data_A1DKB # _chem_comp.id A1DKB _chem_comp.name "3-fluoro-N-hydroxy-4-({4-oxo-1-phenyl-8-[(pyridin-3-yl)methyl]-1,3,8-triazaspiro[4.5]decan-3-yl}methyl)benzamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H28 F N5 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2026-06-16 _chem_comp.pdbx_modified_date 2026-11-06 _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 489.541 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1DKB _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 36KK _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? _chem_comp.pdbx_comp_type ? # 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 A1DKB C12 C1 C 0 1 N N N N N N -20.867 5.778 26.649 2.254 1.767 2.119 C12 A1DKB 1 A1DKB C14 C2 C 0 1 N N N N N N -19.767 4.274 28.257 0.512 2.820 0.493 C14 A1DKB 2 A1DKB C16 C3 C 0 1 N N N N N N -18.913 5.421 30.107 -1.320 1.504 1.023 C16 A1DKB 3 A1DKB C17 C4 C 0 1 N N N N N N -19.624 6.380 29.004 -0.132 1.071 1.847 C17 A1DKB 4 A1DKB C18 C5 C 0 1 N N N N N N -18.714 5.558 31.531 -2.571 1.587 1.894 C18 A1DKB 5 A1DKB C19 C6 C 0 1 N N N N N N -18.409 7.012 31.814 -2.942 0.183 2.381 C19 A1DKB 6 A1DKB C21 C7 C 0 1 N N N N N N -17.110 7.120 29.714 -1.949 -0.831 0.415 C21 A1DKB 7 A1DKB C22 C8 C 0 1 N N N N N N -17.598 5.742 29.556 -1.544 0.538 -0.137 C22 A1DKB 8 A1DKB C23 C9 C 0 1 Y N N N N N -19.695 3.211 30.782 -1.480 3.036 -0.777 C23 A1DKB 9 A1DKB C25 C10 C 0 1 N N N N N N -17.519 8.796 31.047 -3.670 -2.006 1.648 C25 A1DKB 10 A1DKB C26 C11 C 0 1 Y N N N N N -16.381 9.744 31.438 -4.119 -2.786 0.439 C26 A1DKB 11 A1DKB C27 C12 C 0 1 Y N N N N N -15.397 9.299 32.306 -3.230 -3.607 -0.237 C27 A1DKB 12 A1DKB C28 C13 C 0 1 Y N N N N N -14.420 10.213 32.648 -3.687 -4.306 -1.344 C28 A1DKB 13 A1DKB C29 C14 C 0 1 Y N N N N N -14.463 11.510 32.146 -5.005 -4.162 -1.733 C29 A1DKB 14 A1DKB C01 C15 C 0 1 Y N N N N N -20.213 6.050 25.269 3.096 0.812 1.312 C01 A1DKB 15 A1DKB C02 C16 C 0 1 Y N N N N N -19.418 5.128 24.575 3.684 1.239 0.132 C02 A1DKB 16 A1DKB C03 C17 C 0 1 Y N N N N N -18.914 5.452 23.311 4.457 0.367 -0.611 C03 A1DKB 17 A1DKB C04 C18 C 0 1 Y N N N N N -19.223 6.681 22.721 4.644 -0.943 -0.170 C04 A1DKB 18 A1DKB C05 C19 C 0 1 Y N N N N N -20.034 7.582 23.393 4.048 -1.365 1.019 C05 A1DKB 19 A1DKB C06 C20 C 0 1 Y N N N N N -20.538 7.265 24.655 3.283 -0.485 1.755 C06 A1DKB 