data_8AJ0 # _model_server_result.job_id l8xtXWojv5sThLr3NNMtTQ _model_server_result.datetime_utc '2025-01-28 02:38:51' _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 8aj0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8AJ0 # _exptl.entry_id 8AJ0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 551.634 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R,3S)-3-[[(2S)-3-cyclopropyl-2-[2-oxidanylidene-3-(3-phenylpropanoylamino)pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.38 _cell.angle_gamma 90 _cell.entry_id 8AJ0 _cell.length_a 45.253 _cell.length_b 54.376 _cell.length_c 114.192 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AJ0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,E,F,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order covale ? covale1 A SG CYS 145 AAA CYS 145 1_555 C C12 MJ0 . AAA MJ0 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.767 ? covale ? covale2 B SG CYS 145 BBB CYS 145 1_555 F C12 MJ0 . BBB MJ0 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.808 ? metalc ? metalc1 A OG SER 284 AAA SER 284 1_555 E NA NA . AAA NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.049 ? # _chem_comp.formula 'C29 H37 N5 O6' _chem_comp.formula_weight 551.634 _chem_comp.id MJ0 _chem_comp.mon_nstd_flag . _chem_comp.name (2R,3S)-3-[[(2S)-3-cyclopropyl-2-[2-oxidanylidene-3-(3-phenylpropanoylamino)pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(S)-3-((S)-3-cyclopropyl-2-(2-oxo-3-(3-phenylpropanamido)pyridin-1(2H)-yl)propanamido)-N-methyl-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide;RK-90 inhibitor (covalently bound to protein)' # 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 C22 C23 MJ0 sing 237 n n C22 C21 MJ0 sing 238 n n C23 C21 MJ0 sing 239 n n C26 C27 MJ0 doub 240 n y C26 C25 MJ0 sing 241 n y C21 C20 MJ0 sing 242 n n C27 C28 MJ0 sing 243 n y C25 C24 MJ0 doub 244 n y C28 C29 MJ0 doub 245 n y C20 C9 MJ0 sing 246 n n C24 C29 MJ0 sing 247 n y C24 C8 MJ0 sing 248 n n C1 C5 MJ0 doub 249 n n C1 C2 MJ0 sing 250 n n C5 N1 MJ0 sing 251 n n C2 C3 MJ0 doub 252 n n N1 C9 MJ0 sing 253 n n N1 C4 MJ0 sing 254 n n C9 C10 MJ0 sing 255 n n C8 C7 MJ0 sing 256 n n C3 C4 MJ0 sing 257 n n C3 N2 MJ0 sing 258 n n C4 O3 MJ0 doub 259 n n N2 C6 MJ0 sing 260 n n C6 O2 MJ0 doub 261 n n C6 C7 MJ0 sing 262 n n C10 N3 MJ0 sing 263 n n C10 O4 MJ0 doub 264 n n N3 C11 MJ0 sing 265 