data_XDQ
# 
_chem_comp.id                                    XDQ 
_chem_comp.name                                  "(2~{R})-2-[[4-[chloranyl-bis(fluoranyl)methoxy]phenyl]-(2-chloranyl-2-fluoranyl-ethanoyl)amino]-~{N}-(oxan-4-yl)-2-pyrimidin-5-yl-propanamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H21 Cl2 F3 N4 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-10-27 
_chem_comp.pdbx_modified_date                    2025-04-18 
_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                        521.317 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XDQ 
_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        8WTS 
_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_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_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 
XDQ N3  N1  N  0 1 N N N N N N -21.992 39.657 1.238  -2.507 -1.107 -0.890 N3  XDQ 1  
XDQ C4  C1  C  0 1 N N R N N N -22.036 41.225 3.305  -0.848 0.727  -0.850 C4  XDQ 2  
XDQ C6  C2  C  0 1 N N N N N N -23.583 41.134 3.290  -0.043 0.377  -2.103 C6  XDQ 3  
XDQ C7  C3  C  0 1 Y N N N N N -21.441 40.752 4.672  -0.876 2.224  -0.673 C7  XDQ 4  
XDQ C8  C4  C  0 1 Y N N N N N -20.110 41.065 5.045  -1.488 3.038  -1.612 C8  XDQ 5  
XDQ N12 N2  N  0 1 Y N N N N N -19.610 40.612 6.231  -1.492 4.348  -1.423 N12 XDQ 6  
XDQ C13 C5  C  0 1 Y N N N N N -21.194 42.932 1.734  1.106  -0.330 0.256  C13 XDQ 7  
XDQ C15 C6  C  0 1 N N S N N N -20.936 44.911 3.826  -2.431 0.020  1.431  C15 XDQ 8  
XDQ C20 C7  C  0 1 Y N N N N N -22.245 43.475 0.979  1.397  -1.684 0.359  C20 XDQ 9  
XDQ C21 C8  C  0 1 Y N N N N N -22.028 43.794 -0.334 2.707  -2.115 0.296  C21 XDQ 10 
XDQ C22 C9  C  0 1 Y N N N N N -20.804 43.708 -0.950 3.733  -1.196 0.128  C22 XDQ 11 
XDQ O1  O1  O  0 1 N N N N N N -20.137 40.065 2.349  -3.166 0.987  -1.214 O1  XDQ 12 
XDQ C2  C10 C  0 1 N N N N N N -21.352 40.280 2.274  -2.257 0.213  -0.998 C2  XDQ 13 
XDQ N5  N3  N  0 1 N N N N N N -21.588 42.602 3.044  -0.223 0.108  0.321  N5  XDQ 14 
XDQ C9  C11 C  0 1 Y N N N N N -22.193 40.041 5.608  -0.294 2.818  0.436  C9  XDQ 15 
XDQ N10 N4  N  0 1 Y N N N N N -21.663 39.639 6.750  -0.338 4.135  0.558  N10 XDQ 16 
XDQ C11 C12 C  0 1 Y N N N N N -20.402 39.950 7.055  -0.924 4.878  -0.359 C11 XDQ 17 
XDQ C14 C13 C  0 1 N N N N N N -21.631 43.577 4.002  -0.926 -0.040 1.461  C14 XDQ 18 
XDQ O16 O2  O  0 1 N N N N N N -22.122 43.333 5.110  -0.347 -0.220 2.512  O16 XDQ 19 
XDQ F17 F1  F  0 1 N N N N N N -21.374 45.758 4.828  -2.939 -0.380 2.672  F17 XDQ 20 
XDQ C19 C14 C  0 1 Y N N N N N -19.999 42.876 1.103  2.134  0.590  0.094  C19 XDQ 21 
XDQ C23 C15 C  0 1 Y N N N N N -19.786 43.218 -0.186 3.443  0.157  0.025  C23 XDQ 22 
XDQ O24 O3  O  0 1 N N N N N N -20.655 44.130 -2.248 5.023  -1.621 0.065  O24 XDQ 23 
XDQ C25 C16 C  0 1 N N N N N N -19.901 43.552 -3.301 6.028  -0.621 -0.108 C25 XDQ 24 
XDQ F26 F2  F  0 1 N N N N N N -18.561 43.435 -3.008 5.800  0.067  -1.305 F26 XDQ 25 
XDQ F27 F3  F  0 1 N N N N N N -20.260 44.061 -4.620 5.981  0.279  0.962  F27 XDQ 26 
