data_A1L7R # _chem_comp.id A1L7R _chem_comp.name "1-(2-azanylideneethyl)-6-[6,6-bis(fluoranyl)-2-azaspiro[3.3]heptan-2-yl]-5-(3-chloranyl-4-fluoranyl-phenyl)-3-(5-chloranylpyridin-3-yl)pyrimidine-2,4-dione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H18 Cl2 F3 N5 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-02-19 _chem_comp.pdbx_modified_date 2025-05-09 _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 524.323 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1L7R _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 9LVV _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm Y # 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 A1L7R C10 C1 C 0 1 N N N N N N -2.354 -29.181 -13.571 -0.467 -0.520 0.271 C10 A1L7R 1 A1L7R C12 C2 C 0 1 N N N N N N -0.835 -30.132 -15.713 -2.779 -1.007 -0.873 C12 A1L7R 2 A1L7R C13 C3 C 0 1 N N N N N N 0.176 -31.046 -15.105 -3.748 -1.324 0.267 C13 A1L7R 3 A1L7R C14 C4 C 0 1 N N N N N N -0.823 -31.342 -13.989 -2.942 -0.349 1.128 C14 A1L7R 4 A1L7R C15 C5 C 0 1 N N N N N N 0.566 -32.174 -16.051 -5.258 -1.167 0.092 C15 A1L7R 5 A1L7R F01 F1 F 0 1 N N N N N N -2.315 -26.594 -19.537 -2.762 5.259 -1.343 F01 A1L7R 6 A1L7R C02 C6 C 0 1 Y N N N N N -2.394 -26.855 -18.170 -2.054 4.156 -1.015 C02 A1L7R 7 A1L7R C03 C7 C 0 1 Y N N N N N -3.309 -27.762 -17.752 -1.337 4.123 0.171 C03 A1L7R 8 A1L7R CL04 CL1 CL 0 0 N N N N N N -4.308 -28.535 -18.925 -1.352 5.497 1.232 CL04 A1L7R 9 A1L7R C05 C8 C 0 1 Y N N N N N -3.414 -28.075 -16.401 -0.612 2.998 0.510 C05 A1L7R 10 A1L7R C06 C9 C 0 1 Y N N N N N -2.565 -27.461 -15.494 -0.601 1.895 -0.343 C06 A1L7R 11 A1L7R C07 C10 C 0 1 Y N N N N N -1.626 -26.531 -15.901 -1.324 1.934 -1.535 C07 A1L7R 12 A1L7R C08 C11 C 0 1 Y N N N N N -1.566 -26.242 -17.245 -2.051 3.060 -1.862 C08 A1L7R 13 A1L7R C09 C12 C 0 1 N N N N N N -2.833 -27.900 -14.101 0.176 0.685 0.016 C09 A1L7R 14 A1L7R N11 N1 N 0 1 N N N N N N -1.480 -30.069 -14.344 -1.831 -0.610 0.189 N11 A1L7R 15 A1L7R C16 C13 C 0 1 N N N N N N 1.950 -32.128 -15.461 -5.306 -2.695 -0.091 C16 A1L7R 16 A1L7R F17 F2 F 0 1 N N N N N N 2.280 -33.120 -14.554 -6.393 -3.301 0.549 F17 A1L7R 17 A1L7R F18 F3 F 0 1 N N N N N N 2.787 -31.975 -16.469 -5.162 -3.104 -1.421 F18 A1L7R 18 A1L7R C19 C14 C 0 1 N N N N N N 1.620 -30.869 -14.689 -3.999 -2.761 0.719 C19 A1L7R 19 A1L7R N20 N2 N 0 1 N N N N N N -2.706 -29.595 -12.196 0.283 -1.620 0.601 N20 A1L7R 20 A1L7R C21 C15 C 0 1 N N N N N N -2.645 -30.950 -11.658 -0.380 -2.898 0.873 C21 A1L7R 21 A1L7R C22 C16 C 0 1 N N N N N N -4.212 -31.391 -11.538 -0.392 -3.734 -0.381 C22 A1L7R 22 A1L7R N23 N3 N 0 1 N N N N N N -4.517 -32.580 -10.988 0.097 -4.917 -0.366 N23 A1L7R 23 A1L7R C24 C17 C 0 1 N N N N N N -3.549 -28.807 -11.380 1.623 -1.535 0.677 C24 A1L7R 24 A1L7R O25 O1 O 0 1 N N N N N N -3.781 -29.208 -10.312 2.266 -2.525 0.971 O25 A1L7R 25 A1L7R N26 N4 N 0 1 N N N N N N -3.986 -27.551 -11.923 2.267 -0.381 0.435 N26 A1L7R 26 A1L7R C27 C18 C 0 1 Y N N N N N -4.850 -26.809 -11.107 3.665 -0.336 0.525 C27 A1L7R 27 A1L7R C28 C19 C 0 1 Y N N N N N -6.196 -26.998 -11.197 4.283 0.037 1.710 C28 A1L7R 28 A1L7R N29 N5 N 0 1 Y N N N N N -7.022 -26.309 -10.390 5.597 0.081 1.800 N29 A1L7R 29 A1L7R C30 C20 C 0 1 Y N N N N N -6.492 -25.462 -9.469 6.374 -0.225 0.779 C30 A1L7R 30 A1L7R C31 C21 C 0 1 Y N N N N N -5.170 -25.275 -9.354 5.833 -0.607 -0.436 C31 A1L7R 31 A1L7R CL32 CL2 CL 0 0 N N N N N N -4.487 -24.168 -8.115 6.867 -1.007 -1.771 CL32 A1L7R 32 A1L7R C33 C22 C 0 1 Y N N N N N -4.271 -25.946 -10.179 4.455 -0.672 -0.572 C33 A1L7R 33 A1L7R C34 C23 C 0 1 N N N N N N -3.699 -27.069 -13.274 1.586 0.734 0.106 C34 A1L7R 34 A1L7R O35 O2 O 0 1 N N N N N N -4.155 -26.038 -13.669 2.180 1.776 -0.112 O35 A1L7R 35 A1L7R H1 H1 H 0 1 N N N N N N -0.432 -29.176 -16.077 -2.463 -1.883 -1.439 H1 A1L7R 36 A1L7R H2 H2 H 0 1 N N N N N N -1.458 -30.589 -16.496 -3.100 -0.181 -1.508 H2 A1L7R 37 A1L7R H3 H3 H 0 1 N N N N N N -1.440 -32.239 -14.149 -3.313 0.675 1.097 H3 A1L7R 38 A1L7R H4 H4 H 0 1 N N N N N N -0.390 -31.370 -12.978 -2.758 -0.705 2.141 H4 A1L7R 39 A1L7R H5 H5 H 0 1 N N N N N N 0.516 -31.912 -17.118 -5.768 -0.817 0.989 H5 A1L7R 40 A1L7R H6 H6 H 0 1 N N N N N N 0.029 -33.119 -15.880 -5.539 -0.610 -0.802 H6 A1L7R 41 A1L7R H7 H7 H 0 1 N N N N N N -4.150 -28.789 -16.062 -0.053 2.973 1.434 H7 A1L7R 42 A1L7R H8 H8 H 0 1 N N N N N N -0.967 -26.051 -15.193 -1.319 1.082 -2.198 H8 A1L7R 43 A1L7R H9 H9 H 0 1 N N N N N N -0.849 -25.512 -17.590 -2.614 3.089 -2.783 H9 A1L7R 44 A1L7R H10 H10 H 0 1 N N N N N N 1.794 -30.940 -13.605 -3.276 -3.476 0.326 H10 A1L7R 45 A1L7R H11 H11 H 0 1 N N N N N N 2.098 -29.958 -15.078 -4.155 -2.862 1.793 H11 A1L7R 46 A1L7R H12 H12 H 0 1 N N N N N N -2.101 -31.619 -12.341 0.159 -3.428 1.658 H12 A1L7R 47 A1L7R H13 H13 H 0 1 N N N N N N -2.159 -30.959 -10.671 -1.405 -2.714 1.196 H13 A1L7R 48 A1L7R H14 H14 H 0 1 N N N N N N -4.993 -30.737 -11.895 -0.813 -3.335 -1.292 H14 A1L7R 49 A1L7R H16 H16 H 0 1 N N N N N N -5.504 -32.741 -10.968 0.089 -5.455 -1.173 H16 A1L7R 50 A1L7R H19 H19 H 0 1 N N N N N N -6.598 -27.699 -11.914 3.680 0.295 2.569 H19 A1L7R 51 A1L7R H20 H20 H 0 1 N N N N N N -7.156 -24.923 -8.810 7.447 -0.176 0.893 H20 A1L7R 52 A1L7R H21 H21 H 0 1 N N N N N N -3.202 -25.808 -10.105 4.005 -0.970 -1.507 H21 A1L7R 53 # 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 A1L7R F01 C02 SING N N 1 A1L7R CL04 C03 SING N N 2 A1L7R C02 C03 DOUB Y N 3 A1L7R C02 C08 SING Y N 4 