n n O1 C12 MJ0 sing 266 n n C12 C11 MJ0 sing 267 n n C12 C18 MJ0 sing 268 n n C11 C13 MJ0 sing 269 n n C19 N5 MJ0 sing 270 n n C14 C13 MJ0 sing 271 n n C14 C15 MJ0 sing 272 n n C14 C17 MJ0 sing 273 n n O5 C17 MJ0 doub 274 n n C18 N5 MJ0 sing 275 n n C18 O6 MJ0 doub 276 n n C15 C16 MJ0 sing 277 n n C17 N4 MJ0 sing 278 n n N4 C16 MJ0 sing 279 n n N3 H1 MJ0 sing 280 n n C5 H2 MJ0 sing 281 n n C7 H3 MJ0 sing 282 n n C7 H4 MJ0 sing 283 n n C8 H5 MJ0 sing 284 n n C8 H6 MJ0 sing 285 n n C13 H7 MJ0 sing 286 n n C13 H8 MJ0 sing 287 n n C15 H9 MJ0 sing 288 n n C15 H10 MJ0 sing 289 n n C20 H11 MJ0 sing 290 n n C20 H12 MJ0 sing 291 n n C21 H13 MJ0 sing 292 n n C22 H14 MJ0 sing 293 n n C22 H15 MJ0 sing 294 n n C26 H16 MJ0 sing 295 n n C28 H17 MJ0 sing 296 n n C1 H18 MJ0 sing 297 n n C2 H19 MJ0 sing 298 n n N2 H20 MJ0 sing 299 n n C9 H21 MJ0 sing 300 n n C11 H22 MJ0 sing 301 n n C12 H23 MJ0 sing 302 n n C14 H24 MJ0 sing 303 n n C16 H25 MJ0 sing 304 n n C16 H26 MJ0 sing 305 n n N4 H27 MJ0 sing 306 n n O1 H28 MJ0 sing 307 n n N5 H29 MJ0 sing 308 n n C19 H30 MJ0 sing 309 n n C19 H31 MJ0 sing 310 n n C19 H32 MJ0 sing 311 n n C23 H33 MJ0 sing 312 n n C23 H34 MJ0 sing 313 n n C25 H35 MJ0 sing 314 n n C27 H36 MJ0 sing 315 n n C29 H37 MJ0 sing 316 n n # _atom_sites.entry_id 8AJ0 _atom_sites.fract_transf_matrix[1][1] 0.022098 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004448 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01839 _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] 0.008933 _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 2 MJ0 AAA 1 401 401 MJ0 LIG . D 3 CL AAA 1 402 1 CL CL . E 4 NA AAA 1 403 1 NA NA . F 2 MJ0 BBB 1 401 401 MJ0 LIG . G 5 HOH AAA 1 501 96 HOH HOH . G 5 HOH AAA 2 502 74 HOH HOH . G 5 HOH AAA 3 503 64 HOH HOH . G 5 HOH AAA 4 504 65 HOH HOH . G 5 HOH AAA 5 505 10 HOH HOH . G 5 HOH AAA 6 506 89 HOH HOH . G 5 HOH AAA 7 507 84 HOH HOH . G 5 HOH AAA 8 508 33 HOH HOH . G 5 HOH AAA 9 509 85 HOH HOH . G 5 HOH AAA 10 510 95 HOH HOH . G 5 HOH AAA 11 511 73 HOH HOH . G 5 HOH AAA 12 512 4 HOH HOH . G 5 HOH AAA 13 513 78 HOH HOH . G 5 HOH AAA 14 514 87 HOH HOH . G 5 HOH AAA 15 515 22 HOH HOH . G 5 HOH AAA 16 516 6 HOH HOH . G 5 HOH AAA 17 517 26 HOH HOH . G 5 HOH AAA 18 518 11 HOH HOH . G 5 HOH AAA 19 519 82 HOH HOH . G 5 HOH AAA 20 520 14 HOH HOH . G 5 HOH AAA 21 521 15 HOH HOH . G 5 HOH AAA 22 522 77 HOH HOH . G 