.693 C7 YU6 25 YU6 C8 C26 C 0 1 N N N N N N 2.412 -22.736 -23.446 6.391 0.226 0.874 C8 YU6 26 YU6 C9 C27 C 0 1 Y N N N N N 1.354 -23.026 -22.405 6.626 -1.255 0.726 C9 YU6 27 YU6 N16 N1 N 0 1 Y N N N N N 6.439 -17.797 -22.138 -0.345 2.703 -0.371 N16 YU6 28 YU6 N19 N2 N 0 1 Y N N N N N 4.867 -16.231 -21.950 -0.068 0.744 -1.292 N19 YU6 29 YU6 N2 N3 N 0 1 N N N N N N 4.267 -18.994 -23.837 2.876 1.915 -0.752 N2 YU6 30 YU6 N5 N4 N 0 1 N N N N N N 2.543 -21.306 -23.788 5.326 0.647 -0.046 N5 YU6 31 YU6 O33 O1 O 0 1 N N N N N N 8.792 -19.082 -20.949 -1.990 4.405 1.178 O33 YU6 32 YU6 O34 O2 O 0 1 N N N N N N 9.555 -18.385 -18.986 -3.964 3.789 1.986 O34 YU6 33 YU6 CL24 CL1 CL 0 0 N N N N N N 7.660 -12.734 -18.934 -4.282 -1.355 -2.370 CL24 YU6 34 YU6 H47 H1 H 0 1 N N N N N N -0.285 -22.888 -23.778 8.109 -1.021 -0.796 H47 YU6 35 YU6 H48 H2 H 0 1 N N N N N N -2.018 -23.232 -22.063 8.493 -3.441 -1.038 H48 YU6 36 YU6 H50 H3 H 0 1 N N N N N N 1.003 -23.526 -19.068 5.570 -4.206 1.973 H50 YU6 37 YU6 H53 H4 H 0 1 N N N N N N 4.776 -14.693 -19.567 -2.112 -1.247 -0.989 H53 YU6 38 YU6 H54 H5 H 0 1 N N N N N N 7.365 -11.569 -16.389 -6.244 -3.243 -1.537 H54 YU6 39 YU6 H56 H6 H 0 1 N N N N N N 5.373 -11.549 -13.944 -6.964 -5.059 0.882 H56 YU6 40 YU6 H57 H7 H 0 1 N N N N N N 6.338 -12.765 -13.040 -8.082 -3.861 1.578 H57 YU6 41 YU6 H55 H8 H 0 1 N N N N N N 7.167 -11.453 -13.945 -8.047 -4.129 -0.182 H55 YU6 42 YU6 H58 H9 H 0 1 N N N N N N 5.385 -14.673 -14.231 -6.329 -2.601 2.679 H58 YU6 43 YU6 H35 H10 H 0 1 N N N N N N 5.560 -17.644 -24.792 1.966 1.870 -2.645 H35 YU6 44 YU6 H36 H11 H 0 1 N N N N N N 3.974 -16.965 -24.292 1.834 3.420 -1.781 H36 YU6 45 YU6 H49 H12 H 0 1 N N N N N N -1.377 -23.576 -19.709 7.221 -5.034 0.345 H49 YU6 46 YU6 H51 H13 H 0 1 N N N N N N 2.738 -23.139 -20.773 5.201 -1.785 2.229 H51 YU6 47 YU6 H59 H14 H 0 1 N N N N N N 5.473 -16.132 -16.199 -4.600 -0.866 2.460 H59 YU6 48 YU6 H38 H15 H 0 1 N N N N N N 2.983 -19.122 -25.499 4.072 3.596 -1.155 H38 YU6 49 YU6 H37 H16 H 0 1 N N N N N N 4.700 -19.538 -25.823 4.458 2.148 -2.117 H37 YU6 50 YU6 H60 H17 H 0 1 N N N N N N 8.417 -16.417 -18.131 -4.508 1.429 1.341 H60 YU6 51 YU6 H39 H18 H 0 1 N N N N N N 3.179 -21.547 -25.795 6.193 2.529 -0.400 H39 YU6 52 YU6 H40 H19 H 0 1 N N N N N N 4.487 -21.626 -24.567 4.951 2.498 0.876 H40 YU6 53 YU6 H42 H20 H 0 1 N N N N N N 1.979 -20.539 -21.897 3.745 0.415 1.319 H42 YU6 54 YU6 H41 H21 H 0 1 N N N N N N 3.726 -20.918 -22.076 4.130 -1.033 0.358 H41 YU6 55 YU6 H44 H22 H 0 1 N N N N N N 3.344 -18.479 -22.018 3.251 0.064 -1.673 H44 YU6 56 YU6 H43 H23 H 0 1 N N N N N N 2.239 -18.612 -23.428 2.010 0.033 -0.398 H43 YU6 57 YU6 H45 H24 H 0 1 N N N N N N 2.156 -23.289 -24.362 6.093 0.447 1.899 H45 YU6 58 YU6 H46 H25 H 0 1 N N N N N N 3.380 -23.090 -23.063 7.309 0.765 0.638 H46 YU6 59 YU6 H52 H26 H 0 1 N N N N N N 6.954 -18.565 -22.519 -0.172 3.618 -0.102 H52 YU6 60 YU6 H4 H30 H 0 1 N N N N N N 10.221 -19.038 -19.166 -4.053 4.667 2.380 H4 YU6 61 # 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 YU6 C1 N2 SING N N 1 YU6 C1 C15 SING N N 2 YU6 N2 C3 SING N N 3 YU6 N2 C7 SING N N 4 YU6 C3 C4 SING N N 5 YU6 C4 N5 SING N N 6 YU6 N5 C6 SING N N 7 YU6 N5 C8 SING N N 8 YU6 C6 C7 SING N N 9 YU6 C8 C9 SING N N 10 YU6 C9 C10 DOUB Y N 11 YU6 C9 C14 SING Y N 12 YU6 C10 C11 SING Y N 13 YU6 C11 C12 DOUB Y N 14 YU6 C12 C13 SING Y N 15 YU6 C13 C14 DOUB Y N 16 YU6 C15 N16 SING Y N 17 YU6 C15 N19 DOUB Y N 18 YU6 N16 C17 SING Y N 19 YU6 C17 C18 DOUB Y N 20 YU6 C17 C31 SING Y N 21 YU6 C18 N19 SING Y N 22 YU6 C18 C20 SING Y N 23 YU6 C20 C21 DOUB Y N 24 YU6 C21 C22 SING N N 25 YU6 C21 C30 SING Y N 26 YU6 C22 C23 DOUB Y N 27 YU6 C22 C29 SING Y N 28 YU6 C23 CL24 SING N N 29 YU6 C23 C25 SING Y N 30 YU6 C25 C26 DOUB Y N 31 YU6 C26 C27 SING N N 32 YU6 C26 C28 SING Y N 33 YU6 C28 C29 DOUB Y N 34 YU6 C30 C31 DOUB Y N 35 YU6 C31 C32 SING N N 36 YU6 C32 O33 DOUB N N 37 YU6 C32 O34 SING N N 38 YU6 C10 H47 SING N N 39 YU6 C11 H48 SING N N 40 YU6 C13 H50 SING N N 41 YU6 C20 H53 SING N N 42 YU6 C25 H54 SING N N 43 YU6 C27 H56 SING N N 44 YU6 C27 H57 SING N N 45 YU6 C27 H55 SING N N 46 YU6 C28 H58 SING N N 47 YU6 C1 H35 SING N N 48 YU6 C1 H36 SING N N 49 YU6 C12 H49 SING N N 50 YU6 C14 H51 SING N N 51 YU6 C29 H59 SING N N 52 YU6 C3 H38 SING N N 53 YU6 C3 H37 SING N N 54 YU6 C30 H60 SING N N 55 YU6 C4 H39 SING N N 56 YU6 C4 H40 SING N N 57 YU6 C6 H42 SING N N 58 YU6 C6 H41 SING N N 59 YU6 C7 H44 SING N N 60 YU6 C7 H43 SING N N 61 YU6 C8 H45 SING N N 62 YU6 C8 H46 SING N N 63 YU6 N16 H52 SING N N 64 YU6 O34 H4 SING N N 65 # 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 YU6 SMILES ACDLabs 12.01 "Cc1ccc(c(Cl)c1)c1cc2nc([NH]c2c(c1)C(=O)O)CN1CCN(CC1)Cc1ccccc1" YU6 InChI InChI 1.06 "InChI=1S/C27H27ClN4O2/c1-18-7-8-21(23(28)13-18)20-14-22(27(33)34)26-24(15-20)29-25(30-26)17-32-11-9-31(10-12-32)16-19-5-3-2-4-6-19/h2-8,13-15H,9-12,16-17H2,1H3,(H,29,30)(H,33,34)" YU6 InChIKey InChI 1.06 GFNSGOYZMZLPLR-UHFFFAOYSA-N YU6 SMILES_CANONICAL CACTVS 3.385 "Cc1ccc(c(Cl)c1)c2cc3nc(CN4CCN(CC4)Cc5ccccc5)[nH]c3c(c2)C(O)=O" YU6 SMILES CACTVS 3.385 "Cc1ccc(c(Cl)c1)c2cc3nc(CN4CCN(CC4)Cc5ccccc5)[nH]c3c(c2)C(O)=O" YU6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1ccc(c(c1)Cl)c2cc(c3c(c2)nc([nH]3)CN4CCN(CC4)Cc5ccccc5)C(=O)O" YU6 SMILES "OpenEye OEToolkits" 2.0.7 "Cc1ccc(c(c1)Cl)c2cc(c3c(c2)nc([nH]3)CN4CCN(CC4)Cc5ccccc5)C(=O)O" # 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 YU6 "SYSTEMATIC NAME" ACDLabs 12.01 "(5M)-2-[(4-benzylpiperazin-1-yl)methyl]-5-(2-chloro-4-methylphenyl)-1H-benzimidazole-7-carboxylic acid" YU6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "6-(2-chloranyl-4-methyl-phenyl)-2-[[4-(phenylmethyl)piperazin-1-yl]methyl]-3~{H}-benzimidazole-4-carboxylic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YU6 "Create component" 2023-02-21 RCSB YU6 "Initial release" 2024-02-21 RCSB #