data_8J34 # _model_server_result.job_id Wn70ypQ9Ri8oRmiQlc6VsQ _model_server_result.datetime_utc '2025-06-30 17:43:09' _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 8j34 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8J34 # _exptl.entry_id 8J34 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 474.55 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide _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 90 _cell.angle_gamma 90 _cell.entry_id 8J34 _cell.length_a 57.902 _cell.length_b 91.33 _cell.length_c 118.135 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8J34 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 D 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 146 A CYS 148 1_555 C C34 V2M . A V2M 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.862 ? covale ? covale2 B SG CYS 146 B CYS 148 1_555 D C34 V2M . B V2M 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.858 ? # _chem_comp.formula 'C24 H34 N4 O6' _chem_comp.formula_weight 474.55 _chem_comp.id V2M _chem_comp.mon_nstd_flag . _chem_comp.name N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'N-[(2S)-1-({(2S)-4-hydroxy-3-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, bound form' # 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 O37 C36 V2M sing 358 n n C36 C34 V2M sing 359 n n O35 C34 V2M sing 360 n n C20 C18 V2M sing 361 n n C34 C24 V2M sing 362 n n O22 C21 V2M doub 363 n n C17 C18 V2M sing 364 n n C17 C15 V2M sing 365 n n C18 C19 V2M sing 366 n n C24 N23 V2M sing 367 n n C24 C26 V2M sing 368 n n C21 N23 V2M sing 369 n n C21 C15 V2M sing 370 n n C1 O2 V2M sing 371 n n C15 N14 V2M sing 372 n n C29 C30 V2M sing 373 n n C29 C27 V2M sing 374 n n O2 C3 V2M sing 375 n n N14 C12 V2M sing 376 n n C26 C27 V2M sing 377 n n C10 C11 V2M sing 378 n y C10 C9 V2M doub 379 n y C30 N31 V2M sing 380 n n C27 C32 V2M sing 381 n n C3 C11 V2M doub 382 n y C3 C4 V2M sing 383 n y C12 C9 V2M sing 384 n n C12 O13 V2M doub 385 n n C11 C7 V2M sing 386 n y C9 N8 V2M sing 387 n y C4 C5 V2M doub 388 n y N31 C32 V2M sing 389 n n C32 O33 V2M doub 390 n n C7 N8 V2M sing 391 n y C7 C6 V2M doub 392 n y C5 C6 V2M sing 393 n y C1 H1 V2M sing 394 n n C1 H2 V2M sing 395 n n C1 H3 V2M sing 396 n n C4 H4 V2M sing 397 n n C5 H5 V2M sing 398 n n C6 H6 V2M sing 399 n n N8 H7 V2M sing 400 n n C10 H8 V2M sing 401 n n N14 H9 V2M sing 402 n n C15 H10 V2M sing 403 n n C17 H11 V2M sing 404 n n C17 H12 V2M sing 405 n n C18 H13 V2M sing 406 n n C19 H14 V2M sing 407 n n C19 H15 V2M sing 408 n n C19 H16 V2M sing 409 n n C20 H17 V2M sing 410 n n C20 H18 V2M sing 411 n n C20 H19 V2M sing 412 n n N23 H20 V2M sing 413 n n