data_5DV8 # _model_server_result.job_id pscjh76AwZKWzzC-LZXH7g _model_server_result.datetime_utc '2025-07-03 05:15:25' _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 5dv8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5DV8 # _exptl.entry_id 5DV8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 593.672 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[2-({2-[({4-[(4-methylpiperazin-1-yl)methyl]benzoyl}amino)methyl]benzyl}oxy)phenyl]-3-nitrobenzamide _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 5DV8 _cell.length_a 55.27 _cell.length_b 131.296 _cell.length_c 51.968 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DV8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 3 _struct_asym.id C _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 95 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 285 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id CBI _struct_conn.ptnr2_label_comp_id T51 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id T51 _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 1.668 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C34 H35 N5 O5' _chem_comp.formula_weight 593.672 _chem_comp.id T51 _chem_comp.mon_nstd_flag . _chem_comp.name N-[2-({2-[({4-[(4-methylpiperazin-1-yl)methyl]benzoyl}amino)methyl]benzyl}oxy)phenyl]-3-nitrobenzamide _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 OAE NBS T51 sing 290 n n CAT CAP T51 doub 291 n y CAT CBM T51 sing 292 n y CAP CBI T51 sing 293 n y NBS CBM T51 sing 294 n n NBS OAD T51 doub 295 n n CBM CAU T51 doub 296 n y CBI CBP T51 doub 297 n y CAG CAH T51 doub 298 n y CAG CAK T51 sing 299 n y CAH CAL T51 sing 300 n y CAU CBP T51 sing 301 n y CBP CBG T51 sing 302 n n CAK CBK T51 doub 303 n y CBB CBH T51 sing 304 n n CBB NBR T51 sing 305 n n CBH CAM T51 doub 306 n y CBH CAN T51 sing 307 n y CAL CBL T51 doub 308 n y CAM CAR T51 sing 309 n y CAX NBR T51 sing 310 n n CAX CAV T51 sing 311 n n CAN CAS T51 doub 312 n y CAR CBJ T51 doub 313 n y CBK CBL T51 sing 314 n y CBK CAZ T51 sing 315 n n CBG OAC T51 doub 316 n n CBG NBD T51 sing 317 n n NBR CAY T51 sing 318 n n CAS CBJ T51 sing 319 n y CBJ CBF T51 sing 320 n n NBC CBF T51 sing 321 n n NBC CAZ T51 sing 322 n n CBL CBA T51 sing 323 n n NBD CBN T51 sing 324 n n CBF OAB T51 doub 325 n n CAV NBQ T51 sing 326 n n CAY CAW T51 sing 327 n n CAA NBQ T51 sing 328 n n OBE CBA T51 sing 329 n n OBE CBO T51 sing 330 n n NBQ CAW T51 sing 331 n n CBN CBO T51 doub 332 n y CBN CAO T51 sing 333 n y CBO CAQ T51 sing 334 n y CAO CAI T51 doub 335 n y CAQ CAJ T51 doub 336 n y CAI CAJ T51 sing 337 n y CAU H1 T51 sing 338 n n CAT H2 T51 sing 339 n n CAP H3 T51 sing 340 n n CBI H4 T51 sing 341 n n NBD H5 T51 sing 342 n n CAO H6 T51 sing 343 n n CAI H7 T51 sing 344 n n CAJ H8 T51 sing 345 n n CAQ H9 T51 sing 346 n n CBA H10 T51 sing 347 n n