5 HOH AAA 23 523 8 HOH HOH . G 5 HOH AAA 24 524 79 HOH HOH . G 5 HOH AAA 25 525 25 HOH HOH . G 5 HOH AAA 26 526 63 HOH HOH . G 5 HOH AAA 27 527 37 HOH HOH . G 5 HOH AAA 28 528 24 HOH HOH . G 5 HOH AAA 29 529 38 HOH HOH . G 5 HOH AAA 30 530 34 HOH HOH . G 5 HOH AAA 31 531 36 HOH HOH . G 5 HOH AAA 32 532 80 HOH HOH . G 5 HOH AAA 33 533 2 HOH HOH . G 5 HOH AAA 34 534 90 HOH HOH . G 5 HOH AAA 35 535 29 HOH HOH . H 5 HOH BBB 1 501 47 HOH HOH . H 5 HOH BBB 2 502 7 HOH HOH . H 5 HOH BBB 3 503 72 HOH HOH . H 5 HOH BBB 4 504 1 HOH HOH . H 5 HOH BBB 5 505 94 HOH HOH . H 5 HOH BBB 6 506 20 HOH HOH . H 5 HOH BBB 7 507 44 HOH HOH . H 5 HOH BBB 8 508 61 HOH HOH . H 5 HOH BBB 9 509 69 HOH HOH . H 5 HOH BBB 10 510 57 HOH HOH . H 5 HOH BBB 11 511 54 HOH HOH . H 5 HOH BBB 12 512 46 HOH HOH . H 5 HOH BBB 13 513 93 HOH HOH . H 5 HOH BBB 14 514 92 HOH HOH . H 5 HOH BBB 15 515 13 HOH HOH . H 5 HOH BBB 16 516 12 HOH HOH . H 5 HOH BBB 17 517 51 HOH HOH . H 5 HOH BBB 18 518 55 HOH HOH . H 5 HOH BBB 19 519 9 HOH HOH . H 5 HOH BBB 20 520 68 HOH HOH . H 5 HOH BBB 21 521 83 HOH HOH . H 5 HOH BBB 22 522 81 HOH HOH . H 5 HOH BBB 23 523 75 HOH HOH . H 5 HOH BBB 24 524 56 HOH HOH . H 5 HOH BBB 25 525 71 HOH HOH . H 5 HOH BBB 26 526 66 HOH HOH . H 5 HOH BBB 27 527 43 HOH HOH . H 5 HOH BBB 28 528 45 HOH HOH . H 5 HOH BBB 29 529 5 HOH HOH . H 5 HOH BBB 30 530 30 HOH HOH . H 5 HOH BBB 31 531 70 HOH HOH . H 5 HOH BBB 32 532 86 HOH HOH . H 5 HOH BBB 33 533 67 HOH HOH . H 5 HOH BBB 34 534 53 HOH HOH . H 5 HOH BBB 35 535 91 HOH HOH . H 5 HOH BBB 36 536 59 HOH HOH . H 5 HOH BBB 37 537 60 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 N N1 MJ0 . . . C 2 -3.094 -0.401 12.738 1 29.04 0 N1 MJ0 401 AAA 1 HETATM 2 N N3 MJ0 . . . C 2 -1.115 1.803 14.78 1 27.63 0 N3 MJ0 401 AAA 1 HETATM 3 C C4 MJ0 . . . C 2 -2.589 -1.652 13.105 1 26.35 0 C4 MJ0 401 AAA 1 HETATM 4 C C5 MJ0 . . . C 2 -4.402 -0.225 12.374 1 28.54 0 C5 MJ0 401 AAA 1 HETATM 5 C C6 MJ0 . . . C 2 -3.709 -5.01 13.836 1 28.15 0 C6 MJ0 401 AAA 1 HETATM 6 C C7 MJ0 . . . C 2 -2.953 -6.29 14.111 1 28.22 0 C7 MJ0 401 AAA 1 HETATM 7 C C8 MJ0 . . . C 2 -2.521 -7.01 12.85 1 29.31 0 C8 MJ0 401 AAA 1 HETATM 8 C C10 MJ0 . . . C 2 -2.214 1.23 14.273 1 28.8 0 C10 MJ0 401 AAA 1 HETATM 9 C C13 MJ0 . . . C 2 -0.061 1.569 16.973 1 27.14 0 C13 MJ0 401 AAA 1 HETATM 10 C C15 MJ0 . . . C 2 -1.61 -0.429 17.47 1 31.42 0 C15 MJ0 401 AAA 