data_A1D7W # _chem_comp.id A1D7W _chem_comp.name "dodecyl 1H-benzimidazole-5-carboxylate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H30 N2 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-04-16 _chem_comp.pdbx_modified_date 2025-11-28 _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 330.464 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1D7W _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 8Z23 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBC _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 A1D7W C1 C1 C 0 1 N N N N N N -5.173 -22.838 -3.411 12.475 -0.856 0.000 C1 A1D7W 1 A1D7W C2 C2 C 0 1 N N N N N N -6.600 -22.776 -2.899 11.288 0.109 0.000 C2 A1D7W 2 A1D7W C3 C3 C 0 1 N N N N N N -7.498 -21.772 -3.579 9.982 -0.688 0.000 C3 A1D7W 3 A1D7W C4 C4 C 0 1 N N N N N N -6.861 -20.978 -4.696 8.795 0.278 -0.000 C4 A1D7W 4 A1D7W C5 C5 C 0 1 N N N N N N -7.832 -20.245 -5.570 7.489 -0.519 0.000 C5 A1D7W 5 A1D7W C6 C6 C 0 1 N N N N N N -8.918 -21.118 -6.110 6.302 0.446 -0.000 C6 A1D7W 6 A1D7W C7 C7 C 0 1 N N N N N N -10.260 -20.827 -5.537 4.996 -0.351 0.000 C7 A1D7W 7 A1D7W C8 C8 C 0 1 N N N N N N -10.986 -19.742 -6.284 3.809 0.615 -0.000 C8 A1D7W 8 A1D7W C9 C9 C 0 1 N N N N N N -12.027 -19.011 -5.482 2.503 -0.183 -0.000 C9 A1D7W 9 A1D7W C10 C10 C 0 1 N N N N N N -12.821 -19.887 -4.549 1.317 0.783 -0.000 C10 A1D7W 10 A1D7W C11 C11 C 0 1 N N N N N N -13.870 -20.716 -5.241 0.011 -0.014 -0.000 C11 A1D7W 11 A1D7W C12 C12 C 0 1 N N N N N N -14.803 -19.941 -6.145 -1.176 0.951 -0.001 C12 A1D7W 12 A1D7W O1 O1 O 0 1 N N N N N N -15.271 -18.768 -5.443 -2.416 0.195 -0.000 O1 A1D7W 13 A1D7W C13 C13 C 0 1 N N N N N N -15.873 -19.022 -4.290 -3.563 0.901 -0.001 C13 A1D7W 14 A1D7W O2 O2 O 0 1 N N N N N N -16.938 -19.589 -4.230 -3.529 2.115 -0.001 O2 A1D7W 15 A1D7W C14 C14 C 0 1 Y N N N N N -15.113 -18.488 -3.120 -4.861 0.199 -0.000 C14 A1D7W 16 A1D7W C15 C15 C 0 1 Y N N N N N -14.557 -17.194 -3.197 -4.898 -1.202 -0.000 C15 A1D7W 17 A1D7W C16 C16 C 0 1 Y N N N N N -13.869 -16.631 -2.143 -6.092 -1.862 0.001 C16 A1D7W 18 A1D7W C17 C17 C 0 1 Y N N N N N -13.750 -17.386 -0.988 -7.285 -1.148 0.000 C17 A1D7W 19 A1D7W N1 N1 N 0 1 Y N N N N N -13.164 -17.117 0.216 -8.615 -1.510 -0.000 N1 A1D7W 20 A1D7W C18 C18 C 0 1 Y N N N N N -13.330 -18.210 0.975 -9.348 -0.364 -0.001 C18 A1D7W 21 A1D7W N2 N2 N 0 1 Y N N N N N -13.992 -19.182 0.378 -8.561 0.672 -0.001 N2 A1D7W 22 A1D7W C19 C19 C 0 1 Y N N N N N -14.286 -18.675 -0.884 -7.267 0.259 -0.000 C19 A1D7W 23 A1D7W C20 C20 C 0 1 Y N N N N N -14.976 -19.243 -1.955 -6.046 0.930 0.005 C20 A1D7W 24 A1D7W H3 H1 H 0 1 N N N N N N -4.613 -23.599 -2.847 13.405 -0.288 0.000 H3 A1D7W 25 A1D7W H1 H2 H 0 1 N N N N N N -5.178 -23.103 -4.479 12.432 -1.484 0.891 H1 A1D7W 26 A1D7W H2 H3 H 0 1 N N N N N N -4.693 -21.857 -3.279 12.432 -1.484 -0.889 H2 A1D7W 27 A1D7W H4 H4 H 0 1 N N N N N N -7.049 -23.772 -3.028 11.330 0.738 0.890 H4 A1D7W 28 A1D7W H5 H5 H 0 1 N N N N N N -6.564 -22.526 -1.828 11.330 0.737 -0.890 H5 A1D7W 29 A1D7W H6 H6 H 0 1 N N N N N N -8.358 -22.316 -3.998 9.939 -1.316 -0.890 H6 A1D7W 30 A1D7W H7 H7 H 0 1 N N N N N N -7.850 -21.061 -2.817 9.939 -1.315 0.890 H7 A1D7W 31 A1D7W H9 H8 H 0 1 N N N N N N -6.178 -20.241 -4.248 8.837 0.906 0.890 H9 A1D7W 32 A1D7W H8 H9 H 0 1 N N N N N N -6.287 -21.673 -5.327 8.837 0.905 -0.890 H8 A1D7W 33 A1D7W H11 H10 H 0 1 N N N N N N -8.293 -19.439 -4.980 7.447 -1.148 -0.890 H11 A1D7W 34 A1D7W H10 H11 H 0 1 N N N N N N -7.280 -19.810 -6.417 7.447 -1.147 0.890 H10 A1D7W 35 A1D7W H13 H12 H 0 1 N N N N N N -8.968 -20.977 -7.200 6.345 1.074 0.890 H13 A1D7W 36 A1D7W H12 H13 H 0 1 N N N N N N -8.665 -22.165 -5.887 6.345 1.074 -0.890 H12 A1D7W 37 A1D7W H14 H14 H 0 1 N N N N N N -10.865 -21.745 -5.573 4.954 -0.979 -0.890 H14 A1D7W 38 A1D7W H15 H15 H 0 1 N N N N N N -10.135 -20.511 -4.491 4.954 -0.979 0.890 H15 A1D7W 39 A1D7W H17 H16 H 0 1 N N N N N N -10.243 -19.008 -6.629 3.852 1.243 0.890 H17 A1D7W 40 A1D7W H16 H17 H 0 1 N N N N N N -11.482 -20.198 -7.153 3.852 1.242 -0.891 H16 A1D7W 41 A1D7W H19 H18 H 0 1 N N N N N N -11.521 -18.240 -4.883 2.461 -0.811 -0.890 H19 A1D7W 42 A1D7W H18 H19 H 0 1 N N N N N N -12.727 -18.531 -6.182 2.461 -0.810 0.890 H18 A1D7W 43 A1D7W H20 H20 H 0 1 N N N N N N -12.125 -20.566 -4.035 1.359 1.411 0.889 H20 A1D7W 44 A1D7W H21 H21 H 0 1 N N N N N N -13.320 -19.244 -3.809 1.359 1.411 -0.891 H21 A1D7W 45 A1D7W H23 H22 H 0 1 N N N N N N -13.358 -21.476 -5.850 -0.032 -0.642 -0.890 H23 A1D7W 46 A1D7W H22 H23 H 0 1 N N N N N N -14.477 -21.212 -4.469 -0.032 -0.642 0.890 H22 A1D7W 47 A1D7W H25 H24 H 0 1 N N N N N N -14.266 -19.636 -7.055 -1.134 1.579 0.889 H25 A1D7W 48 A1D7W H24 H25 H 0 1 N N N N N N -15.660 -20.573 -6.419 -1.134 1.579 -0.891 H24 A1D7W 49 A1D7W H26 H26 H 0 1 N N N N N N -14.674 -16.627 -4.109 -3.975 -1.763 -0.001 H26 A1D7W 50 A1D7W H27 H27 H 0 1 N N N N N N -13.441 -15.642 -2.215 -6.110 -2.942 0.001 H27 A1D7W 51 A1D7W H28 H28 H 0 1 N N N N N N -12.702 -16.271 0.480 -8.963 -2.415 -0.001 H28 A1D7W 52 A1D7W H29 H29 H 0 1 N N N N N N -12.955 -18.287 1.985 -10.427 -0.321 -0.002 H29 A1D7W 53 A1D7W H30 H31 H 0 1 N N N N N N -15.392 -20.237 -1.884 -6.018 2.010 0.009 H30 A1D7W 54 # 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 A1D7W C1 C2 SING N N 1 A1D7W C2 C3 SING N N 2 A1D7W C3 C4 SING N N 3 A1D7W C4 C5 SING N N 4 A1D7W C5 C6 SING N N 5 A1D7W C6 C7 SING N N 6 A1D7W C7 C8 SING N N 7 A1D7W C8 C9 SING N N 8 A1D7W C9 C10 SING N N 9 A1D7W C10 C11 SING N N 10 A1D7W C11 C12 SING N N 11 A1D7W C12 O1 SING N N 12 A1D7W O1 C13 SING N N 13 A1D7W C13 O2 DOUB N N 14 A1D7W C13 C14 SING N N 15 A1D7W C14 C15 DOUB Y N 16 A1D7W C15 C16 SING Y N 17 A1D7W C16 C17 DOUB Y N 18 A1D7W C17 N1 SING Y N 19 A1D7W N1 C18 SING Y N 20 A1D7W C18 N2 DOUB Y N 21 A1D7W N2 C19 SING Y N 22 A1D7W C19 C20 DOUB Y N 23 A1D7W C14 C20 SING Y N 24 A1D7W C17 C19 SING Y N 25 A1D7W C1 H3 SING N N 26 A1D7W C1 H1 SING N N 27 A1D7W C1 H2 SING N N 28 A1D7W C2 H4 SING N N 29 A1D7W C2 H5 SING N N 30 A1D7W C3 H6 SING N N 31 A1D7W C3 H7 SING N N 32 A1D7W C4 H9 SING N N 33 A1D7W C4 H8 SING N N 34 A1D7W C5 H11 SING N N 35 A1D7W C5 H10 SING N N 36 A1D7W C6 H13 SING N N 37 A1D7W C6 H12 SING N N 38 A1D7W C7 H14 SING N N 39 A1D7W C7 H15 SING N N 40 A1D7W C8 H17 SING N N 41 A1D7W C8 H16 SING N N 42 A1D7W C9 H19 SING N N 43 A1D7W C9 H18 SING N N 44 A1D7W C10 H20 SING N N 45 A1D7W C10 H21 SING N N 46 A1D7W C11 H23 SING N N 47 A1D7W C11 H22 SING N N 48 A1D7W C12 H25 SING N N 49 A1D7W C12 H24 SING N N 50 A1D7W C15 H26 SING N N 51 A1D7W C16 H27 SING N N 52 A1D7W N1 H28 SING N N 53 A1D7W C18 H29 SING N N 54 A1D7W C20 H30 SING N N 55 # 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 A1D7W InChI InChI 1.06 "InChI=1S/C20H30N2O2/c1-2-3-4-5-6-7-8-9-10-11-14-24-20(23)17-12-13-18-19(15-17)22-16-21-18/h12-13,15-16H,2-11,14H2,1H3,(H,21,22)" A1D7W InChIKey InChI 1.06 VXKKXAFRWVJMCS-UHFFFAOYSA-N A1D7W SMILES_CANONICAL CACTVS 3.385 "CCCCCCCCCCCCOC(=O)c1ccc2[nH]cnc2c1" A1D7W SMILES CACTVS 3.385 "CCCCCCCCCCCCOC(=O)c1ccc2[nH]cnc2c1" A1D7W SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCCCCCCCCCCOC(=O)c1ccc2c(c1)nc[nH]2" A1D7W SMILES "OpenEye OEToolkits" 2.0.7 "CCCCCCCCCCCCOC(=O)c1ccc2c(c1)nc[nH]2" # _pdbx_chem_comp_identifier.comp_id A1D7W _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 "dodecyl 1~{H}-benzimidazole-5-carboxylate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1D7W "Create component" 2024-04-16 PDBC A1D7W "Initial release" 2025-12-03 RCSB #