data_XL5
# 
_chem_comp.id                                    XL5 
_chem_comp.name                                  "N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-3-fluorophenyl]propanamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H21 Cl2 F N4 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-11-05 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        495.331 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XL5 
_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        6BIU 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
XL5 C1  C1  C  0 1 Y N N N N N 20.913 -2.770  -8.630  5.954  -0.756 0.212  C1  XL5 1  
XL5 C2  C2  C  0 1 Y N N N N N 19.715 -3.462  -8.615  4.589  -0.984 0.105  C2  XL5 2  
XL5 C3  C3  C  0 1 Y N N N N N 19.519 -4.571  -7.782  3.745  0.037  -0.290 C3  XL5 3  
XL5 C4  C4  C  0 1 Y N N N N N 20.567 -4.975  -6.968  4.258  1.288  -0.580 C4  XL5 4  
XL5 C5  C5  C  0 1 Y N N N N N 21.777 -4.285  -6.980  5.623  1.520  -0.474 C5  XL5 5  
XL5 C6  C6  C  0 1 Y N N N N N 21.947 -3.190  -7.810  6.471  0.498  -0.078 C6  XL5 6  
XL5 O1  O1  O  0 1 N N N N N N 20.947 -1.703  -9.477  6.783  -1.759 0.605  O1  XL5 7  
XL5 O2  O2  O  0 1 N N N N N N 22.788 -4.693  -6.172  6.127  2.750  -0.759 O2  XL5 8  
XL5 C7  C7  C  0 1 N N N N N N 22.098 -0.869  -9.523  8.176  -1.452 0.693  C7  XL5 9  
XL5 C8  C8  C  0 1 N N N N N N 24.063 -4.871  -6.769  7.540  2.918  -0.628 C8  XL5 10 
XL5 CL1 CL1 CL 0 0 N N N N N N 18.452 -2.911  -9.671  3.941  -2.554 0.468  CL1 XL5 11 
XL5 CL2 CL2 CL 0 0 N N N N N N 20.354 -6.350  -5.926  3.196  2.568  -1.076 CL2 XL5 12 
XL5 C9  C9  C  0 1 N N N N N N 18.229 -5.336  -7.788  2.263  -0.214 -0.407 C9  XL5 13 
XL5 O3  O3  O  0 1 N N N N N N 18.452 -6.532  -8.554  1.632  0.071  0.844  O3  XL5 14 
XL5 C10 C10 C  0 1 Y N N N N N 17.621 -7.604  -8.353  0.285  -0.105 0.910  C10 XL5 15 
XL5 C11 C11 C  0 1 Y N N N N N 16.325 -7.505  -7.865  -0.408 0.149  2.088  C11 XL5 16 
XL5 N1  N1  N  0 1 Y N N N N N 15.559 -8.585  -7.725  -1.718 -0.033 2.116  N1  XL5 17 
XL5 C12 C12 C  0 1 Y N N N N N 16.100 -9.766  -8.081  -2.368 -0.452 1.041  C12 XL5 18 
XL5 N2  N2  N  0 1 Y N N N N N 17.347 -9.945  -8.556  -1.740 -0.703 -0.098 N2  XL5 19 
XL5 C13 C13 C  0 1 Y N N N N N 18.103 -8.850  -8.688  -0.431 -0.537 -0.200 C13 XL5 20 
XL5 N3  N3  N  0 1 N N N N N N 15.340 -10.878 -7.918  -3.741 -0.632 1.109  N3  XL5 21 
XL5 C14 C14 C  0 1 Y N N N N N 14.025 -10.971 -7.427  -4.463 -0.958 -0.047 C14 XL5 22 
XL5 C15 C15 C  0 1 Y N N N N N 13.037 -11.541 -8.236  -5.503 -0.135 -0.478 C15 XL5 23 
XL5 C16 C16 C  0 1 Y N N N N N 11.717 -11.622 -7.715  -6.213 -0.463 -1.624 C16 XL5 24 
XL5 C17 C17 C  0 1 Y N N N N N 11.430 -11.122 -6.454  -5.890 -1.603 -2.335 C17 XL5 25 
XL5 C18 C18 C  0 1 Y N N N N N 12.416 -10.561 -5.669  -4.860 -2.421 -1.909 C18 XL5 26 
XL5 C19 C19 C  0 1 Y N N N N N 13.696 -10.492 -6.167  -4.142 -2.099 -0.771 C19 XL5 27 
