data_6S9W # _model_server_result.job_id 1Asvt1d-3AcBTUWa9cnEpQ _model_server_result.datetime_utc '2025-02-05 14:10:25' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6s9w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6S9W # _exptl.entry_id 6S9W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 562.661 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ~{N}-[3-[1-[[4-(5-methyl-6-oxidanylidene-3-phenyl-1~{H}-pyrazin-2-yl)phenyl]methyl]piperidin-4-yl]-2-oxidanylidene-1~{H}-benzimidazol-5-yl]propanamide _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6S9W _cell.length_a 70.07 _cell.length_b 71.03 _cell.length_c 91.34 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6S9W _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 310 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 310 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id CBL _struct_conn.ptnr2_label_comp_id L1Z _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id L1Z _struct_conn.ptnr2_auth_seq_id 501 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.83 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C33 H34 N6 O3' _chem_comp.formula_weight 562.661 _chem_comp.id L1Z _chem_comp.mon_nstd_flag . _chem_comp.name ~{N}-[3-[1-[[4-(5-methyl-6-oxidanylidene-3-phenyl-1~{H}-pyrazin-2-yl)phenyl]methyl]piperidin-4-yl]-2-oxidanylidene-1~{H}-benzimidazol-5-yl]propanamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag CBO CAB L1Z sing 173 n n CAL CAM L1Z doub 174 n y CAL CAK L1Z sing 175 n y CAM CAG L1Z sing 176 n y CAB NAC L1Z doub 177 n n CAB CAA L1Z sing 178 n n NAC CAD L1Z sing 179 n n CAK CAJ L1Z doub 180 n y OBP CAA L1Z doub 181 n n CAA NAF L1Z sing 182 n n CAG CAD L1Z sing 183 n n CAG CAI L1Z doub 184 n y CAD CAE L1Z doub 185 n n NAF CAE L1Z sing 186 n n CAJ CAI L1Z sing 187 n y CAE CAH L1Z sing 188 n n CAR CAH L1Z doub 189 n y CAR CAQ L1Z sing 190 n y CAH CAN L1Z sing 191 n y CAQ CAP L1Z doub 192 n y CAN CAO L1Z doub 193 n y CAP CAO L1Z sing 194 n y CAP CAS L1Z sing 195 n n CAS NAT L1Z sing 196 n n CAU NAT L1Z sing 197 n n CAU CAV L1Z sing 198 n n NAT CAY L1Z sing 199 n n CAV CAW L1Z sing 200 n n CAY CAX L1Z sing 201 n n CAW CAX L1Z sing 202 n n CAW NAZ L1Z sing 203 n n NAZ CBA L1Z sing 204 n n NAZ CBD L1Z sing 205 n n OBN CBA L1Z doub 206 n n CBA NBB L1Z sing 207 n n CBH CBD L1Z doub 208 n y CBH CBG L1Z sing 209 n y CBD CBC L1Z sing 210 n y NBI CBG L1Z sing 211 n n NBI CBJ L1Z sing 212 n n CBG CBF L1Z doub 213 n y NBB CBC L1Z