20 A1DKB C07 C21 C 0 1 N N N N N N -18.697 7.063 21.328 5.470 -1.882 -0.961 C07 A1DKB 21 A1DKB C31 C22 C 0 1 Y N N N N N -16.399 11.081 31.003 -5.425 -2.697 -0.006 C31 A1DKB 22 A1DKB C32 C23 C 0 1 Y N N N N N -20.954 2.918 31.285 -2.847 2.942 -1.004 C32 A1DKB 23 A1DKB C33 C24 C 0 1 Y N N N N N -21.117 1.827 32.137 -3.350 3.138 -2.275 C33 A1DKB 24 A1DKB C34 C25 C 0 1 Y N N N N N -20.020 1.030 32.478 -2.493 3.427 -3.322 C34 A1DKB 25 A1DKB C35 C26 C 0 1 Y N N N N N -18.760 1.337 31.971 -1.132 3.521 -3.099 C35 A1DKB 26 A1DKB C36 C27 C 0 1 Y N N N N N -18.602 2.429 31.118 -0.623 3.327 -1.831 C36 A1DKB 27 A1DKB F11 F1 F 0 1 N N N N N N -19.096 3.947 25.115 3.501 2.508 -0.292 F11 A1DKB 28 A1DKB N09 N1 N 0 1 N N N N N N -18.513 6.025 20.311 5.648 -3.147 -0.533 N09 A1DKB 29 A1DKB N13 N2 N 0 1 N N N N N N -20.091 5.429 27.865 0.917 1.858 1.527 N13 A1DKB 30 A1DKB N15 N3 N 0 1 N N N N N N -19.521 4.383 29.901 -0.969 2.844 0.509 N15 A1DKB 31 A1DKB N20 N4 N 0 1 N N N N N N -17.305 7.577 31.067 -3.167 -0.693 1.224 N20 A1DKB 32 A1DKB N30 N5 N 0 1 Y N N N N N -15.435 11.929 31.338 -5.824 -3.372 -1.066 N30 A1DKB 33 A1DKB O08 O1 O 0 1 N N N N N N -18.505 8.200 21.048 5.987 -1.512 -1.997 O08 A1DKB 34 A1DKB O10 O2 O 0 1 N N N N N N -18.060 6.366 19.020 6.439 -4.046 -1.289 O10 A1DKB 35 A1DKB O24 O3 O 0 1 N N N N N N -19.840 7.545 28.996 -0.122 0.170 2.659 O24 A1DKB 36 A1DKB H121 H1 H 0 0 N N N N N N -21.429 6.690 26.901 2.173 1.404 3.143 H121 A1DKB 37 A1DKB H122 H2 H 0 0 N N N N N N -21.570 4.946 26.491 2.720 2.752 2.118 H122 A1DKB 38 A1DKB H142 H3 H 0 0 N N N N N N -20.574 3.559 28.040 0.905 3.809 0.728 H142 A1DKB 39 A1DKB H141 H4 H 0 0 N N N N N N -18.844 3.948 27.756 0.872 2.496 -0.483 H141 A1DKB 40 A1DKB H182 H5 H 0 0 N N N N N N -19.625 5.255 32.068 -2.375 2.230 2.752 H182 A1DKB 41 A1DKB H181 H6 H 0 0 N N N N N N -17.872 4.929 31.854 -3.394 1.999 1.310 H181 A1DKB 42 A1DKB H192 H7 H 0 0 N N N N N N -19.310 7.598 31.581 -2.130 -0.218 2.988 H192 A1DKB 43 A1DKB H191 H8 H 0 0 N N N N N N -18.176 7.107 32.885 -3.852 0.235 2.980 H191 A1DKB 44 A1DKB H212 H9 H 0 0 N N N N N N -17.661 7.779 29.027 -2.138 -1.515 -0.412 H212 A1DKB 45 A1DKB H211 H10 H 0 0 N N N N N N -16.037 7.153 29.473 -1.144 -1.225 1.036 H211 A1DKB 46 A1DKB H222 H11 H 0 0 N N N N N N -17.632 5.527 28.478 -2.337 0.920 -0.780 H222 A1DKB 47 A1DKB H221 H12 H 