XL5 N4  N4  N  0 1 N N N N N N 13.443 -12.070 -9.484  -5.829 1.021  0.244  N4  XL5 28 
XL5 C20 C20 C  0 1 N N N N N N 12.796 -12.016 -10.660 -7.111 1.431  0.315  C20 XL5 29 
XL5 C21 C21 C  0 1 N N N N N N 13.547 -12.665 -11.802 -7.478 2.609  1.180  C21 XL5 30 
XL5 C22 C22 C  0 1 N N N N N N 14.870 -11.994 -12.108 -8.983 2.864  1.083  C22 XL5 31 
XL5 O4  O4  O  0 1 N N N N N N 11.712 -11.491 -10.796 -7.969 0.852  -0.317 O4  XL5 32 
XL5 F1  F1  F  0 1 N N N N N N 14.668 -9.937  -5.410  -3.132 -2.897 -0.360 F1  XL5 33 
XL5 H1  H1  H  0 1 N N N N N N 22.889 -2.662  -7.818  7.532  0.677  0.004  H1  XL5 34 
XL5 H2  H2  H  0 1 N N N N N N 21.941 -0.067  -10.259 8.723  -2.338 1.017  H2  XL5 35 
XL5 H3  H3  H  0 1 N N N N N N 22.270 -0.427  -8.531  8.541  -1.137 -0.285 H3  XL5 36 
XL5 H4  H4  H  0 1 N N N N N N 22.973 -1.468  -9.814  8.326  -0.648 1.413  H4  XL5 37 
XL5 H5  H5  H  0 1 N N N N N N 24.783 -5.201  -6.006  7.810  3.942  -0.885 H5  XL5 38 
XL5 H6  H6  H  0 1 N N N N N N 23.994 -5.632  -7.561  7.838  2.710  0.400  H6  XL5 39 
XL5 H7  H7  H  0 1 N N N N N N 24.400 -3.919  -7.204  8.052  2.229  -1.301 H7  XL5 40 
XL5 H8  H8  H  0 1 N N N N N N 17.435 -4.733  -8.252  1.845  0.431  -1.180 H8  XL5 41 
XL5 H9  H9  H  0 1 N N N N N N 17.939 -5.595  -6.759  2.091  -1.257 -0.671 H9  XL5 42 
XL5 H10 H10 H  0 1 N N N N N N 15.932 -6.536  -7.595  0.116  0.490  2.969  H10 XL5 43 
XL5 H11 H11 H  0 1 N N N N N N 19.111 -8.944  -9.064  0.075  -0.744 -1.131 H11 XL5 44 
XL5 H12 H12 H  0 1 N N N N N N 15.770 -11.742 -8.180  -4.202 -0.532 1.956  H12 XL5 45 
XL5 H13 H13 H  0 1 N N N N N N 10.934 -12.075 -8.304  -7.019 0.173  -1.959 H13 XL5 46 
XL5 H14 H14 H  0 1 N N N N N N 10.418 -11.173 -6.080  -6.445 -1.857 -3.226 H14 XL5 47 
XL5 H15 H15 H  0 1 N N N N N N 12.187 -10.184 -4.683  -4.612 -3.311 -2.469 H15 XL5 48 
XL5 H16 H16 H  0 1 N N N N N N 14.323 -12.544 -9.491  -5.133 1.525  0.692  H16 XL5 49 
XL5 H17 H17 H  0 1 N N N N N N 12.917 -12.622 -12.703 -7.211 2.397  2.216  H17 XL5 50 
XL5 H18 H18 H  0 1 N N N N N N 13.741 -13.716 -11.540 -6.937 3.492  0.840  H18 XL5 51 
XL5 H19 H19 H  0 1 N N N N N N 15.361 -12.514 -12.944 -9.248 3.716  1.709  H19 XL5 52 
XL5 H20 H20 H  0 1 N N N N N N 14.693 -10.944 -12.382 -9.250 3.076  0.048  H20 XL5 53 
XL5 H21 H21 H  0 1 N N N N N N 15.517 -12.037 -11.219 -9.524 1.981  1.424  H21 XL5 54 
# 
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 
XL5 C22 C21 SING N N 1  
XL5 C21 C20 SING N N 2  
XL5 O4  C20 DOUB N N 3  
XL5 C20 N4  SING N N 4  
XL5 CL1 C2  SING N N 5  
XL5 C7  O1  SING N N 6  
XL5 N4  C15 SING N N 7  
XL5 O1  C1  SING N N 8  
XL5 C13 N2  DOUB Y N 9  
XL5 C13 C10 SING Y N 10 
XL5 C1  C2  DOUB Y N 11 
XL5 C1  C6  SING Y N 12 
XL5 C2  C3  SING Y N 13 
XL5 N2  C12 SING Y N 14 
XL5 O3  C10 SING N N 15 
XL5 O3  C9  SING N N 16 
XL5 C10 C11 DOUB Y N 17 
XL5 C15 C16 DOUB Y N 18 
XL5 C15 C14 SING Y N 19 
XL5 C12 N3  SING N N 20 
XL5 C12 N1  DOUB Y N 21 
XL5 N3  C14 SING N N 22 
XL5 C11 N1  SING Y N 23 