CBA H11 T51 sing 348 n n CAL H12 T51 sing 349 n n CAH H13 T51 sing 350 n n CAG H14 T51 sing 351 n n CAK H15 T51 sing 352 n n CAZ H16 T51 sing 353 n n CAZ H17 T51 sing 354 n n NBC H18 T51 sing 355 n n CAS H19 T51 sing 356 n n CAN H20 T51 sing 357 n n CAR H21 T51 sing 358 n n CAM H22 T51 sing 359 n n CBB H23 T51 sing 360 n n CBB H24 T51 sing 361 n n CAX H26 T51 sing 362 n n CAX H27 T51 sing 363 n n CAV H28 T51 sing 364 n n CAV H29 T51 sing 365 n n CAA H31 T51 sing 366 n n CAA H32 T51 sing 367 n n CAA H33 T51 sing 368 n n CAW H34 T51 sing 369 n n CAW H35 T51 sing 370 n n CAY H36 T51 sing 371 n n CAY H37 T51 sing 372 n n # _atom_sites.entry_id 5DV8 _atom_sites.fract_transf_matrix[1][1] 0.018093 _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] 0.007616 _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] 0.019243 _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 C 3 T51 A 1 501 501 T51 T51 . D 4 HOH A 1 601 611 HOH HOH . D 4 HOH A 2 602 621 HOH HOH . D 4 HOH A 3 603 633 HOH HOH . D 4 HOH A 4 604 624 HOH HOH . D 4 HOH A 5 605 606 HOH HOH . D 4 HOH A 6 606 620 HOH HOH . D 4 HOH A 7 607 607 HOH HOH . D 4 HOH A 8 608 630 HOH HOH . D 4 HOH A 9 609 634 HOH HOH . D 4 HOH A 10 610 635 HOH HOH . D 4 HOH A 11 611 612 HOH HOH . D 4 HOH A 12 612 605 HOH HOH . D 4 HOH A 13 613 617 HOH HOH . D 4 HOH A 14 614 636 HOH HOH . D 4 HOH A 15 615 618 HOH HOH . D 4 HOH A 16 616 608 HOH HOH . D 4 HOH A 17 617 622 HOH HOH . D 4 HOH A 18 618 628 HOH HOH . D 4 HOH A 19 619 603 HOH HOH . D 4 HOH A 20 620 602 HOH HOH . D 4 HOH A 21 621 609 HOH HOH . D 4 HOH A 22 622 639 HOH HOH . D 4 HOH A 23 623 627 HOH HOH . D 4 HOH A 24 624 614 HOH HOH . D 4 HOH A 25 625 613 HOH HOH . D 4 HOH A 26 626 631 HOH HOH . D 4 HOH A 27 627 629 HOH HOH . D 4 HOH A 28 628 604 HOH HOH . D 4 HOH A 29 629 610 HOH HOH . D 4 HOH A 30 630 626 HOH HOH . D 4 HOH A 31 631 619 HOH HOH . D 4 HOH A 32 632 615 HOH HOH . D 4 HOH A 33 633 632 HOH HOH . D 4 HOH A 34 634 616 HOH HOH . D 4 HOH A 35 635 638 HOH HOH . D 4 HOH A 36 636 625 HOH HOH . D 4 HOH A 37 637 623 HOH HOH . D 4 HOH A 38 638 637 HOH HOH . D 4 HOH A 39 639 601 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 O OAD T51 . . . C 3 -18.895 18.065 -26.055 1 72.94 ? OAD T51 501 A 1 HETATM 2 N NBS T51 . . . C 3 -19.201 19.059 -26.98 1 64.87 ? NBS T51 501 A 1 HETATM 3 O OAE T51 . . . C 3 -18.448 19.18 -28.144 1 73.99 ? OAE T51 501 A 1 HETATM 4 C CBM T51 . . . C 3 -20.265 19.936 -26.739 1 52.87 ? CBM T51 501 A 1 HETATM 5 C CAU T51 . . . C 3 -20.687 20.106 -25.463 1 52.7 ? CAU T51 501 A 1 HETATM 6 C CAT T51 . . . C 3 -20.834 20.6 -27.817 1 49.57 ? CAT T51 501 A 1 HETATM 7 C CAP T51 . . . C 3 -21.884 21.472 -27.601 1 49.43 ? CAP T51 501 A 1 HETATM 8 C CBI T51 . . . C 3 -22.323 21.645 -26.301 1 45.76 ? CBI T51 501 A 1 HETATM 9 C CBP T51 . . . C 3 -21.724 20.969 -25.241 1 