0 0 N N N N N N -16.868 5.077 30.040 -0.624 0.441 -0.713 H221 A1DKB 48 A1DKB H251 H13 H 0 0 N N N N N N -17.821 9.056 30.022 -4.512 -1.871 2.327 H251 A1DKB 49 A1DKB H252 H14 H 0 0 N N N N N N -18.355 8.990 31.735 -2.876 -2.552 2.158 H252 A1DKB 50 A1DKB H271 H15 H 0 0 N N N N N N -15.394 8.291 32.694 -2.205 -3.699 0.090 H271 A1DKB 51 A1DKB H281 H16 H 0 0 N N N N N N -13.618 9.919 33.309 -3.022 -4.953 -1.895 H281 A1DKB 52 A1DKB H291 H17 H 0 0 N N N N N N -13.680 12.201 32.421 -5.370 -4.703 -2.594 H291 A1DKB 53 A1DKB H031 H18 H 0 0 N N N N N N -18.283 4.749 22.788 4.915 0.699 -1.531 H031 A1DKB 54 A1DKB H051 H19 H 0 0 N N N N N N -20.276 8.531 22.939 4.189 -2.379 1.365 H051 A1DKB 55 A1DKB H061 H20 H 0 0 N N N N N N -21.185 7.964 25.163 2.822 -0.811 2.676 H061 A1DKB 56 A1DKB H311 H21 H 0 0 N N N N N N -17.214 11.425 30.384 -6.125 -2.064 0.518 H311 A1DKB 57 A1DKB H321 H22 H 0 0 N N N N N N -21.802 3.531 31.018 -3.517 2.716 -0.187 H321 A1DKB 58 A1DKB H331 H23 H 0 0 N N N N N N -22.094 1.596 32.535 -4.413 3.065 -2.453 H331 A1DKB 59 A1DKB H341 H24 H 0 0 N N N N N N -20.149 0.180 33.132 -2.889 3.580 -4.315 H341 A1DKB 60 A1DKB H351 H25 H 0 0 N N N N N N -17.907 0.731 32.238 -0.466 3.747 -3.919 H351 A1DKB 61 A1DKB H361 H26 H 0 0 N N N N N N -17.627 2.665 30.719 0.441 3.401 -1.657 H361 A1DKB 62 A1DKB H091 H27 H 0 0 N N N N N N -18.710 5.070 20.533 5.235 -3.442 0.294 H091 A1DKB 63 A1DKB H101 H29 H 0 0 N N N N N N -17.937 7.306 18.965 6.509 -4.929 -0.903 H101 A1DKB 64 # 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 A1DKB C01 C02 DOUB Y N 1 A1DKB C02 C03 SING Y N 2 A1DKB C03 C04 DOUB Y N 3 A1DKB C04 C05 SING Y N 4 A1DKB C05 C06 DOUB Y N 5 A1DKB C06 C01 SING Y N 6 A1DKB C04 C07 SING N N 7 A1DKB C07 O08 DOUB N N 8 A1DKB C07 N09 SING N N 9 A1DKB N09 O10 SING N N 10 A1DKB C02 F11 SING N N 11 A1DKB C01 C12 SING N N 12 A1DKB C12 N13 SING N N 13 A1DKB N13 C14 SING N N 14 A1DKB C14 N15 SING N N 15 A1DKB N15 C16 SING N N 16 A1DKB C16 C17 SING N N 17 A1DKB C17 N13 SING N N 18 A1DKB C16 C18 SING N N 19 A1DKB C18 C19 SING N N 20 A1DKB C19 N20 SING N N 21 A1DKB N20 C21 SING N N 22 A1DKB C21 C22 SING N N 23 A1DKB C22 C16 SING N N 24 A1DKB N15 C23 SING N N 25 A1DKB C17 O24 DOUB N N 26 A1DKB N20 C25 SING N N 27 A1DKB C25 C26 SING N N 28 A1DKB C26 C27 DOUB Y N 29 A1DKB C27 C28 SING Y N 30 A1DKB C28 C29 DOUB Y N 31 A1DKB