data_Y5T
# 
_chem_comp.id                                    Y5T 
_chem_comp.name                                  "2-chloro-N-(2-methylpyridin-4-yl)-5-nitrobenzamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H10 Cl 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                        291.690 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y5T 
_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        8FKE 
_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 
Y5T C10 C1  C  0  1 Y N N N N N -5.065 1.230  15.310 -3.221 0.594  -0.111 C10 Y5T 1  
Y5T C15 C2  C  0  1 Y N N N N N -6.797 2.290  16.519 -3.069 -1.797 0.031  C15 Y5T 2  
Y5T C16 C3  C  0  1 Y N N N N N -7.146 2.979  15.366 -1.694 -1.712 0.122  C16 Y5T 3  
Y5T N20 N1  N  0  1 Y N N N N N -5.812 5.500  8.258  5.114  1.120  0.109  N20 Y5T 4  
Y5T C01 C4  C  0  1 N N N N N N -8.205 5.861  8.234  5.374  -0.942 -1.179 C01 Y5T 5  
Y5T C02 C5  C  0  1 Y N N N N N -6.973 5.353  8.922  4.530  0.099  -0.490 C02 Y5T 6  
Y5T C03 C6  C  0  1 Y N N N N N -7.032 4.776  10.174 3.156  -0.028 -0.492 C03 Y5T 7  
Y5T C04 C7  C  0  1 Y N N N N N -5.851 4.316  10.750 2.385  0.941  0.149  C04 Y5T 8  
Y5T C06 C8  C  0  1 N N N N N N -6.831 3.551  12.927 0.398  -0.359 0.193  C06 Y5T 9  
Y5T C08 C9  C  0  1 Y N N N N N -6.473 2.775  14.165 -1.073 -0.460 0.097  C08 Y5T 10 
Y5T C09 C10 C  0  1 Y N N N N N -5.397 1.922  14.163 -1.849 0.695  -0.021 C09 Y5T 11 
Y5T C14 C11 C  0  1 Y N N N N N -5.739 1.403  16.493 -3.831 -0.649 -0.085 C14 Y5T 12 
Y5T C18 C12 C  0  1 Y N N N N N -4.655 4.476  10.062 3.041  2.003  0.769  C18 Y5T 13 
Y5T C19 C13 C  0  1 Y N N N N N -4.679 5.065  8.830  4.419  2.057  0.726  C19 Y5T 14 
Y5T N05 N2  N  0  1 N N N N N N -5.828 3.710  12.031 0.994  0.849  0.169  N05 Y5T 15 
Y5T N11 N3  N  1  1 N N N N N N -3.944 0.289  15.265 -4.045 1.818  -0.229 N11 Y5T 16 
Y5T O07 O1  O  0  1 N N N N N N -7.978 3.936  12.741 1.071  -1.367 0.295  O07 Y5T 17 
Y5T O12 O2  O  -1 1 N N N N N N -3.655 -0.317 16.287 -5.258 1.731  -0.304 O12 Y5T 18 
Y5T O13 O3  O  0  1 N N N N N N -3.356 0.141  14.205 -3.511 2.912  -0.252 O13 Y5T 19 
Y5T CL1 CL1 CL 0  0 N Y N N N N -8.218 4.351  15.652 -0.739 -3.154 0.268  CL1 Y5T 20 
Y5T H1  H1  H  0  1 N N N N N N -7.351 2.447  17.433 -3.551 -2.764 0.050  H1  Y5T 21 
Y5T H2  H2  H  0  1 N N N N N N -7.931 6.287  7.257  5.626  -1.732 -0.471 H2  Y5T 22 
Y5T H3  H3  H  0  1 N N N N N N -8.911 5.031  8.087  4.818  -1.366 -2.015 H3  Y5T 23 
Y5T H4  H4  H  0  1 N N N N N N -8.677 6.638  8.853  6.290  -0.480 -1.548 H4  Y5T 24 
Y5T H5  H5  H  0  1 N N N N N N -7.973 4.683  10.695 2.685  -0.866 -0.984 H5  Y5T 25 
Y5T H6  H6  H  0  1 N N N N N N -4.811 1.793  13.265 -1.375 1.665  -0.041 H6  Y5T 26 
Y5T H7  H7  H  0  1 N N N N N N -5.449 0.860  17.380 -4.906 -0.721 -0.156 H7  Y5T 27 