C24 H21 V2M sing 414 n n C26 H22 V2M sing 415 n n C26 H23 V2M sing 416 n n C27 H24 V2M sing 417 n n C29 H25 V2M sing 418 n n C29 H26 V2M sing 419 n n C30 H27 V2M sing 420 n n C30 H28 V2M sing 421 n n N31 H29 V2M sing 422 n n C34 H30 V2M sing 423 n n O35 H31 V2M sing 424 n n C36 H32 V2M sing 425 n n C36 H33 V2M sing 426 n n O37 H34 V2M sing 427 n n # _atom_sites.entry_id 8J34 _atom_sites.fract_transf_matrix[1][1] 0.017271 _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] 0.010949 _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] 0.008465 _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 V2M A 1 401 401 V2M V2M . D 2 V2M B 1 401 401 V2M V2M . E 3 HOH A 1 501 7 HOH HOH . E 3 HOH A 2 502 20 HOH HOH . E 3 HOH A 3 503 53 HOH HOH . E 3 HOH A 4 504 58 HOH HOH . E 3 HOH A 5 505 61 HOH HOH . E 3 HOH A 6 506 40 HOH HOH . E 3 HOH A 7 507 19 HOH HOH . E 3 HOH A 8 508 35 HOH HOH . E 3 HOH A 9 509 62 HOH HOH . E 3 HOH A 10 510 30 HOH HOH . E 3 HOH A 11 511 26 HOH HOH . E 3 HOH A 12 512 5 HOH HOH . E 3 HOH A 13 513 17 HOH HOH . E 3 HOH A 14 514 24 HOH HOH . E 3 HOH A 15 515 18 HOH HOH . E 3 HOH A 16 516 34 HOH HOH . E 3 HOH A 17 517 6 HOH HOH . E 3 HOH A 18 518 44 HOH HOH . E 3 HOH A 19 519 23 HOH HOH . E 3 HOH A 20 520 1 HOH HOH . E 3 HOH A 21 521 4 HOH HOH . E 3 HOH A 22 522 33 HOH HOH . E 3 HOH A 23 523 57 HOH HOH . E 3 HOH A 24 524 11 HOH HOH . E 3 HOH A 25 525 9 HOH HOH . E 3 HOH A 26 526 63 HOH HOH . E 3 HOH A 27 527 38 HOH HOH . E 3 HOH A 28 528 55 HOH HOH . E 3 HOH A 29 529 31 HOH HOH . E 3 HOH A 30 530 22 HOH HOH . E 3 HOH A 31 531 52 HOH HOH . E 3 HOH A 32 532 27 HOH HOH . E 3 HOH A 33 533 14 HOH HOH . E 3 HOH A 34 534 42 HOH HOH . E 3 HOH A 35 535 25 HOH HOH . E 3 HOH A 36 536 36 HOH HOH . E 3 HOH A 37 537 49 HOH HOH . E 3 HOH A 38 538 43 HOH HOH . E 3 HOH A 39 539 47 HOH HOH . F 3 HOH B 1 501 45 HOH HOH . F 3 HOH B 2 502 48 HOH HOH . F 3 HOH B 3 503 56 HOH HOH . F 3 HOH B 4 504 51 HOH HOH . F 3 HOH B 5 505 39 HOH HOH . F 3 HOH B 6 506 29 HOH HOH . F 3 HOH B 7 507 65 HOH HOH . F 3 HOH B 8 508 13 HOH HOH . F 3 HOH B 9 509 8 HOH HOH . F 3 HOH B 10 510 59 HOH HOH . F 3 HOH B 11 511 2 HOH HOH . F 3 HOH B 12 512 3 HOH HOH . F 3 HOH B 13 513 41 HOH HOH . F 3 HOH B 14 514 16 HOH HOH . F 3 HOH B 15 515 50 HOH HOH . F 3 HOH B 16 516 46 HOH HOH . F 3 HOH B 17 517 37 HOH HOH . F 3 HOH B 18 518 21 HOH HOH . F 3 HOH B 19 519 32 HOH HOH . F 3 HOH B 20 520 12 HOH HOH . F 3 HOH B 21 521 15 HOH HOH . F 3 HOH B 22 522 10 HOH HOH . F 3 HOH B 23 523 28 HOH HOH . F 3 HOH B 24 524 54 HOH HOH . F 3 HOH B 25 525 60 HOH HOH . F 3 HOH B 26 526 64 HOH HOH . F 3 HOH B 27 527 66 