A1L7R C03 C05 SING Y N 5 A1L7R C08 C07 DOUB Y N 6 A1L7R F18 C16 SING N N 7 A1L7R C05 C06 DOUB Y N 8 A1L7R C15 C16 SING N N 9 A1L7R C15 C13 SING N N 10 A1L7R C07 C06 SING Y N 11 A1L7R C12 C13 SING N N 12 A1L7R C12 N11 SING N N 13 A1L7R C06 C09 SING N N 14 A1L7R C16 C19 SING N N 15 A1L7R C16 F17 SING N N 16 A1L7R C13 C19 SING N N 17 A1L7R C13 C14 SING N N 18 A1L7R N11 C14 SING N N 19 A1L7R N11 C10 SING N N 20 A1L7R C09 C10 DOUB N N 21 A1L7R C09 C34 SING N N 22 A1L7R O35 C34 DOUB N N 23 A1L7R C10 N20 SING N N 24 A1L7R C34 N26 SING N N 25 A1L7R N20 C21 SING N N 26 A1L7R N20 C24 SING N N 27 A1L7R N26 C24 SING N N 28 A1L7R N26 C27 SING N N 29 A1L7R C21 C22 SING N N 30 A1L7R C22 N23 DOUB N N 31 A1L7R C24 O25 DOUB N N 32 A1L7R C28 C27 DOUB Y N 33 A1L7R C28 N29 SING Y N 34 A1L7R C27 C33 SING Y N 35 A1L7R N29 C30 DOUB Y N 36 A1L7R C33 C31 DOUB Y N 37 A1L7R C30 C31 SING Y N 38 A1L7R C31 CL32 SING N N 39 A1L7R C12 H1 SING N N 40 A1L7R C12 H2 SING N N 41 A1L7R C14 H3 SING N N 42 A1L7R C14 H4 SING N N 43 A1L7R C15 H5 SING N N 44 A1L7R C15 H6 SING N N 45 A1L7R C05 H7 SING N N 46 A1L7R C07 H8 SING N N 47 A1L7R C08 H9 SING N N 48 A1L7R C19 H10 SING N N 49 A1L7R C19 H11 SING N N 50 A1L7R C21 H12 SING N N 51 A1L7R C21 H13 SING N N 52 A1L7R C22 H14 SING N N 53 A1L7R N23 H16 SING N N 54 A1L7R C28 H19 SING N N 55 A1L7R C30 H20 SING N N 56 A1L7R C33 H21 SING N N 57 # 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 A1L7R InChI InChI 1.06 "InChI=1S/C23H18Cl2F3N5O2/c24-14-6-15(8-30-7-14)33-20(34)18(13-1-2-17(26)16(25)5-13)19(32(4-3-29)21(33)35)31-11-22(12-31)9-23(27,28)10-22/h1-3,5-8,29H,4,9-12H2" A1L7R InChIKey InChI 1.06 RXJZRRLUUSKVDH-UHFFFAOYSA-N A1L7R SMILES_CANONICAL CACTVS 3.385 "Fc1ccc(cc1Cl)C2=C(N3CC4(C3)CC(F)(F)C4)N(CC=N)C(=O)N(C2=O)c5cncc(Cl)c5" A1L7R SMILES CACTVS 3.385 "Fc1ccc(cc1Cl)C2=C(N3CC4(C3)CC(F)(F)C4)N(CC=N)C(=O)N(C2=O)c5cncc(Cl)c5" A1L7R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1C2=C(N(C(=O)N(C2=O)c3cc(cnc3)Cl)CC=N)N4CC5(C4)CC(C5)(F)F)Cl)F" A1L7R SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1C2=C(N(C(=O)N(C2=O)c3cc(cnc3)Cl)CC=N)N4CC5(C4)CC(C5)(F)F)Cl)F" # _pdbx_chem_comp_identifier.comp_id A1L7R _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 "1-(2-azanylideneethyl)-6-[6,6-bis(fluoranyl)-2-azaspiro[3.3]heptan-2-yl]-5-(3-chloranyl-4-fluoranyl-phenyl)-3-(5-chloranylpyridin-3-yl)pyrimidine-2,4-dione" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1L7R "Create component" 2025-02-19 PDBJ A1L7R "Modify PCM" 2025-02-19 PDBJ A1L7R "Initial release" 2025-05-14 RCSB # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id A1L7R _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C22 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #