data_D84 # _chem_comp.id D84 _chem_comp.name "5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]methyl}-1H-benzimidazol-6-yl)pyridin-2(1H)-one" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C31 H26 F2 N4 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-10-23 _chem_comp.pdbx_modified_date 2021-01-08 _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 556.559 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D84 _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 6BCW _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 D84 C10 C1 C 0 1 Y N N -9.808 -1.039 15.624 -3.744 -1.427 -0.496 C10 D84 1 D84 C11 C2 C 0 1 Y N N -10.709 -1.136 14.567 -4.215 -2.160 -1.576 C11 D84 2 D84 C12 C3 C 0 1 Y N N -10.453 -2.023 13.533 -5.558 -2.131 -1.899 C12 D84 3 D84 C13 C4 C 0 1 Y N N -9.288 -2.794 13.527 -6.436 -1.372 -1.150 C13 D84 4 D84 C14 C5 C 0 1 Y N N -8.399 -2.724 14.595 -5.970 -0.636 -0.067 C14 D84 5 D84 F F1 F 0 1 N N N -11.320 -1.877 24.305 2.619 2.955 0.923 F D84 6 D84 C15 C6 C 0 1 Y N N -8.666 -1.838 15.632 -4.621 -0.665 0.259 C15 D84 7 D84 C16 C7 C 0 1 N N N -6.156 -3.079 15.570 -8.278 0.318 0.369 C16 D84 8 D84 C17 C8 C 0 1 N N N -4.997 -3.961 15.098 -8.732 1.545 1.190 C17 D84 9 D84 O1 O1 O 0 1 N N N -9.994 -0.192 16.695 -2.424 -1.461 -0.175 O1 D84 10 D84 C1 C9 C 0 1 Y N N -11.245 -2.181 21.224 0.855 1.884 -0.990 C1 D84 11 D84 N1 N1 N 0 1 N N N -7.210 -3.462 14.641 -6.859 0.132 0.693 N1 D84 12 D84 O3 O2 O 0 1 N N N -19.423 -3.676 23.025 9.197 0.646 0.555 O3 D84 13 D84 C28 C10 C 0 1 N N N -18.587 -3.226 22.205 8.078 0.159 0.552 C28 D84 14 D84 N3 N2 N 0 1 N N N -18.979 -2.297 21.323 7.276 0.317 1.622 N3 D84 15 D84 C27 C11 C 0 1 N N N -18.110 -1.787 20.438 6.026 -0.210 1.638 C27 D84 16 D84 C29 C12 C 0 1 N N N -17.262 -3.663 22.234 7.630 -0.560 -0.570 C29 D84 17 D84 C30 C13 C 0 1 N N N -16.347 -3.168 21.316 6.379 -1.100 -0.564 C30 D84 18 D84 C26 C14 C 0 1 N N N -16.776 -2.208 20.408 5.556 -0.915 0.568 C26 D84 19 D84 C23 C15 C 0 1 Y N N -15.871 -1.616 19.390 4.188 -1.489 0.596 C23 D84 20 D84 C22 C16 C 0 1 Y N N -16.437 -1.373 18.150 3.871 -2.490 1.519 C22 D84 21 D84 C21 C17 C 0 1 Y N N -15.673 -0.791 17.148 2.616 -3.022 1.560 C21 D84 22 D84 C24 C18 C 0 1 Y N N -14.541 -1.245 19.651 3.224 -1.025 -0.291 C24 D84 23 D84 C25 C19 C 0 1 Y N N -13.772 -0.661 18.639 1.948 -1.565 -0.259 C25 D84 24 D84 N N3 N 0 1 Y N N -12.497 -0.246 18.542 0.791 -1.338 -0.979 N D84 25 D84 C7 C20 C 0 1 N N N -11.483 -0.304 19.590 0.619 -0.370 -2.064 C7 D84 26 D84 C6 C21 C 0 1 Y N N -11.154 -1.746 19.922 0.026 0.902 -1.513 C6 D84 27 D84 C5 C22 C 0 1 Y N N -10.759 -2.637 18.937 -1.342 1.090 -1.528 C5 D84 28 D84 C4 C23 C 0 1 Y N N -10.469 -3.962 19.260 -1.887 2.256 -1.022 C4 D84 29 D84 C3 C24 C 0 1 Y N N -10.586 -4.402 20.571 -1.063 3.237 -0.501 C3 D84 30 D84 C2 C25 C 0 1 Y N N -10.989 -3.506 21.552 0.306 3.054 -0.484 C2 D84 31 D84 O O3 O 0 1 N N N -11.695 -1.297 22.162 2.201 1.699 -0.969 O D84 32 D84 C C26 C 0 1 N N N -10.991 -0.963 23.348 2.991 2.750 -0.410 C D84 33 D84 F1 F2 F 0 1 N N N -11.431 0.269 23.753 2.786 3.927 -1.138 F1 D84 34 D84 C20 C27 C 0 1 Y N N -14.341 -0.461 17.387 1.633 -2.568 0.675 C20 D84 35 D84 N2 N4 N 0 1 Y N N -13.407 0.096 16.586 0.330 -2.894 0.481 N2 D84 36 D84 C8 C28 C 0 1 Y N N -12.278 0.225 17.304 -0.159 -2.183 -0.493 C8 D84 37 D84 C9 C29 C 0 1 N N N -11.001 0.812 16.761 -1.577 -2.268 -0.997 C9 D84 38 D84 C19 C30 C 0 1 N N N -6.947 -4.492 13.854 -6.522 0.794 1.813 C19 D84 39 D84 O2 O4 O 0 1 N N N -7.683 -4.979 13.018 -5.415 0.806 2.308 O2 D84 40 D84 C18 C31 C 0 1 N N N -5.565 -5.017 14.152 -7.729 1.527 2.366 C18 D84 41 D84 H1 H1 H 0 1 N N N -11.600 -0.525 14.553 -3.531 -2.754 -2.164 H1 D84 42 D84 H2 H2 H 0 1 N N N -11.162 -2.119 12.724 -5.923 -2.702 -2.741 H2 D84 43 D84 H3 H3 H 0 1 N N N -9.077 -3.446 12.692 -7.485 -1.351 -1.405 H3 D84 44 D84 H4 H4 H 0 1 N N N -7.976 -1.767 16.460 -4.257 -0.097 1.103 H4 D84 45 D84 H5 H5 H 0 1 N N N -5.910 -2.011 15.480 -8.850 -0.563 0.661 H5 D84 46 D84 H6 H6 H 0 1 N N N -6.435 -3.305 16.610 -8.400 0.510 -0.697 H6 D84 47 D84 H7 H7 H 0 1 N N N -4.523 -4.450 15.962 -8.635 2.461 0.608 H7 D84 48 D84 H8 H8 H 0 1 N N N -4.252 -3.348 14.570 -9.755 1.419 1.547 H8 D84 49 D84 H9 H9 H 0 1 N N N -18.446 -1.038 19.736 5.398 -0.072 2.506 H9 D84 50 D84 H10 H10 H 0 1 N N N -16.949 -4.387 22.972 8.272 -0.683 -1.430 H10 D84 51 D84 H11 H11 H 0 1 N N N -15.326 -3.520 21.307 6.019 -1.655 -1.417 H11 D84 52 D84 H13 H13 H 0 1 N N N -17.468 -1.635 17.963 4.626 -2.845 2.204 H13 D84 53 D84 H14 H14 H 0 1 N N N -16.112 -0.594 16.181 2.381 -3.795 2.277 H14 D84 54 D84 H15 H15 H 0 1 N N N -14.114 -1.410 20.629 3.467 -0.248 -1.000 H15 D84 55 D84 H16 H16 H 0 1 N N N -10.572 0.206 19.243 1.587 -0.153 -2.515 H16 D84 56 D84 H17 H17 H 0 1 N N N -11.863 0.199 20.492 -0.049 -0.784 -2.819 H17 D84 57 D84 H18 H18 H 0 1 N N N -10.675 -2.303 17.913 -1.988 0.325 -1.934 H18 D84 58 D84 H19 H19 H 0 1 N N N -10.152 -4.648 18.488 -2.957 2.401 -1.035 H19 D84 59 D84 H20 H20 H 0 1 N N N -10.366 -5.428 20.825 -1.490 4.147 -0.107 H20 D84 60 D84 H21 H21 H 0 1 N N N -11.104 -3.840 22.573 0.948 3.818 -0.072 H21 D84 61 D84 H22 H22 H 0 1 N N N -9.907 -0.955 23.160 4.045 2.475 -0.454 H22 D84 62 D84 H23 H23 H 0 1 N N N -10.663 1.624 17.422 -1.914 -3.304 -0.959 H23 D84 63 D84 H24 H24 H 0 1 N N N -11.184 1.212 15.753 -1.620 -1.909 -2.025 H24 D84 64 D84 H25 H25 H 0 1 N N N -5.612 -6.002 14.640 -7.459 2.543 2.654 H25 D84 65 D84 H26 H26 H 0 1 N N N -4.963 -5.091 13.234 -8.146 0.987 3.216 H26 D84 66 D84 H27 H27 H 0 1 N N N -19.928 -1.981 21.325 7.595 0.815 2.390 H27 D84 67 # # 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 D84 O2 C19 DOUB N N 1 D84 C13 C12 DOUB Y N 2 D84 C13 C14 SING Y N 3 D84 C12 C11 SING Y N 4 D84 C19 C18 SING N N 5 D84 C19 N1 SING N N 6 D84 C18 C17 SING N N 7 