XL5 C6  C5  DOUB Y N 24 
XL5 C9  C3  SING N N 25 
XL5 C3  C4  DOUB Y N 26 
XL5 C16 C17 SING Y N 27 
XL5 C14 C19 DOUB Y N 28 
XL5 C5  C4  SING Y N 29 
XL5 C5  O2  SING N N 30 
XL5 C4  CL2 SING N N 31 
XL5 C8  O2  SING N N 32 
XL5 C17 C18 DOUB Y N 33 
XL5 C19 C18 SING Y N 34 
XL5 C19 F1  SING N N 35 
XL5 C6  H1  SING N N 36 
XL5 C7  H2  SING N N 37 
XL5 C7  H3  SING N N 38 
XL5 C7  H4  SING N N 39 
XL5 C8  H5  SING N N 40 
XL5 C8  H6  SING N N 41 
XL5 C8  H7  SING N N 42 
XL5 C9  H8  SING N N 43 
XL5 C9  H9  SING N N 44 
XL5 C11 H10 SING N N 45 
XL5 C13 H11 SING N N 46 
XL5 N3  H12 SING N N 47 
XL5 C16 H13 SING N N 48 
XL5 C17 H14 SING N N 49 
XL5 C18 H15 SING N N 50 
XL5 N4  H16 SING N N 51 
XL5 C21 H17 SING N N 52 
XL5 C21 H18 SING N N 53 
XL5 C22 H19 SING N N 54 
XL5 C22 H20 SING N N 55 
XL5 C22 H21 SING N N 56 
# 
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 
XL5 SMILES           ACDLabs              12.01 "c1(c(c(c(Cl)c(OC)c1)COc3cnc(Nc2c(cccc2NC(CC)=O)F)nc3)Cl)OC"                                                                                                            
XL5 InChI            InChI                1.03  "InChI=1S/C22H21Cl2FN4O4/c1-4-18(30)28-15-7-5-6-14(25)21(15)29-22-26-9-12(10-27-22)33-11-13-19(23)16(31-2)8-17(32-3)20(13)24/h5-10H,4,11H2,1-3H3,(H,28,30)(H,26,27,29)" 
XL5 InChIKey         InChI                1.03  QQZLOGCMIZJHHI-UHFFFAOYSA-N                                                                                                                                             
XL5 SMILES_CANONICAL CACTVS               3.385 "CCC(=O)Nc1cccc(F)c1Nc2ncc(OCc3c(Cl)c(OC)cc(OC)c3Cl)cn2"                                                                                                                
XL5 SMILES           CACTVS               3.385 "CCC(=O)Nc1cccc(F)c1Nc2ncc(OCc3c(Cl)c(OC)cc(OC)c3Cl)cn2"                                                                                                                
XL5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CCC(=O)Nc1cccc(c1Nc2ncc(cn2)OCc3c(c(cc(c3Cl)OC)OC)Cl)F"                                                                                                                
XL5 SMILES           "OpenEye OEToolkits" 2.0.6 "CCC(=O)Nc1cccc(c1Nc2ncc(cn2)OCc3c(c(cc(c3Cl)OC)OC)Cl)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 
XL5 "SYSTEMATIC NAME" ACDLabs              12.01 "N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-3-fluorophenyl]propanamide"               
XL5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "~{N}-[2-[[5-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]methoxy]pyrimidin-2-yl]amino]-3-fluoranyl-phenyl]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 
XL5 "Create component" 2017-11-05 RCSB 
XL5 "Initial release"  2019-07-10 RCSB 
XL5 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            XL5 
_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      ? 
# 