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 C1 V2M . . . C 2 25.158 -9.804 8.905 1 34.68 ? C1 V2M 401 A 1 HETATM 2 O O2 V2M . . . C 2 25.137 -10.078 7.513 1 32.55 ? O2 V2M 401 A 1 HETATM 3 C C3 V2M . . . C 2 24.777 -9.064 6.676 1 34.2 ? C3 V2M 401 A 1 HETATM 4 C C4 V2M . . . C 2 24.736 -7.744 7.053 1 29.99 ? C4 V2M 401 A 1 HETATM 5 C C5 V2M . . . C 2 24.352 -6.758 6.136 1 33.02 ? C5 V2M 401 A 1 HETATM 6 C C6 V2M . . . C 2 24.002 -7.056 4.849 1 32.38 ? C6 V2M 401 A 1 HETATM 7 C C7 V2M . . . C 2 24.04 -8.392 4.467 1 32.25 ? C7 V2M 401 A 1 HETATM 8 N N8 V2M . . . C 2 23.742 -8.981 3.272 1 30.64 ? N8 V2M 401 A 1 HETATM 9 C C9 V2M . . . C 2 23.927 -10.338 3.381 1 29.17 ? C9 V2M 401 A 1 HETATM 10 C C10 V2M . . . C 2 24.345 -10.633 4.651 1 29.43 ? C10 V2M 401 A 1 HETATM 11 C C11 V2M . . . C 2 24.426 -9.409 5.364 1 30.74 ? C11 V2M 401 A 1 HETATM 12 C C12 V2M . . . C 2 23.665 -11.174 2.208 1 29.61 ? C12 V2M 401 A 1 HETATM 13 O O13 V2M . . . C 2 23.288 -10.682 1.148 1 29.52 ? O13 V2M 401 A 1 HETATM 14 N N14 V2M . . . C 2 23.871 -12.486 2.367 1 28.63 ? N14 V2M 401 A 1 HETATM 15 C C15 V2M . . . C 2 23.519 -13.438 1.33 1 26.13 ? C15 V2M 401 A 1 HETATM 16 C C17 V2M . . . C 2 24 -14.825 1.75 1 26.21 ? C17 V2M 401 A 1 HETATM 17 C C18 V2M . . . C 2 25.398 -14.871 2.362 1 28 ? C18 V2M 401 A 1 HETATM 18 C C19 V2M . . . C 2 25.651 -16.2 3.047 1 26.41 ? C19 V2M 401 A 1 HETATM 19 C C20 V2M . . . C 2 26.457 -14.599 1.307 1 27.31 ? C20 V2M 401 A 1 HETATM 20 C C21 V2M . . . C 2 22.011 -13.467 1.08 1 30.34 ? C21 V2M 401 A 1 HETATM 21 O O22 V2M . . . C 2 21.23 -13.4 2.019 1 29.44 ? O22 V2M 401 A 1 HETATM 22 N N23 V2M . . . C 2 21.599 -13.625 -0.18 1 25.16 ? N23 V2M 401 A 1 HETATM 23 C C24 V2M . . . C 2 20.312 -13.601 -0.762 1 28.82 ? C24 V2M 401 A 1 HETATM 24 C C26 V2M . . . C 2 19.917 -12.55 -1.588 1 27.26 ? C26 V2M 401 A 1 HETATM 25 C C27 V2M . . . C 2 19.779 -11.204 -0.898 1 31.06 ? C27 V2M 401 A 1 HETATM 26 C C29 V2M . . . C 2 18.657 -11.217 0.122 1 27.41 ? C29 V2M 401 A 1 HETATM 27 C C30 V2M . . . C 2 18.08 -9.82 0.08 1 29.1 ? C30 V2M 401 A 1 HETATM 28 N N31 V2M . . . C 2 18.441 -9.36 -1.252 1 30.6 ? N31 V2M 401 A 1 HETATM 29 C C32 V2M . . . C 2 19.391 -10.068 -1.821 1 29.31 ? C32 V2M 401 A 1 HETATM 30 O O33 V2M . . . C 2 19.922 -9.811 -2.878 1 24.96 ? O33 V2M 401 A 1 HETATM 31 C C34 V2M . . . C 2 20.245 -15.06 -1.593 1 30.97 ? C34 V2M 401 A 1 HETATM 32 O O35 V2M . . . C 2 18.928 -15.133 -1.804 1 27.48 ? O35 V2M 401 A 1 HETATM 33 C C36 V2M . . . C 2 20.689 -15.904 -0.687 1 28.41 ? C36 V2M 401 A 1 HETATM 34 O O37 V2M . . . C 2 20.885 -17.448 -0.972 1 28.81 ? O37 V2M 401 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 34 #