Y5T H8  H8  H  0  1 N N N N N N -3.723 4.141  10.493 2.478  2.773  1.276  H8  Y5T 28 
Y5T H9  H9  H  0  1 N N N N N N -3.749 5.185  8.295  4.936  2.876  1.204  H9  Y5T 29 
Y5T H10 H10 H  0  1 N N N N N N -4.941 3.346  12.315 0.455  1.656  0.165  H10 Y5T 30 
# 
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 
Y5T C01 C02 SING N N 1  
Y5T N20 C19 DOUB Y N 2  
Y5T N20 C02 SING Y N 3  
Y5T C19 C18 SING Y N 4  
Y5T C02 C03 DOUB Y N 5  
Y5T C18 C04 DOUB Y N 6  
Y5T C03 C04 SING Y N 7  
Y5T C04 N05 SING N N 8  
Y5T N05 C06 SING N N 9  
Y5T O07 C06 DOUB N N 10 
Y5T C06 C08 SING N N 11 
Y5T C09 C08 DOUB Y N 12 
Y5T C09 C10 SING Y N 13 
Y5T C08 C16 SING Y N 14 
Y5T O13 N11 DOUB N N 15 
Y5T N11 C10 SING N N 16 
Y5T N11 O12 SING N N 17 
Y5T C10 C14 DOUB Y N 18 
Y5T C16 C15 DOUB Y N 19 
Y5T C14 C15 SING Y N 20 
Y5T C16 CL1 SING N N 21 
Y5T C15 H1  SING N N 22 
Y5T C01 H2  SING N N 23 
Y5T C01 H3  SING N N 24 
Y5T C01 H4  SING N N 25 
Y5T C03 H5  SING N N 26 
Y5T C09 H6  SING N N 27 
Y5T C14 H7  SING N N 28 
Y5T C18 H8  SING N N 29 
Y5T C19 H9  SING N N 30 
Y5T N05 H10 SING N N 31 
# 
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 
Y5T SMILES           ACDLabs              12.01 "Cc1cc(NC(=O)c2cc(ccc2Cl)[N+]([O-])=O)ccn1"                                                             
Y5T InChI            InChI                1.06  "InChI=1S/C13H10ClN3O3/c1-8-6-9(4-5-15-8)16-13(18)11-7-10(17(19)20)2-3-12(11)14/h2-7H,1H3,(H,15,16,18)" 
Y5T InChIKey         InChI                1.06  SQONBECQQLGCLE-UHFFFAOYSA-N                                                                             
Y5T SMILES_CANONICAL CACTVS               3.385 "Cc1cc(NC(=O)c2cc(ccc2Cl)[N+]([O-])=O)ccn1"                                                             
Y5T SMILES           CACTVS               3.385 "Cc1cc(NC(=O)c2cc(ccc2Cl)[N+]([O-])=O)ccn1"                                                             
Y5T SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cc(ccn1)NC(=O)c2cc(ccc2Cl)[N+](=O)[O-]"                                                             
Y5T SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1cc(ccn1)NC(=O)c2cc(ccc2Cl)[N+](=O)[O-]"                                                             
# 
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 
Y5T "SYSTEMATIC NAME" ACDLabs              12.01 "2-chloro-N-(2-methylpyridin-4-yl)-5-nitrobenzamide"        
Y5T "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-chloranyl-~{N}-(2-methylpyridin-4-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 
Y5T "Create component" 2023-01-05 RCSB 
Y5T "Initial release"  2024-04-17 RCSB 
Y5T "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y5T 
_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               C16 
_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      ? 
# 