XDQ CL2 CL1 CL 0 0 N N N N N N -20.307 41.866 -3.244 7.652  -1.403 -0.164 CL2 XDQ 27 
XDQ C29 C17 C  0 1 N N N N N N -21.312 38.760 0.292  -3.883 -1.602 -0.985 C29 XDQ 28 
XDQ C30 C18 C  0 1 N N N N N N -22.286 37.651 -0.055 -3.868 -3.094 -1.332 C30 XDQ 29 
XDQ C31 C19 C  0 1 N N N N N N -20.894 39.556 -0.941 -4.592 -1.406 0.358  C31 XDQ 30 
XDQ C32 C20 C  0 1 N N N N N N -20.343 38.527 -1.962 -6.002 -1.997 0.273  C32 XDQ 31 
XDQ O33 O4  O  0 1 N N N N N N -21.509 37.757 -2.296 -5.917 -3.379 -0.081 O33 XDQ 32 
XDQ C34 C21 C  0 1 N N N N N N -21.828 36.846 -1.261 -5.306 -3.619 -1.352 C34 XDQ 33 
XDQ H1  H1  H  0 1 N N N N N N -22.971 39.820 1.118  -1.776 -1.730 -0.754 H1  XDQ 34 
XDQ H2  H2  H  0 1 N N N N N N -23.999 41.824 4.039  -0.350 1.024  -2.925 H2  XDQ 35 
XDQ H3  H3  H  0 1 N N N N N N -23.957 41.407 2.292  1.019  0.519  -1.905 H3  XDQ 36 
XDQ H4  H4  H  0 1 N N N N N N -23.892 40.106 3.528  -0.226 -0.664 -2.373 H4  XDQ 37 
XDQ H5  H5  H  0 1 N N N N N N -19.492 41.662 4.391  -1.955 2.610  -2.487 H5  XDQ 38 
XDQ H6  H6  H  0 1 N N N N N N -21.091 45.313 2.814  -2.806 -0.647 0.654  H6  XDQ 39 
XDQ H8  H8  H  0 1 N N N N N N -23.213 43.639 1.429  0.599  -2.399 0.490  H8  XDQ 40 
XDQ H9  H9  H  0 1 N N N N N N -22.869 44.133 -0.920 2.934  -3.168 0.376  H9  XDQ 41 
XDQ H10 H10 H  0 1 N N N N N N -23.227 39.815 5.395  0.188  2.214  1.191  H10 XDQ 42 
XDQ H11 H11 H  0 1 N N N N N N -20.012 39.648 8.016  -0.944 5.951  -0.232 H11 XDQ 43 
XDQ H12 H12 H  0 1 N N N N N N -19.150 42.531 1.674  1.909  1.643  0.017  H12 XDQ 44 
XDQ H13 H13 H  0 1 N N N N N N -18.802 43.103 -0.615 4.242  0.872  -0.105 H13 XDQ 45 
XDQ H14 H14 H  0 1 N N N N N N -20.418 38.326 0.763  -4.415 -1.052 -1.762 H14 XDQ 46 
XDQ H15 H15 H  0 1 N N N N N N -23.267 38.097 -0.277 -3.415 -3.235 -2.313 H15 XDQ 47 
XDQ H16 H16 H  0 1 N N N N N N -22.377 36.976 0.809  -3.291 -3.636 -0.583 H16 XDQ 48 
XDQ H17 H17 H  0 1 N N N N N N -20.113 40.285 -0.677 -4.031 -1.914 1.143  H17 XDQ 49 
XDQ H18 H18 H  0 1 N N N N N N -21.761 40.085 -1.364 -4.655 -0.342 0.585  H18 XDQ 50 
XDQ H19 H19 H  0 1 N N N N N N -19.567 37.894 -1.507 -6.496 -1.899 1.240  H19 XDQ 51 
XDQ H20 H20 H  0 1 N N N N N N -19.932 39.030 -2.850 -6.575 -1.462 -0.484 H20 XDQ 52 
XDQ H21 H21 H  0 1 N N N N N N -22.634 36.174 -1.590 -5.871 -3.106 -2.130 H21 XDQ 53 
XDQ H22 H22 H  0 1 N N N N N N -20.940 36.252 -0.999 -5.298 -4.690 -1.555 H22 XDQ 54 
XDQ CL1 CL2 CL 0 0 N N N N N N -19.060 44.617 4.020  -2.960 1.707  1.081  CL1 XDQ 55 
# 
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 
XDQ F27 C25 SING N N 1  
XDQ C25 CL2 SING N N 2  
XDQ C25 F26 SING N N 3  
XDQ C25 O24 SING N N 4  
XDQ O33 C32 SING N N 5  
XDQ O33 C34 SING N N 6  
XDQ O24 C22 SING N N 7  
XDQ C32 C31 SING N N 8  
XDQ C34 C30 SING N N 9  
XDQ C22 C21 DOUB Y N 10 
XDQ C22 C23 SING Y N 11 
XDQ C31 C29 SING N N 12 
XDQ C21 C20 SING Y N 13 
XDQ C23 C19 DOUB Y N 14 
XDQ C30 C29 SING N N 15 
XDQ C29 N3  SING N N 16 
XDQ C20 C13 DOUB Y N 17 
XDQ C19 C13 SING Y N 18 