sing 214 n n CBC CBE L1Z doub 215 n y OBM CBJ L1Z doub 216 n n CBJ CBK L1Z sing 217 n n CBF CBE L1Z sing 218 n y CBK CBL L1Z sing 219 n n CAI H1 L1Z sing 220 n n CAJ H2 L1Z sing 221 n n CAK H3 L1Z sing 222 n n CAL H4 L1Z sing 223 n n CAM H5 L1Z sing 224 n n CAN H6 L1Z sing 225 n n CAO H7 L1Z sing 226 n n CAQ H8 L1Z sing 227 n n CAR H9 L1Z sing 228 n n CAS H10 L1Z sing 229 n n CAS H11 L1Z sing 230 n n CAU H12 L1Z sing 231 n n CAU H13 L1Z sing 232 n n CAV H14 L1Z sing 233 n n CAV H15 L1Z sing 234 n n CAW H16 L1Z sing 235 n n CAX H17 L1Z sing 236 n n CAX H18 L1Z sing 237 n n CAY H19 L1Z sing 238 n n CAY H20 L1Z sing 239 n n CBE H21 L1Z sing 240 n n CBF H22 L1Z sing 241 n n CBH H23 L1Z sing 242 n n CBK H24 L1Z sing 243 n n CBK H25 L1Z sing 244 n n CBL H26 L1Z sing 245 n n CBL H27 L1Z sing 246 n n CBL H28 L1Z sing 247 n n CBO H29 L1Z sing 248 n n CBO H30 L1Z sing 249 n n CBO H31 L1Z sing 250 n n NAF H32 L1Z sing 251 n n NBB H34 L1Z sing 252 n n NBI H35 L1Z sing 253 n n # _atom_sites.entry_id 6S9W _atom_sites.fract_transf_matrix[1][1] 0.014271 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014079 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.010948 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 L1Z A 1 501 501 L1Z DRG . C 3 HOH A 1 601 7 HOH HOH . C 3 HOH A 2 602 11 HOH HOH . C 3 HOH A 3 603 4 HOH HOH . C 3 HOH A 4 604 13 HOH HOH . C 3 HOH A 5 605 3 HOH HOH . C 3 HOH A 6 606 5 HOH HOH . C 3 HOH A 7 607 16 HOH HOH . C 3 HOH A 8 608 2 HOH HOH . C 3 HOH A 9 609 20 HOH HOH . C 3 HOH A 10 610 9 HOH HOH . C 3 HOH A 11 611 1 HOH HOH . C 3 HOH A 12 612 10 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C CAA L1Z . . . B 2 -17.734 -16.376 7.926 1 46.32 ? CAA L1Z 501 A 1 HETATM 2 C CAB L1Z . . . B 2 -18.135 -15.426 6.997 1 46.75 ? CAB L1Z 501 A 1 HETATM 3 C CAD L1Z . . . B 2 -16.847 -13.75 8.044 1 48.35 ? CAD L1Z 501 A 1 HETATM 4 C CAE L1Z . . . B 2 -16.403 -14.671 9.019 1 42.57 ? CAE L1Z 501 A 1 HETATM 5 C CAG L1Z . . . B 2 -16.485 -12.398 7.983 1 41.34 ? CAG L1Z 501 A 1 HETATM 6 C CAH L1Z . . . B 2 -15.527 -14.366 10.07 1 38.59 ? CAH L1Z 501 A 1 HETATM 7 C CAI L1Z . . . B 2 -16.659 -11.54 9.066 1 32.23 ? CAI L1Z 501 A 1 HETATM 8 C CAJ L1Z . . . B 2 -16.293 -10.2 8.963 1 36.29 ? CAJ L1Z 501 A 1 HETATM 9 C CAK L1Z . . . B 2 -15.77 -9.701 7.772 1 46.1 ? CAK L1Z 501 A 1 HETATM 10 C CAL L1Z . . . B 2 -15.611 -10.552 6.687 1 37.02 ? CAL L1Z 501 A 1 HETATM 11 C CAM L1Z . . . B 2 -15.975 -11.889 6.793 1 37.47 ? CAM L1Z 501 A 1 HETATM 12 C CAN L1Z . . . B 2 -15.831 -14.775 11.367 1 41.57 ? CAN L1Z 501 A 1 HETATM 13 C CAO L1Z . . . B 2 -14.962 -14.484 12.42 1 40.36 ? CAO L1Z 501 A 1 HETATM 14 C CAP L1Z . . . B 2 -13.772 -13.797 12.183 1 49.34 ? CAP L1Z 501 A 1 HETATM 15 C CAQ L1Z . . . B 2 -13.463 -13.402 10.89 1 30.27 ? CAQ L1Z 501 A 1 HETATM 16 C CAR L1Z . . . B 2 -14.328 -13.695 9.844 1 39.05 ? CAR L1Z 501 A 1 HETATM 17 C CAS L1Z . . . B 2 -12.885 -13.486 13.216 1 43.21 ? CAS L1Z 501 A 1 HETATM 18 C CAU L1Z . . . B 2 -11.845 -15.619 13.586 1 50.71 ? CAU L1Z 501 A 1 HETATM 19 C CAV L1Z . . . B 2 -11.664 -16.779 14.548 1 56.7 ? CAV L1Z 501 A 1 HETATM 20 C CAW L1Z . . . B 2 -11.084 -16.259 15.857 1 63.75 ? CAW L1Z 501 A 1 HETATM 21 C CAX L1Z . . . B 2 -11.983 -15.177 16.43 1 51.95 ? CAX L1Z 501 A 1 HETATM 22 C CAY L1Z . . . B 2 -12.132 -14.07 15.407 1 51.96 ? CAY L1Z 501 A 1 HETATM 23 C CBA L1Z . . . B 2 -11.672 -18.318 17.275 1 77.83 ? CBA L1Z 501 A 1 HETATM 24 C CBC L1Z . . . B 2 -9.79 -18.579 18.275 1 80.13 ? CBC L1Z 501 A 1 HETATM 25 C CBD L1Z . . . B 2 -9.7 -17.522 17.463 1 81.34 ? CBD L1Z 501 A 1 HETATM 26 C CBE L1Z . . . B 2 -8.741 -18.951 19.017 1 83.63 ? CBE L1Z 501 A 1 HETATM 27 C CBF L1Z . . . B 2 -7.53 -18.258 18.96 1 86.2 ? CBF L1Z 501 A 1 HETATM 28 C CBG L1Z . . . B 2 -7.445 -17.139 18.131 1 92.99 ? CBG L1Z 501 A 1 HETATM 29 C CBH L1Z . . . B 2 -8.57 -16.826 17.377 1 91.13 ? CBH L1Z 501 A 1 HETATM 30 C CBJ L1Z . . . B 2 -5.542 -15.78 18.845 1 97.66 ? CBJ L1Z 501 A 1 HETATM 31 C CBK L1Z . . . B 2 -5.75 -16.011 20.351 1 97.57 ? CBK L1Z 501 A 1 HETATM 32 C CBL L1Z . . . B 2 -4.371 -16.19 21.001 1 89.52 ? CBL L1Z 501 A 1 HETATM 33 C CBO L1Z . . . B 2 -19.005 -15.791 5.973 1 46.39 ? CBO L1Z 501 A 1 HETATM 34 N NAC L1Z . . . B 2 -17.686 -14.165 7.08 1 42.87 ? NAC L1Z 501 A 1 HETATM 35 N NAF L1Z . . . B 2 -16.862 -15.995 8.949 1 44.09 ? NAF L1Z 501 A 1 HETATM 36 N NAT L1Z . . . B 2 -12.729 -14.594 14.167 1 49.13 ? NAT L1Z 501 A 1 HETATM 37 N NAZ L1Z . . . B 2 -10.863 -17.357 16.837 1 77.1 ? NAZ L1Z 501 A 1 HETATM 38 N NBB L1Z . . . B 2 -11.024 -19.077 18.159 1 78.87 ? NBB L1Z 501 A 1 HETATM 39 N NBI L1Z . . . B 2 -6.357 -16.366 17.921 1 98.44 ? NBI L1Z 501 A 1 HETATM 40 O OBM L1Z . . . B 2 -4.604 -15.067 18.492 1 91.93 ? OBM L1Z 501 A 1 HETATM 41 O OBN L1Z . . . B 2 -12.841 -18.488 16.921 1 78.09 ? OBN L1Z 501 A 1 HETATM 42 O OBP L1Z . . . B 2 -18.138 -17.536 7.858 1 48.99 ? OBP L1Z 501 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 42 #