data_D49 # _chem_comp.id D49 _chem_comp.name "2-[4-[(2~{R})-4-[4-(6-carboxy-1~{H}-benzimidazol-2-yl)phenoxy]-2-oxidanyl-butoxy]phenyl]-1~{H}-benzimidazole-5-carboxylic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C32 H26 N4 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-02-15 _chem_comp.pdbx_modified_date 2019-05-24 _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 578.571 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D49 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 6NXZ _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.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 D49 O7 O1 O 0 1 N N N -2.158 0.256 3.447 -2.728 -1.023 0.241 O7 D49 1 D49 C8 C1 C 0 1 N N N -0.818 -0.285 3.349 -1.877 0.124 0.295 C8 D49 2 D49 C9 C2 C 0 1 N N R 0.239 0.812 3.383 -0.417 -0.326 0.363 C9 D49 3 D49 O10 O2 O 0 1 N N N 3.684 -0.783 2.881 2.812 1.584 0.175 O10 D49 4 D49 C11 C3 C 0 1 Y N N 4.406 -1.925 2.608 4.149 1.352 0.118 C11 D49 5 D49 O35 O3 O 0 1 N N N 0.193 1.693 2.233 -0.190 -1.023 1.590 O35 D49 6 D49 C36 C4 C 0 1 N N N 1.684 0.340 3.593 0.498 0.898 0.296 C36 D49 7 D49 C37 C5 C 0 1 N N N 2.243 -0.844 2.834 1.958 0.441 0.238 C37 D49 8 D49 H2 H2 H 0 1 N N N -0.726 -0.839 2.403 -2.029 0.732 -0.598 H2 D49 9 D49 H3 H3 H 0 1 N N N -0.648 -0.970 4.193 -2.118 0.713 1.180 H3 D49 10 D49 H4 H4 H 0 1 N N N -0.001 1.430 4.261 -0.201 -0.988 -0.476 H4 D49 11 D49 H8 H8 H 0 1 N N N 0.127 1.175 1.439 -0.363 -0.494 2.381 H8 D49 12 D49 H9 H9 H 0 1 N N N 1.780 0.098 4.662 0.264 1.478 -0.597 H9 D49 13 D49 H10 H10 H 0 1 N N N 2.330 1.197 3.352 0.345 1.515 1.181 H10 D49 14 D49 H11 H11 H 0 1 N N N 1.905 -0.807 1.788 2.111 -0.176 -0.647 H11 D49 15 D49 H12 H12 H 0 1 N N N 1.896 -1.779 3.299 2.192 -0.139 1.130 H12 D49 16 D49 C1 C6 C 0 1 Y N N ? ? ? 5.036 2.420 0.055 C1 D49 17 D49 C2 C7 C 0 1 Y N N ? ? ? 6.393 2.189 -0.002 C2 D49 18 D49 C3 C8 C 0 1 Y N N ? ? ? 6.877 0.879 0.004 C3 D49 19 D49 C4 C9 C 0 1 Y N N ? ? ? 5.982 -0.192 0.067 C4 D49 20 D49 C5 C10 C 0 1 Y N N ? ? ? 4.627 0.048 0.130 C5 D49 21 D49 C13 C11 C 0 1 Y N N ? ? ? 8.331 0.626 -0.058 C13 D49 22 D49 N1 N1 N 0 1 Y N N ? ? ? 8.915 -0.610 -0.059 N1 D49 23 D49 C7 C12 C 0 1 Y N N ? ? ? 10.283 -0.412 -0.127 C7 D49 24 D49 C10 C13 C 0 1 Y N N ? ? ? 10.475 0.983 -0.166 C10 D49 25 D49 N2 N2 N 0 1 Y N N ? ? ? 9.256 1.555 -0.127 N2 D49 26 D49 C6 C23 C 0 1 Y N N ? ? ? 11.776 1.501 -0.238 C6 D49 27 D49 C12 C26 C 0 1 Y N N ? ? ? 12.846 0.660 -0.270 C12 D49 28 D49 C14 C14 C 0 1 Y N N ? ? ? 12.661 -0.729 -0.231 C14 D49 29 D49 C15 C15 C 0 1 Y N N ? ? ? 11.373 -1.262 -0.160 C15 D49 30 D49 C16 C16 C 0 1 N N N ? ? ? 13.828 -1.628 -0.266 C16 D49 31 D49 O2 O4 O 0 1 N N N ? ? ? 