C29 N30 SING Y N 32 A1DKB N30 C31 DOUB Y N 33 A1DKB C31 C26 SING Y N 34 A1DKB C23 C32 DOUB Y N 35 A1DKB C32 C33 SING Y N 36 A1DKB C33 C34 DOUB Y N 37 A1DKB C34 C35 SING Y N 38 A1DKB C35 C36 DOUB Y N 39 A1DKB C36 C23 SING Y N 40 A1DKB C12 H121 SING N N 41 A1DKB C12 H122 SING N N 42 A1DKB C14 H142 SING N N 43 A1DKB C14 H141 SING N N 44 A1DKB C18 H182 SING N N 45 A1DKB C18 H181 SING N N 46 A1DKB C19 H192 SING N N 47 A1DKB C19 H191 SING N N 48 A1DKB C21 H212 SING N N 49 A1DKB C21 H211 SING N N 50 A1DKB C22 H222 SING N N 51 A1DKB C22 H221 SING N N 52 A1DKB C25 H251 SING N N 53 A1DKB C25 H252 SING N N 54 A1DKB C27 H271 SING N N 55 A1DKB C28 H281 SING N N 56 A1DKB C29 H291 SING N N 57 A1DKB C03 H031 SING N N 58 A1DKB C05 H051 SING N N 59 A1DKB C06 H061 SING N N 60 A1DKB C31 H311 SING N N 61 A1DKB C32 H321 SING N N 62 A1DKB C33 H331 SING N N 63 A1DKB C34 H341 SING N N 64 A1DKB C35 H351 SING N N 65 A1DKB C36 H361 SING N N 66 A1DKB N09 H091 SING N N 67 A1DKB O10 H101 SING N N 68 # 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 A1DKB SMILES ACDLabs 14.52 "ONC(=O)c1ccc(CN2CN(c3ccccc3)C3(CCN(CC3)Cc3cccnc3)C2=O)c(F)c1" A1DKB InChI InChI 1.06 "InChI=1S/C27H28FN5O3/c28-24-15-21(25(34)30-36)8-9-22(24)18-32-19-33(23-6-2-1-3-7-23)27(26(32)35)10-13-31(14-11-27)17-20-5-4-12-29-16-20/h1-9,12,15-16,36H,10-11,13-14,17-19H2,(H,30,34)" A1DKB InChIKey InChI 1.06 FYNCIRXZCMNTRN-UHFFFAOYSA-N A1DKB SMILES_CANONICAL CACTVS 3.385 "ONC(=O)c1ccc(CN2CN(c3ccccc3)C4(CCN(CC4)Cc5cccnc5)C2=O)c(F)c1" A1DKB SMILES CACTVS 3.385 "ONC(=O)c1ccc(CN2CN(c3ccccc3)C4(CCN(CC4)Cc5cccnc5)C2=O)c(F)c1" A1DKB SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1ccc(cc1)N2CN(C(=O)C23CCN(CC3)Cc4cccnc4)Cc5ccc(cc5F)C(=O)NO" A1DKB SMILES "OpenEye OEToolkits" 3.1.0.0 "c1ccc(cc1)N2CN(C(=O)C23CCN(CC3)Cc4cccnc4)Cc5ccc(cc5F)C(=O)NO" # 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 A1DKB "SYSTEMATIC NAME" ACDLabs 14.52 "3-fluoro-N-hydroxy-4-({4-oxo-1-phenyl-8-[(pyridin-3-yl)methyl]-1,3,8-triazaspiro[4.5]decan-3-yl}methyl)benzamide" A1DKB "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "3-fluoranyl-~{N}-oxidanyl-4-[[4-oxidanylidene-1-phenyl-8-(pyridin-3-ylmethyl)-1,3,8-triazaspiro[4.5]decan-3-yl]methyl]benzamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1DKB "Create component" 2026-06-16 RCSB A1DKB "Initial release" 2026-11-11 RCSB #