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      ? 
# 
