data_Y5F
# 
_chem_comp.id                                    Y5F 
_chem_comp.name                                  "2-chloro-N-(5-cyanopyridin-3-yl)-5-nitrobenzamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H7 Cl N4 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                        302.673 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y5F 
_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        8FKC 
_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 
Y5F C02 C1  C  0  1 N N N N N N -4.261 5.727  7.541  -5.306 0.630  0.670  C02 Y5F 1  
Y5F C03 C2  C  0  1 Y N N N N N -5.360 5.473  8.417  -4.360 -0.342 0.211  C03 Y5F 2  
Y5F C04 C3  C  0  1 Y N N N N N -6.633 5.966  8.125  -4.794 -1.519 -0.402 C04 Y5F 3  
Y5F C06 C4  C  0  1 Y N N N N N -7.490 5.044  10.022 -2.626 -2.246 -0.693 C06 Y5F 4  
Y5F C07 C5  C  0  1 Y N N N N N -6.258 4.521  10.401 -2.111 -1.100 -0.099 C07 Y5F 5  
Y5F C09 C6  C  0  1 N N N N N N -7.050 3.283  12.350 -0.186 0.298  -0.083 C09 Y5F 6  
Y5F C11 C7  C  0  1 Y N N N N N -6.608 2.560  13.586 1.282  0.464  -0.049 C11 Y5F 7  
Y5F C12 C8  C  0  1 Y N N N N N -5.597 1.634  13.475 2.110  -0.650 0.095  C12 Y5F 8  
Y5F C13 C9  C  0  1 Y N N N N N -5.148 0.981  14.600 3.480  -0.488 0.125  C13 Y5F 9  
Y5F C17 C10 C  0  1 Y N N N N N -5.645 1.257  15.849 4.034  0.775  0.014  C17 Y5F 10 
Y5F C18 C11 C  0  1 Y N N N N N -6.639 2.209  15.982 3.220  1.885  -0.128 C18 Y5F 11 
Y5F C19 C12 C  0  1 Y N N N N N -7.101 2.874  14.851 1.847  1.737  -0.166 C19 Y5F 12 
Y5F C21 C13 C  0  1 Y N N N N N -5.177 4.732  9.581  -2.986 -0.125 0.364  C21 Y5F 13 
Y5F N01 N1  N  0  1 N N N N N N -3.382 5.953  6.857  -6.056 1.401  1.034  N01 Y5F 14 
Y5F N05 N2  N  0  1 Y N N N N N -7.684 5.764  8.914  -3.927 -2.416 -0.826 N05 Y5F 15 
Y5F N08 N3  N  0  1 N N N N N N -6.055 3.750  11.565 -0.728 -0.930 0.031  N08 Y5F 16 
Y5F N14 N4  N  1  1 N N N N N N -4.111 -0.037 14.463 4.360  -1.668 0.277  N14 Y5F 17 
Y5F O10 O1  O  0  1 N N N N N N -8.238 3.362  12.046 -0.905 1.270  -0.213 O10 Y5F 18 
Y5F O15 O2  O  0  1 N N N N N N -3.723 -0.592 15.486 3.874  -2.781 0.375  O15 Y5F 19 
Y5F O16 O3  O  -1 1 N N N N N N -3.693 -0.308 13.351 5.569  -1.527 0.304  O16 Y5F 20 
Y5F H1  H1  H  0  1 N N N N N N -6.770 6.537  7.218  -5.851 -1.697 -0.529 H1  Y5F 21 
Y5F H2  H2  H  0  1 N N N N N N -8.340 4.857  10.662 -1.951 -3.008 -1.054 H2  Y5F 22 
Y5F H3  H3  H  0  1 N N N N N N -5.158 1.421  12.511 1.680  -1.637 0.182  H3  Y5F 23 
Y5F H4  H4  H  0  1 N N N N N N -5.265 0.738  16.716 5.107  0.896  0.039  H4  Y5F 24 
Y5F H5  H5  H  0  1 N N N N N N -7.052 2.434  16.954 3.659  2.868  -0.214 H5  Y5F 25 
Y5F H7  H7  H  0  1 N N N N N N -4.206 4.332  9.834  -2.615 0.777  0.829  H7  Y5F 26 
Y5F H8  H8  H  0  1 N N N N N N -5.114 3.535  11.826 -0.159 -1.697 0.203  H8  Y5F 27 
Y5F CL1 CL1 CL 0  0 N Y N N N N -8.361 4.115  14.878 0.827  3.129  -0.352 CL1 Y5F 28 
# 
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 
Y5F N01 C02 TRIP N N 1  
Y5F C02 C03 SING N N 2  
Y5F C04 C03 DOUB Y N 3  
Y5F C04 N05 SING Y N 4  
Y5F C03 C21 SING Y N 5  
Y5F N05 C06 DOUB Y N 6  
Y5F C21 C07 DOUB Y N 7  
Y5F C06 C07 SING Y N 8  
Y5F C07 N08 SING N N 9  
Y5F N08 C09 SING N N 10 
Y5F O10 C09 DOUB N N 11 
Y5F C09 C11 SING N N 12 
Y5F O16 N14 SING N N 13 
Y5F C12 C11 DOUB Y N 14 
Y5F C12 C13 SING Y N 15 
Y5F C11 C19 SING Y N 16 
Y5F N14 C13 SING N N 17 
Y5F N14 O15 DOUB N N 18 
Y5F C13 C17 DOUB Y N 19 
Y5F C19 C18 DOUB Y N 20 
Y5F C17 C18 SING Y N 21 
Y5F C04 H1  SING N N 22 
Y5F C06 H2  SING N N 23 
Y5F C12 H3  SING N N 24 
Y5F C17 H4  SING N N 25 
Y5F C18 H5  SING N N 26 
Y5F C21 H7  SING N N 27 
Y5F N08 H8  SING N N 28 
Y5F C19 CL1 SING N N 29 
# 
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 
Y5F SMILES           ACDLabs              12.01 "O=C(Nc1cc(cnc1)C#N)c1cc(ccc1Cl)[N+]([O-])=O"                                                          
Y5F InChI            InChI                1.06  "InChI=1S/C13H7ClN4O3/c14-12-2-1-10(18(20)21)4-11(12)13(19)17-9-3-8(5-15)6-16-7-9/h1-4,6-7H,(H,17,19)" 
Y5F InChIKey         InChI                1.06  QDJGFGPMRNZDNJ-UHFFFAOYSA-N                                                                            
Y5F SMILES_CANONICAL CACTVS               3.385 "[O-][N+](=O)c1ccc(Cl)c(c1)C(=O)Nc2cncc(c2)C#N"                                                        
Y5F SMILES           CACTVS               3.385 "[O-][N+](=O)c1ccc(Cl)c(c1)C(=O)Nc2cncc(c2)C#N"                                                        
Y5F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1[N+](=O)[O-])C(=O)Nc2cc(cnc2)C#N)Cl"                                                        
Y5F SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1[N+](=O)[O-])C(=O)Nc2cc(cnc2)C#N)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 
Y5F "SYSTEMATIC NAME" ACDLabs              12.01 "2-chloro-N-(5-cyanopyridin-3-yl)-5-nitrobenzamide"        
Y5F "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-chloranyl-~{N}-(5-cyanopyridin-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 
Y5F "Create component" 2023-01-05 RCSB 
Y5F "Initial release"  2024-04-17 RCSB 
Y5F "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y5F 
_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      ? 
# 