15.072 -1.115 -0.336 O2 D49 32 D49 O1 O5 O 0 1 N N N ? ? ? 13.669 -2.832 -0.233 O1 D49 33 D49 C17 C17 C 0 1 Y N N ? ? ? -4.065 -0.796 0.176 C17 D49 34 D49 C18 C18 C 0 1 Y N N ? ? ? -4.948 -1.868 0.121 C18 D49 35 D49 C19 C19 C 0 1 Y N N ? ? ? -6.305 -1.642 0.056 C19 D49 36 D49 C20 C20 C 0 1 Y N N ? ? ? -6.794 -0.334 0.045 C20 D49 37 D49 C21 C21 C 0 1 Y N N ? ? ? -5.904 0.741 0.101 C21 D49 38 D49 C22 C22 C 0 1 Y N N ? ? ? -4.548 0.507 0.171 C22 D49 39 D49 C32 C32 C 0 1 Y N N ? ? ? -8.250 -0.087 -0.025 C32 D49 40 D49 N3 N3 N 0 1 Y N N ? ? ? -8.839 1.149 -0.042 N3 D49 41 D49 C24 C24 C 0 1 Y N N ? ? ? -10.201 0.953 -0.113 C24 D49 42 D49 C25 C25 C 0 1 Y N N ? ? ? -10.396 -0.442 -0.139 C25 D49 43 D49 N4 N4 N 0 1 Y N N ? ? ? -9.169 -1.018 -0.088 N4 D49 44 D49 C27 C27 C 0 1 Y N N ? ? ? -11.692 -0.954 -0.210 C27 D49 45 D49 C28 C28 C 0 1 Y N N ? ? ? -12.773 -0.078 -0.256 C28 D49 46 D49 C29 C29 C 0 1 Y N N ? ? ? -12.560 1.307 -0.230 C29 D49 47 D49 C30 C30 C 0 1 Y N N ? ? ? -11.294 1.811 -0.159 C30 D49 48 D49 C31 C31 C 0 1 N N N ? ? ? -14.147 -0.610 -0.332 C31 D49 49 D49 O3 O6 O 0 1 N N N ? ? ? -14.334 -1.811 -0.354 O3 D49 50 D49 O4 O7 O 0 1 N N N ? ? ? -15.196 0.235 -0.376 O4 D49 51 D49 H1 H1 H 0 1 N N N ? ? ? 4.661 3.433 0.051 H1 D49 52 D49 H5 H5 H 0 1 N N N ? ? ? 7.081 3.019 -0.052 H5 D49 53 D49 H6 H6 H 0 1 N N N ? ? ? 6.353 -1.206 0.072 H6 D49 54 D49 H7 H7 H 0 1 N N N ? ? ? 3.935 -0.780 0.179 H7 D49 55 D49 H13 H13 H 0 1 N N N ? ? ? 8.458 -1.464 -0.019 H13 D49 56 D49 H14 H14 H 0 1 N N N ? ? ? 11.929 2.570 -0.269 H14 D49 57 D49 H15 H15 H 0 1 N N N ? ? ? 13.845 1.066 -0.326 H15 D49 58 D49 H16 H16 H 0 1 N N N ? ? ? 11.229 -2.332 -0.130 H16 D49 59 D49 H17 H17 H 0 1 N N N ? ? ? 15.807 -1.744 -0.356 H17 D49 60 D49 H18 H18 H 0 1 N N N ? ? ? -4.569 -2.879 0.129 H18 D49 61 D49 H19 H19 H 0 1 N N N ? ? ? -6.991 -2.475 0.012 H19 D49 62 D49 H20 H20 H 0 1 N N N ? ? ? -6.278 1.754 0.093 H20 D49 63 D49 H21 H21 H 0 1 N N N ? ? ? -3.859 1.337 0.215 H21 D49 64 D49 H22 H22 H 0 1 N N N ? ? ? -8.382 2.004 -0.009 H22 D49 65 D49 H23 H23 H 0 1 N N N ? ? ? -11.855 -2.021 -0.231 H23 D49 66 D49 H24 H24 H 0 1 N N N ? ? ? -13.404 1.980 -0.266 H24 D49 67 D49 H25 H25 H 0 1 N N N ? ? ? -11.141 2.880 -0.140 H25 D49 68 D49 H26 H26 H 0 1 N N N ? ? ? -16.077 -0.160 -0.425 H26 D49 69 # # 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 D49 O35 C9 SING N N 1 D49 C11 O10 SING N N 2 D49 C37 O10 SING N N 3 D49 C37 C36 SING N N 4 D49 C8 C9 SING N N 5 D49 C8 O7 SING N N 6 D49 C9 C36 SING N N 7 D49 C8 H2 SING N N 8 D49 C8 H3 SING N N 9 D49 C9 H4 SING N N 10 D49 O35 H8 SING N N 11 D49 C36 H9 SING N N 12 D49 C36 H10 SING N N 13 D49 C37 