XDQ N3  C2  SING N N 19 
XDQ C13 N5  SING N N 20 
XDQ C2  O1  DOUB N N 21 
XDQ C2  C4  SING N N 22 
XDQ N5  C4  SING N N 23 
XDQ N5  C14 SING N N 24 
XDQ C6  C4  SING N N 25 
XDQ C4  C7  SING N N 26 
XDQ C15 C14 SING N N 27 
XDQ C15 F17 SING N N 28 
XDQ C14 O16 DOUB N N 29 
XDQ C7  C8  DOUB Y N 30 
XDQ C7  C9  SING Y N 31 
XDQ C8  N12 SING Y N 32 
XDQ C9  N10 DOUB Y N 33 
XDQ N12 C11 DOUB Y N 34 
XDQ N10 C11 SING Y N 35 
XDQ N3  H1  SING N N 36 
XDQ C6  H2  SING N N 37 
XDQ C6  H3  SING N N 38 
XDQ C6  H4  SING N N 39 
XDQ C8  H5  SING N N 40 
XDQ C15 H6  SING N N 41 
XDQ C20 H8  SING N N 42 
XDQ C21 H9  SING N N 43 
XDQ C9  H10 SING N N 44 
XDQ C11 H11 SING N N 45 
XDQ C19 H12 SING N N 46 
XDQ C23 H13 SING N N 47 
XDQ C29 H14 SING N N 48 
XDQ C30 H15 SING N N 49 
XDQ C30 H16 SING N N 50 
XDQ C31 H17 SING N N 51 
XDQ C31 H18 SING N N 52 
XDQ C32 H19 SING N N 53 
XDQ C32 H20 SING N N 54 
XDQ C34 H21 SING N N 55 
XDQ C34 H22 SING N N 56 
XDQ C15 CL1 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 
XDQ InChI            InChI                1.06  "InChI=1S/C21H21Cl2F3N4O4/c1-20(13-10-27-12-28-11-13,19(32)29-14-6-8-33-9-7-14)30(18(31)17(22)24)15-2-4-16(5-3-15)34-21(23,25)26/h2-5,10-12,14,17H,6-9H2,1H3,(H,29,32)/t17-,20-/m1/s1" 
XDQ InChIKey         InChI                1.06  YWLKYOUHSKWUGZ-YLJYHZDGSA-N                                                                                                                                                            
XDQ SMILES_CANONICAL CACTVS               3.385 "C[C@](N(C(=O)[C@@H](F)Cl)c1ccc(OC(F)(F)Cl)cc1)(C(=O)NC2CCOCC2)c3cncnc3"                                                                                                               
XDQ SMILES           CACTVS               3.385 "C[C](N(C(=O)[CH](F)Cl)c1ccc(OC(F)(F)Cl)cc1)(C(=O)NC2CCOCC2)c3cncnc3"                                                                                                                  
XDQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@](c1cncnc1)(C(=O)NC2CCOCC2)N(c3ccc(cc3)OC(F)(F)Cl)C(=O)C(F)Cl"                                                                                                                   
XDQ SMILES           "OpenEye OEToolkits" 2.0.7 "CC(c1cncnc1)(C(=O)NC2CCOCC2)N(c3ccc(cc3)OC(F)(F)Cl)C(=O)C(F)Cl"                                                                                                                       
# 
_pdbx_chem_comp_identifier.comp_id           XDQ 
_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        "(2~{R})-2-[[4-[chloranyl-bis(fluoranyl)methoxy]phenyl]-(2-chloranyl-2-fluoranyl-ethanoyl)amino]-~{N}-(oxan-4-yl)-2-pyrimidin-5-yl-propanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
XDQ "Create component" 2023-10-27 PDBJ 
XDQ "Modify PCM"       2024-09-27 PDBE 
XDQ "Initial release"  2025-04-23 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            XDQ 
_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               C15 
_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      ? 
# 