1 HETATM 11 C C17 MJ0 . . . C 2 0.754 -0.797 17.517 1 31.92 0 C17 MJ0 401 AAA 1 HETATM 12 C C20 MJ0 . . . C 2 -2.523 1.872 11.807 1 29.34 0 C20 MJ0 401 AAA 1 HETATM 13 C C21 MJ0 . . . C 2 -2.313 1.448 10.366 1 32.95 0 C21 MJ0 401 AAA 1 HETATM 14 C C22 MJ0 . . . C 2 -2.539 2.399 9.225 1 31.31 0 C22 MJ0 401 AAA 1 HETATM 15 C C24 MJ0 . . . C 2 -3.658 -7.554 12.017 1 32.83 0 C24 MJ0 401 AAA 1 HETATM 16 C C26 MJ0 . . . C 2 -5.373 -7.241 10.346 1 31.19 0 C26 MJ0 401 AAA 1 HETATM 17 C C28 MJ0 . . . C 2 -5.125 -9.367 11.394 1 34.06 0 C28 MJ0 401 AAA 1 HETATM 18 C C1 MJ0 . . . C 2 -5.258 -1.259 12.307 1 26.8 0 C1 MJ0 401 AAA 1 HETATM 19 C C2 MJ0 . . . C 2 -4.801 -2.528 12.625 1 26.9 0 C2 MJ0 401 AAA 1 HETATM 20 C C3 MJ0 . . . C 2 -3.477 -2.703 13.037 1 25.56 0 C3 MJ0 401 AAA 1 HETATM 21 N N2 MJ0 . . . C 2 -2.976 -3.969 13.398 1 26.63 0 N2 MJ0 401 AAA 1 HETATM 22 C C9 MJ0 . . . C 2 -2.196 0.763 12.82 1 28.56 0 C9 MJ0 401 AAA 1 HETATM 23 C C11 MJ0 . . . C 2 -1.061 2.349 16.124 1 28.98 0 C11 MJ0 401 AAA 1 HETATM 24 C C12 MJ0 . . . C 2 -0.787 3.864 16.052 1 30.59 0 C12 MJ0 401 AAA 1 HETATM 25 C C14 MJ0 . . . C 2 -0.313 0.076 16.886 1 30.17 0 C14 MJ0 401 AAA 1 HETATM 26 C C16 MJ0 . . . C 2 -1.216 -1.331 18.625 1 32.69 0 C16 MJ0 401 AAA 1 HETATM 27 N N4 MJ0 . . . C 2 0.221 -1.514 18.466 1 32.3 0 N4 MJ0 401 AAA 1 HETATM 28 O O1 MJ0 . . . C 2 -1.54 4.547 15.055 1 29.03 0 O1 MJ0 401 AAA 1 HETATM 29 C C18 MJ0 . . . C 2 -0.958 4.503 17.413 1 30.16 0 C18 MJ0 401 AAA 1 HETATM 30 N N5 MJ0 . . . C 2 -1.865 5.451 17.58 1 38.16 0 N5 MJ0 401 AAA 1 HETATM 31 C C19 MJ0 . . . C 2 -3.103 5.561 16.826 1 43.21 0 C19 MJ0 401 AAA 1 HETATM 32 C C23 MJ0 . . . C 2 -1.155 1.973 9.569 1 32.41 0 C23 MJ0 401 AAA 1 HETATM 33 O O2 MJ0 . . . C 2 -4.917 -4.937 13.949 1 29.89 0 O2 MJ0 401 AAA 1 HETATM 34 O O3 MJ0 . . . C 2 -1.415 -1.744 13.431 1 25.51 0 O3 MJ0 401 AAA 1 HETATM 35 O O4 MJ0 . . . C 2 -3.211 1.018 14.958 1 29.3 0 O4 MJ0 401 AAA 1 HETATM 36 O O5 MJ0 . . . C 2 1.949 -0.841 17.17 1 34.01 0 O5 MJ0 401 AAA 1 HETATM 37 O O6 MJ0 . . . C 2 -0.17 4.157 18.292 1 30.99 0 O6 MJ0 401 AAA 1 HETATM 38 C C25 MJ0 . . . C 2 -4.321 -6.748 11.101 1 33.29 0 C25 MJ0 401 AAA 1 HETATM 39 C C27 MJ0 . . . C 2 -5.774 -8.546 10.495 1 33.45 0 C27 MJ0 401 AAA 1 HETATM 40 C C29 MJ0 . . . C 2 -4.069 -8.876 12.147 1 35.64 0 C29 MJ0 401 AAA 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 40 #