H11 SING N N 14 D49 C37 H12 SING N N 15 D49 C11 C1 SING Y N 16 D49 C1 C2 DOUB Y N 17 D49 C2 C3 SING Y N 18 D49 C3 C4 DOUB Y N 19 D49 C4 C5 SING Y N 20 D49 C5 C11 DOUB Y N 21 D49 C3 C13 SING N N 22 D49 C13 N1 SING Y N 23 D49 N1 C7 SING Y N 24 D49 C7 C10 DOUB Y N 25 D49 C10 N2 SING Y N 26 D49 N2 C13 DOUB Y N 27 D49 C10 C6 SING Y N 28 D49 C6 C12 DOUB Y N 29 D49 C12 C14 SING Y N 30 D49 C14 C15 DOUB Y N 31 D49 C15 C7 SING Y N 32 D49 C14 C16 SING N N 33 D49 C16 O2 SING N N 34 D49 C16 O1 DOUB N N 35 D49 O7 C17 SING N N 36 D49 C17 C18 SING Y N 37 D49 C18 C19 DOUB Y N 38 D49 C19 C20 SING Y N 39 D49 C20 C21 DOUB Y N 40 D49 C21 C22 SING Y N 41 D49 C22 C17 DOUB Y N 42 D49 C20 C32 SING N N 43 D49 C32 N3 SING Y N 44 D49 N3 C24 SING Y N 45 D49 C24 C25 DOUB Y N 46 D49 C25 N4 SING Y N 47 D49 N4 C32 DOUB Y N 48 D49 C25 C27 SING Y N 49 D49 C27 C28 DOUB Y N 50 D49 C28 C29 SING Y N 51 D49 C29 C30 DOUB Y N 52 D49 C30 C24 SING Y N 53 D49 C28 C31 SING N N 54 D49 C31 O3 DOUB N N 55 D49 C31 O4 SING N N 56 D49 C1 H1 SING N N 57 D49 C2 H5 SING N N 58 D49 C4 H6 SING N N 59 D49 C5 H7 SING N N 60 D49 N1 H13 SING N N 61 D49 C6 H14 SING N N 62 D49 C12 H15 SING N N 63 D49 C15 H16 SING N N 64 D49 O2 H17 SING N N 65 D49 C18 H18 SING N N 66 D49 C19 H19 SING N N 67 D49 C21 H20 SING N N 68 D49 C22 H21 SING N N 69 D49 N3 H22 SING N N 70 D49 C27 H23 SING N N 71 D49 C29 H24 SING N N 72 D49 C30 H25 SING N N 73 D49 O4 H26 SING N N 74 # # 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 D49 InChI InChI 1.03 "InChI=1S/C32H26N4O7/c37-22(17-43-24-9-3-19(4-10-24)30-34-26-12-6-21(32(40)41)16-28(26)36-30)13-14-42-23-7-1-18(2-8-23)29-33-25-11-5-20(31(38)39)15-27(25)35-29/h1-12,15-16,22,37H,13-14,17H2,(H,33,35)(H,34,36)(H,38,39)(H,40,41)/t22-/m1/s1" D49 InChIKey InChI 1.03 QQYJHKTWHJAQJJ-JOCHJYFZSA-N D49 SMILES_CANONICAL CACTVS 3.385 "O[C@H](CCOc1ccc(cc1)c2[nH]c3cc(ccc3n2)C(O)=O)COc4ccc(cc4)c5[nH]c6ccc(cc6n5)C(O)=O" D49 SMILES CACTVS 3.385 "O[CH](CCOc1ccc(cc1)c2[nH]c3cc(ccc3n2)C(O)=O)COc4ccc(cc4)c5[nH]c6ccc(cc6n5)C(O)=O" D49 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1c2[nH]c3cc(ccc3n2)C(=O)O)OCC[C@H](COc4ccc(cc4)c5[nH]c6ccc(cc6n5)C(=O)O)O" D49 SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1c2[nH]c3cc(ccc3n2)C(=O)O)OCCC(COc4ccc(cc4)c5[nH]c6ccc(cc6n5)C(=O)O)O" # _pdbx_chem_comp_identifier.comp_id D49 _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-[4-[(2~{R})-4-[4-(6-carboxy-1~{H}-benzimidazol-2-yl)phenoxy]-2-oxidanyl-butoxy]phenyl]-1~{H}-benzimidazole-5-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 D49 "Create component" 2019-02-15 RCSB D49 "Modify formula" 2019-03-04 RCSB D49 "Initial release" 2019-05-29 RCSB ##