D84 C11 C10 DOUB Y N 8 D84 C14 N1 SING N N 9 D84 C14 C15 DOUB Y N 10 D84 N1 C16 SING N N 11 D84 C17 C16 SING N N 12 D84 C10 C15 SING Y N 13 D84 C10 O1 SING N N 14 D84 N2 C8 DOUB Y N 15 D84 N2 C20 SING Y N 16 D84 O1 C9 SING N N 17 D84 C9 C8 SING N N 18 D84 C21 C20 DOUB Y N 19 D84 C21 C22 SING Y N 20 D84 C8 N SING Y N 21 D84 C20 C25 SING Y N 22 D84 C22 C23 DOUB Y N 23 D84 N C25 SING Y N 24 D84 N C7 SING N N 25 D84 C25 C24 DOUB Y N 26 D84 C5 C4 DOUB Y N 27 D84 C5 C6 SING Y N 28 D84 C4 C3 SING Y N 29 D84 C23 C24 SING Y N 30 D84 C23 C26 SING N N 31 D84 C7 C6 SING N N 32 D84 C6 C1 DOUB Y N 33 D84 C26 C27 DOUB N N 34 D84 C26 C30 SING N N 35 D84 C27 N3 SING N N 36 D84 C3 C2 DOUB Y N 37 D84 C1 C2 SING Y N 38 D84 C1 O SING N N 39 D84 C30 C29 DOUB N N 40 D84 N3 C28 SING N N 41 D84 O C SING N N 42 D84 C28 C29 SING N N 43 D84 C28 O3 DOUB N N 44 D84 C F1 SING N N 45 D84 C F SING N N 46 D84 C11 H1 SING N N 47 D84 C12 H2 SING N N 48 D84 C13 H3 SING N N 49 D84 C15 H4 SING N N 50 D84 C16 H5 SING N N 51 D84 C16 H6 SING N N 52 D84 C17 H7 SING N N 53 D84 C17 H8 SING N N 54 D84 C27 H9 SING N N 55 D84 C29 H10 SING N N 56 D84 C30 H11 SING N N 57 D84 C22 H13 SING N N 58 D84 C21 H14 SING N N 59 D84 C24 H15 SING N N 60 D84 C7 H16 SING N N 61 D84 C7 H17 SING N N 62 D84 C5 H18 SING N N 63 D84 C4 H19 SING N N 64 D84 C3 H20 SING N N 65 D84 C2 H21 SING N N 66 D84 C H22 SING N N 67 D84 C9 H23 SING N N 68 D84 C9 H24 SING N N 69 D84 C18 H25 SING N N 70 D84 C18 H26 SING N N 71 D84 N3 H27 SING N N 72 # # 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 D84 SMILES ACDLabs 12.01 "c1(cc(ccc1)N2CCCC2=O)OCc5n(c4cc(C3=CNC(=O)C=C3)ccc4n5)Cc6c(cccc6)OC(F)F" D84 InChI InChI 1.03 "InChI=1S/C31H26F2N4O4/c32-31(33)41-27-8-2-1-5-22(27)18-37-26-15-20(21-11-13-29(38)34-17-21)10-12-25(26)35-28(37)19-40-24-7-3-6-23(16-24)36-14-4-9-30(36)39/h1-3,5-8,10-13,15-17,31H,4,9,14,18-19H2,(H,34,38)" D84 InChIKey InChI 1.03 DNTKSNFCNRDJAC-UHFFFAOYSA-N D84 SMILES_CANONICAL CACTVS 3.385 "FC(F)Oc1ccccc1Cn2c(COc3cccc(c3)N4CCCC4=O)nc5ccc(cc25)C6=CNC(=O)C=C6" D84 SMILES CACTVS 3.385 "FC(F)Oc1ccccc1Cn2c(COc3cccc(c3)N4CCCC4=O)nc5ccc(cc25)C6=CNC(=O)C=C6" D84 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc(c(c1)Cn2c3cc(ccc3nc2COc4cccc(c4)N5CCCC5=O)C6=CNC(=O)C=C6)OC(F)F" D84 SMILES "OpenEye OEToolkits" 2.0.6 "c1ccc(c(c1)Cn2c3cc(ccc3nc2COc4cccc(c4)N5CCCC5=O)C6=CNC(=O)C=C6)OC(F)F" # # 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 D84 "SYSTEMATIC NAME" ACDLabs 12.01 "5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]methyl}-1H-benzimidazol-6-yl)pyridin-2(1H)-one" D84 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "5-[3-[[2-[bis(fluoranyl)methoxy]phenyl]methyl]-2-[[3-(2-oxidanylidenepyrrolidin-1-yl)phenoxy]methyl]benzimidazol-5-yl]-1~{H}-pyridin-2-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site D84 "Create component" 2017-10-23 RCSB D84 "Initial release" 2021-01-13 RCSB ##