data_Y62 # _chem_comp.id Y62 _chem_comp.name "2-chloro-N-(5-cyanopyridin-2-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 Y62 _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 8FKG _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 Y62 C14 C1 C 0 1 Y N N N N N -4.585 4.696 9.997 -2.820 -1.817 -0.029 C14 Y62 1 Y62 C13 C2 C 0 1 Y N N N N N -4.716 5.313 8.772 -4.198 -1.787 0.030 C13 Y62 2 Y62 C12 C3 C 0 1 Y N N N N N -5.970 5.741 8.359 -4.838 -0.539 0.032 C12 Y62 3 Y62 C15 C4 C 0 1 N N N N N N -6.156 6.391 7.090 -6.266 -0.455 0.092 C15 Y62 4 Y62 C11 C5 C 0 1 Y N N N N N -7.050 5.535 9.220 -4.062 0.620 -0.025 C11 Y62 5 Y62 C01 C6 C 0 1 Y N N N N N -5.358 2.000 14.114 2.123 -0.738 -0.030 C01 Y62 6 Y62 C02 C7 C 0 1 Y N N N N N -5.002 1.330 15.264 3.501 -0.759 0.022 C02 Y62 7 Y62 C03 C8 C 0 1 Y N N N N N -5.577 1.603 16.482 4.213 0.426 0.074 C03 Y62 8 Y62 C04 C9 C 0 1 Y N N N N N -6.562 2.570 16.537 3.550 1.640 0.073 C04 Y62 9 Y62 C05 C10 C 0 1 Y N N N N N -6.939 3.238 15.381 2.170 1.676 0.021 C05 Y62 10 Y62 C06 C11 C 0 1 Y N N N N N -6.378 2.924 14.145 1.446 0.482 -0.031 C06 Y62 11 Y62 C07 C12 C 0 1 N N N N N N -6.736 3.674 12.895 -0.030 0.512 -0.087 C07 Y62 12 Y62 C09 C13 C 0 1 Y N N N N N -5.721 4.523 10.784 -2.115 -0.618 -0.083 C09 Y62 13 Y62 N08 N1 N 0 1 N N N N N N -5.695 3.901 12.042 -0.726 -0.641 -0.137 N08 Y62 14 Y62 N10 N2 N 0 1 Y N N N N N -6.935 4.941 10.403 -2.749 0.546 -0.079 N10 Y62 15 Y62 N16 N3 N 0 1 N N N N N N -6.303 6.912 6.085 -7.399 -0.388 0.139 N16 Y62 16 Y62 N18 N4 N 1 1 N N N N N N -3.955 0.309 15.190 4.220 -2.053 0.023 N18 Y62 17 Y62 O17 O1 O 0 1 N N N N N N -7.903 3.965 12.648 -0.617 1.577 -0.088 O17 Y62 18 Y62 O19 O2 O -1 1 N N N N N N -3.636 -0.270 16.218 3.595 -3.097 -0.022 O19 Y62 19 Y62 O20 O3 O 0 1 N N N N N N -3.452 0.076 14.101 5.437 -2.073 0.069 O20 Y62 20 Y62 H1 H1 H 0 1 N N N N N N -3.620 4.353 10.340 -2.294 -2.760 -0.028 H1 Y62 21 Y62 H2 H2 H 0 1 N N N N N N -3.853 5.462 8.140 -4.770 -2.702 0.072 H2 Y62 22 Y62 H3 H3 H 0 1 N N N N N N -8.027 5.875 8.909 -4.543 1.587 -0.024 H3 Y62 23 Y62 H4 H4 H 0 1 N N N N N N -4.837 1.801 13.189 1.569 -1.665 -0.074 H4 Y62 24 Y62 H5 H5 H 0 1 N N N N N N -5.267 1.076 17.372 5.292 0.403 0.115 H5 Y62 25 Y62 H6 H6 H 0 1 N N N N N N -7.037 2.805 17.478 4.112 2.561 0.114 H6 Y62 26 Y62 H8 H8 H 0 1 N N N N N N -4.799 3.584 12.353 -0.258 -1.487 -0.211 H8 Y62 27 Y62 CL1 CL1 CL 0 0 N Y N N N N -8.080 4.583 15.498 1.339 3.200 0.021 CL1 Y62 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 Y62 N16 C15 TRIP N N 1 Y62 C15 C12 SING N N 2 Y62 C12 C13 DOUB Y N 3 Y62 C12 C11 SING Y N 4 Y62 C13 C14 SING Y N 5 Y62 C11 N10 DOUB Y N 6 Y62 C14 C09 DOUB Y N 7 Y62 N10 C09 SING Y N 8 Y62 C09 N08 SING N N 9 Y62 N08 C07 SING N N 10 Y62 O17 C07 DOUB N N 11 Y62 C07 C06 SING N N 12 Y62 O20 N18 DOUB N N 13 Y62 C01 C06 DOUB Y N 14 Y62 C01 C02 SING Y N 15 Y62 C06 C05 SING Y N 16 Y62 N18 C02 SING N N 17 Y62 N18 O19 SING N N 18 Y62 C02 C03 DOUB Y N 19 Y62 C05 C04 DOUB Y N 20 Y62 C03 C04 SING Y N 21 Y62 C14 H1 SING N N 22 Y62 C13 H2 SING N N 23 Y62 C11 H3 SING N N 24 Y62 C01 H4 SING N N 25 Y62 C03 H5 SING N N 26 Y62 C04 H6 SING N N 27 Y62 N08 H8 SING N N 28 Y62 C05 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 Y62 SMILES ACDLabs 12.01 "O=C(Nc1ccc(cn1)C#N)c1cc(ccc1Cl)[N+]([O-])=O" Y62 InChI InChI 1.06 "InChI=1S/C13H7ClN4O3/c14-11-3-2-9(18(20)21)5-10(11)13(19)17-12-4-1-8(6-15)7-16-12/h1-5,7H,(H,16,17,19)" Y62 InChIKey InChI 1.06 WLQNMMZWQLFUOW-UHFFFAOYSA-N Y62 SMILES_CANONICAL CACTVS 3.385 "[O-][N+](=O)c1ccc(Cl)c(c1)C(=O)Nc2ccc(cn2)C#N" Y62 SMILES CACTVS 3.385 "[O-][N+](=O)c1ccc(Cl)c(c1)C(=O)Nc2ccc(cn2)C#N" Y62 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1[N+](=O)[O-])C(=O)Nc2ccc(cn2)C#N)Cl" Y62 SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1[N+](=O)[O-])C(=O)Nc2ccc(cn2)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 Y62 "SYSTEMATIC NAME" ACDLabs 12.01 "2-chloro-N-(5-cyanopyridin-2-yl)-5-nitrobenzamide" Y62 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-chloranyl-~{N}-(5-cyanopyridin-2-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 Y62 "Create component" 2023-01-05 RCSB Y62 "Initial release" 2024-04-17 RCSB Y62 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id Y62 _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 C05 _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 ? #