data_Y5X
# 
_chem_comp.id                                    Y5X 
_chem_comp.name                                  "2-chloro-N-(5-fluoropyridin-3-yl)-5-nitrobenzamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H7 Cl F N3 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-01-05 
_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                        295.654 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y5X 
_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        8FKF 
_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 
Y5X C13 C1  C  0  1 Y N N N N N -5.059 0.930  14.710 3.294  0.582  0.071  C13 Y5X 1  
Y5X C10 C2  C  0  1 Y N N N N N -4.958 4.710  9.525  -3.146 -0.057 0.465  C10 Y5X 2  
Y5X N14 N1  N  1  1 N N N N N N -4.032 -0.101 14.619 4.125  1.803  0.175  N14 Y5X 3  
Y5X C17 C3  C  0  1 Y N N N N N -5.586 1.232  15.945 3.900  -0.659 -0.021 C17 Y5X 4  
Y5X C18 C4  C  0  1 Y N N N N N -6.560 2.215  16.012 3.132  -1.805 -0.119 C18 Y5X 5  
Y5X C02 C5  C  0  1 N N N N N N -6.863 3.215  12.345 -0.338 -0.367 -0.030 C02 Y5X 6  
Y5X C04 C6  C  0  1 Y N N N N N -6.010 4.541  10.415 -2.321 0.947  -0.034 C04 Y5X 7  
Y5X C05 C7  C  0  1 Y N N N N N -7.222 5.141  10.086 -2.898 2.057  -0.638 C05 Y5X 8  
Y5X C07 C8  C  0  1 Y N N N N N -6.374 6.048  8.161  -5.018 1.226  -0.287 C07 Y5X 9  
Y5X C08 C9  C  0  1 Y N N N N N -5.140 5.479  8.394  -4.519 0.092  0.332  C08 Y5X 10 
Y5X C11 C10 C  0  1 Y N N N N N -6.434 2.525  13.609 1.136  -0.469 -0.023 C11 Y5X 11 
Y5X C12 C11 C  0  1 Y N N N N N -5.448 1.568  13.554 1.919  0.683  0.070  C12 Y5X 12 
Y5X C19 C12 C  0  1 Y N N N N N -6.962 2.870  14.854 1.754  -1.718 -0.127 C19 Y5X 13 
Y5X F09 F1  F  0  1 N N N N N N -4.113 5.668  7.520  -5.358 -0.862 0.791  F09 Y5X 14 
Y5X N03 N2  N  0  1 N N N N N N -5.868 3.718  11.561 -0.930 0.840  0.071  N03 Y5X 15 
Y5X N06 N3  N  0  1 Y N N N N N -7.399 5.894  8.997  -4.208 2.163  -0.739 N06 Y5X 16 
Y5X O01 O1  O  0  1 N N N N N N -8.059 3.391  12.130 -1.016 -1.371 -0.127 O01 Y5X 17 
Y5X O15 O2  O  -1 1 N N N N N N -3.565 -0.361 13.520 3.593  2.895  0.256  O15 Y5X 18 
Y5X O16 O3  O  0  1 N N N N N N -3.723 -0.691 15.645 5.339  1.714  0.181  O16 Y5X 19 
Y5X H1  H1  H  0  1 N N N N N N -4.003 4.243  9.717  -2.728 -0.932 0.940  H1  Y5X 20 
Y5X H2  H2  H  0  1 N N N N N N -5.251 0.719  16.834 4.977  -0.733 -0.016 H2  Y5X 21 
Y5X H3  H3  H  0  1 N N N N N N -7.006 2.472  16.962 3.612  -2.771 -0.191 H3  Y5X 22 
Y5X H4  H4  H  0  1 N N N N N N -8.064 4.990  10.746 -2.267 2.841  -1.029 H4  Y5X 23 
Y5X H5  H5  H  0  1 N N N N N N -6.514 6.640  7.269  -6.086 1.348  -0.394 H5  Y5X 24 
Y5X H6  H6  H  0  1 N N N N N N -4.983 1.319  12.612 1.448  1.652  0.151  H6  Y5X 25 
Y5X H8  H8  H  0  1 N N N N N N -4.933 3.480  11.823 -0.392 1.633  0.216  H8  Y5X 26 
Y5X CL1 CL1 CL 0  0 N Y N N N N -8.241 4.091  14.974 0.791  -3.158 -0.244 CL1 Y5X 27 
# 
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 
Y5X F09 C08 SING N N 1  
Y5X C07 C08 DOUB Y N 2  
Y5X C07 N06 SING Y N 3  
Y5X C08 C10 SING Y N 4  
Y5X N06 C05 DOUB Y N 5  
Y5X C10 C04 DOUB Y N 6  
Y5X C05 C04 SING Y N 7  
Y5X C04 N03 SING N N 8  
Y5X N03 C02 SING N N 9  
Y5X O01 C02 DOUB N N 10 
Y5X C02 C11 SING N N 11 
Y5X O15 N14 SING N N 12 
Y5X C12 C11 DOUB Y N 13 
Y5X C12 C13 SING Y N 14 
Y5X C11 C19 SING Y N 15 
Y5X N14 C13 SING N N 16 
Y5X N14 O16 DOUB N N 17 
Y5X C13 C17 DOUB Y N 18 
Y5X C19 C18 DOUB Y N 19 
Y5X C17 C18 SING Y N 20 
Y5X C10 H1  SING N N 21 
Y5X C17 H2  SING N N 22 
Y5X C18 H3  SING N N 23 
Y5X C05 H4  SING N N 24 
Y5X C07 H5  SING N N 25 
Y5X C12 H6  SING N N 26 
Y5X N03 H8  SING N N 27 
Y5X C19 CL1 SING N N 28 
# 
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 
Y5X SMILES           ACDLabs              12.01 "O=C(Nc1cc(F)cnc1)c1cc(ccc1Cl)[N+]([O-])=O"                                                      
Y5X InChI            InChI                1.06  "InChI=1S/C12H7ClFN3O3/c13-11-2-1-9(17(19)20)4-10(11)12(18)16-8-3-7(14)5-15-6-8/h1-6H,(H,16,18)" 
Y5X InChIKey         InChI                1.06  YYVSYARVIWSRBD-UHFFFAOYSA-N                                                                      
Y5X SMILES_CANONICAL CACTVS               3.385 "[O-][N+](=O)c1ccc(Cl)c(c1)C(=O)Nc2cncc(F)c2"                                                    
Y5X SMILES           CACTVS               3.385 "[O-][N+](=O)c1ccc(Cl)c(c1)C(=O)Nc2cncc(F)c2"                                                    
Y5X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1[N+](=O)[O-])C(=O)Nc2cc(cnc2)F)Cl"                                                    
Y5X SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1[N+](=O)[O-])C(=O)Nc2cc(cnc2)F)Cl"                                                    
# 
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 
Y5X "SYSTEMATIC NAME" ACDLabs              12.01 "2-chloro-N-(5-fluoropyridin-3-yl)-5-nitrobenzamide"           
Y5X "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-chloranyl-~{N}-(5-fluoranylpyridin-3-yl)-5-nitro-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 
Y5X "Create component" 2023-01-05 RCSB 
Y5X "Initial release"  2024-04-17 RCSB 
Y5X "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y5X 
_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               C19 
_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      ? 
# 