50.42 ? CBP T51 501 A 1 HETATM 10 C CBG T51 . . . C 3 -22.097 21.055 -23.802 1 47.78 ? CBG T51 501 A 1 HETATM 11 O OAC T51 . . . C 3 -22.061 20.092 -23.142 1 50.06 ? OAC T51 501 A 1 HETATM 12 N NBD T51 . . . C 3 -22.423 22.119 -23.169 1 48.09 ? NBD T51 501 A 1 HETATM 13 C CBN T51 . . . C 3 -22.534 22.21 -21.824 1 46.06 ? CBN T51 501 A 1 HETATM 14 C CAO T51 . . . C 3 -22.019 21.316 -20.852 1 45.14 ? CAO T51 501 A 1 HETATM 15 C CAI T51 . . . C 3 -22.189 21.625 -19.52 1 42.67 ? CAI T51 501 A 1 HETATM 16 C CAJ T51 . . . C 3 -22.843 22.812 -19.144 1 42.89 ? CAJ T51 501 A 1 HETATM 17 C CAQ T51 . . . C 3 -23.34 23.691 -20.091 1 46.44 ? CAQ T51 501 A 1 HETATM 18 C CBO T51 . . . C 3 -23.169 23.392 -21.431 1 48.35 ? CBO T51 501 A 1 HETATM 19 O OBE T51 . . . C 3 -23.642 24.25 -22.413 1 53.21 ? OBE T51 501 A 1 HETATM 20 C CBA T51 . . . C 3 -24.911 24.962 -22.243 1 50.86 ? CBA T51 501 A 1 HETATM 21 C CBL T51 . . . C 3 -25.193 25.667 -23.541 1 47.82 ? CBL T51 501 A 1 HETATM 22 C CAL T51 . . . C 3 -26.111 25.119 -24.428 1 46.78 ? CAL T51 501 A 1 HETATM 23 C CAH T51 . . . C 3 -26.369 25.749 -25.645 1 44.63 ? CAH T51 501 A 1 HETATM 24 C CAG T51 . . . C 3 -25.702 26.941 -25.963 1 43 ? CAG T51 501 A 1 HETATM 25 C CAK T51 . . . C 3 -24.781 27.484 -25.071 1 42.14 ? CAK T51 501 A 1 HETATM 26 C CBK T51 . . . C 3 -24.523 26.843 -23.864 1 46.43 ? CBK T51 501 A 1 HETATM 27 C CAZ T51 . . . C 3 -23.535 27.402 -22.875 1 45.18 ? CAZ T51 501 A 1 HETATM 28 N NBC T51 . . . C 3 -22.701 28.44 -23.422 1 47.9 ? NBC T51 501 A 1 HETATM 29 C CBF T51 . . . C 3 -22.871 29.724 -23.121 1 51.82 ? CBF T51 501 A 1 HETATM 30 O OAB T51 . . . C 3 -23.744 30.089 -22.363 1 54.14 ? OAB T51 501 A 1 HETATM 31 C CBJ T51 . . . C 3 -21.933 30.781 -23.615 1 56.55 ? CBJ T51 501 A 1 HETATM 32 C CAS T51 . . . C 3 -22.324 32.115 -23.644 1 60.37 ? CAS T51 501 A 1 HETATM 33 C CAN T51 . . . C 3 -21.421 33.092 -24.052 1 63.72 ? CAN T51 501 A 1 HETATM 34 C CAR T51 . . . C 3 -20.612 30.446 -23.936 1 60.81 ? CAR T51 501 A 1 HETATM 35 C CAM T51 . . . C 3 -19.717 31.421 -24.343 1 63.81 ? CAM T51 501 A 1 HETATM 36 C CBH T51 . . . C 3 -20.13 32.742 -24.406 1 69.19 ? CBH T51 501 A 1 HETATM 37 C CBB T51 . . . C 3 -19.141 33.789 -24.83 1 79.06 ? CBB T51 501 A 1 HETATM 38 N NBR T51 . . . C 3 -18.251 34.113 -23.723 1 91.21 ? NBR T51 501 A 1 HETATM 39 C CAX T51 . . . C 3 -17.011 34.767 -24.161 1 94.57 ? CAX T51 501 A 1 HETATM 40 C CAV T51 . . . C 3 -16.105 35.076 -22.967 1 96.6 ? CAV T51 501 A 1 HETATM 41 N NBQ T51 . . . C 3 -16.754 36.004 -22.017 1 96.72 ? NBQ T51 501 A 1 HETATM 42 C CAA T51 . . . C 3 -16.786 37.386 -22.563 1 92.34 ? CAA T51 501 A 1 HETATM 43 C CAW T51 . . . C 3 -18.112 35.523 -21.652 1 92.09 ? CAW T51 501 A 1 HETATM 44 C CAY T51 . . . C 3 -18.955 35.078 -22.853 1 92.63 ? CAY T51 501 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #