data_5Y9L
#
_model_server_result.job_id            kruaL99MoUOsRrwBd1LWYg 
_model_server_result.datetime_utc      '2024-11-29 11:57:22' 
_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          5y9l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    5Y9L 
#
_exptl.entry_id    5Y9L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              501.963 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '3-[2-[(3Z,6R)-6-[(5-chloranyl-2-methoxy-phenyl)methyl]-3-(dimethylhydrazinylidene)-7-oxidanylidene-1,4-diazepan-1-yl]ethanoylamino]benzoic acid' 
_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            5Y9L 
_cell.length_a            58.895 
_cell.length_b            90.926 
_cell.length_c            92.03 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5Y9L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_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,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                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
disulf ? disulf1 A SG CYS 7 A CYS 22 1_555 A SG CYS 136 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? 
disulf ? disulf2 A SG CYS 26 A CYS 42 1_555 A SG CYS 42 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf3 A SG CYS 108 A CYS 129 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
disulf ? disulf4 A SG CYS 115 A CYS 136 1_555 A SG CYS 182 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? 
disulf ? disulf5 A SG CYS 147 A CYS 168 1_555 A SG CYS 161 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf6 A SG CYS 172 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
#
_chem_comp.formula           'C24 H28 Cl N5 O5' 
_chem_comp.formula_weight    501.963 
_chem_comp.id                8R3 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '3-[2-[(3Z,6R)-6-[(5-chloranyl-2-methoxy-phenyl)methyl]-3-(dimethylhydrazinylidene)-7-oxidanylidene-1,4-diazepan-1-yl]ethanoylamino]benzoic acid' 
_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
C8 C7 8R3 doub 1 n y 
C8 C9 8R3 sing 2 n y 
C7 C6 8R3 sing 3 n y 
C24 O23 8R3 sing 4 n n 
CL2 C9 8R3 sing 5 n n 
C9 C10 8R3 doub 6 n y 
C6 O23 8R3 sing 7 n n 
C6 C5 8R3 doub 8 n y 
C10 C5 8R3 sing 9 n y 
C5 C4 8R3 sing 10 n n 
C4 C3 8R3 sing 11 n n 
C63 N62 8R3 sing 12 n n 
C3 C11 8R3 sing 13 n n 
C3 C1 8R3 sing 14 n n 
C11 N12 8R3 sing 15 n n 
N12 C13 8R3 sing 16 n n 
N62 N14 8R3 sing 17 n n 
N62 C68 8R3 sing 18 n n 
C13 N14 8R3 doub 19 z n 
C13 C15 8R3 sing 20 n n 
C15 N16 8R3 sing 21 n n 
C1 N16 8R3 sing 22 n n 
C1 O2 8R3 doub 23 n n 
O33 C31 8R3 doub 24 n n 
N16 C17 8R3 sing 25 n n 
O30 C19 8R3 doub 26 n n 
C31 O32 8R3 sing 27 n n 
C31 C26 8R3 sing 28 n n 
C19 C17 8R3 sing 29 n n 
C19 N20 8R3 sing 30 n n 
C25 C26 8R3 doub 31 n y 
C25 C21 8R3 sing 32 n y 
C26 C27 8R3 sing 33 n y 
N20 C21 8R3 sing 34 n n 
C21 C29 8R3 doub 35 n y 
C27 C28 8R3 doub 36 n y 
C29 C28 8R3 sing 37 n y 
O32 H1 8R3 sing 38 n n 
C25 H2 8R3 sing 39 n n 
C27 H3 8R3 sing 40 n n 
C28 H4 8R3 sing 41 n n 
C29 H5 8R3 sing 42 n n 
N20 H6 8R3 sing 43 n n 
C17 H7 8R3 sing 44 n n 
C17 H8 8R3 sing 45 n n 
C15 H9 8R3 sing 46 n n 
C15 H10 8R3 sing 47 n n 
C68 H12 8R3 sing 48 n n 
C68 H13 8R3 sing 49 n n 
C68 H14 8R3 sing 50 n n 
C63 H15 8R3 sing 51 n n 
C63 H16 8R3 sing 52 n n 
C63 H17 8R3 sing 53 n n 
C11 H18 8R3 sing 54 n n 
C11 H19 8R3 sing 55 n n 
C3 H20 8R3 sing 56 n n 
C4 H21 8R3 sing 57 n n 
C4 H22 8R3 sing 58 n n 
C10 H23 8R3 sing 59 n n 
C24 H24 8R3 sing 60 n n 
C24 H25 8R3 sing 61 n n 
C24 H26 8R3 sing 62 n n 
C7 H27 8R3 sing 63 n n 
C8 H28 8R3 sing 64 n n 
N12 H30 8R3 sing 65 n n 
#
_atom_sites.entry_id                     5Y9L 
_atom_sites.fract_transf_matrix[1][1]    0.016979 
_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]    0.010998 
_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]    0.010866 
_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 8R3 A 1 301 301 8R3 ASB . 
C 3 CL A 1 302 1 CL CL . 
D 4 HOH A 1 401 13 HOH HOH . 
D 4 HOH A 2 402 10 HOH HOH . 
D 4 HOH A 3 403 6 HOH HOH . 
D 4 HOH A 4 404 14 HOH HOH . 
D 4 HOH A 5 405 40 HOH HOH . 
D 4 HOH A 6 406 43 HOH HOH . 
D 4 HOH A 7 407 2 HOH HOH . 
D 4 HOH A 8 408 49 HOH HOH . 
D 4 HOH A 9 409 16 HOH HOH . 
D 4 HOH A 10 410 22 HOH HOH . 
D 4 HOH A 11 411 33 HOH HOH . 
D 4 HOH A 12 412 12 HOH HOH . 
D 4 HOH A 13 413 4 HOH HOH . 
D 4 HOH A 14 414 11 HOH HOH . 
D 4 HOH A 15 415 32 HOH HOH . 
D 4 HOH A 16 416 26 HOH HOH . 
D 4 HOH A 17 417 8 HOH HOH . 
D 4 HOH A 18 418 9 HOH HOH . 
D 4 HOH A 19 419 24 HOH HOH . 
D 4 HOH A 20 420 23 HOH HOH . 
D 4 HOH A 21 421 42 HOH HOH . 
D 4 HOH A 22 422 7 HOH HOH . 
D 4 HOH A 23 423 5 HOH HOH . 
D 4 HOH A 24 424 30 HOH HOH . 
D 4 HOH A 25 425 29 HOH HOH . 
D 4 HOH A 26 426 18 HOH HOH . 
D 4 HOH A 27 427 38 HOH HOH . 
D 4 HOH A 28 428 21 HOH HOH . 
D 4 HOH A 29 429 25 HOH HOH . 
D 4 HOH A 30 430 31 HOH HOH . 
D 4 HOH A 31 431 35 HOH HOH . 
D 4 HOH A 32 432 20 HOH HOH . 
D 4 HOH A 33 433 19 HOH HOH . 
D 4 HOH A 34 434 47 HOH HOH . 
D 4 HOH A 35 435 41 HOH HOH . 
D 4 HOH A 36 436 34 HOH HOH . 
D 4 HOH A 37 437 27 HOH HOH . 
D 4 HOH A 38 438 36 HOH HOH . 
D 4 HOH A 39 439 63 HOH HOH . 
D 4 HOH A 40 440 57 HOH HOH . 
D 4 HOH A 41 441 62 HOH HOH . 
D 4 HOH A 42 442 3 HOH HOH . 
D 4 HOH A 43 443 44 HOH HOH . 
D 4 HOH A 44 444 46 HOH HOH . 
D 4 HOH A 45 445 48 HOH HOH . 
D 4 HOH A 46 446 50 HOH HOH . 
D 4 HOH A 47 447 28 HOH HOH . 
D 4 HOH A 48 448 66 HOH HOH . 
D 4 HOH A 49 449 65 HOH HOH . 
D 4 HOH A 50 450 15 HOH HOH . 
D 4 HOH A 51 451 64 HOH HOH . 
D 4 HOH A 52 452 61 HOH HOH . 
D 4 HOH A 53 453 56 HOH HOH . 
D 4 HOH A 54 454 55 HOH HOH . 
D 4 HOH A 55 455 1 HOH HOH . 
D 4 HOH A 56 456 59 HOH HOH . 
D 4 HOH A 57 457 39 HOH HOH . 
D 4 HOH A 58 458 67 HOH HOH . 
D 4 HOH A 59 459 51 HOH HOH . 
D 4 HOH A 60 460 58 HOH HOH . 
D 4 HOH A 61 461 60 HOH HOH . 
D 4 HOH A 62 462 45 HOH HOH . 
D 4 HOH A 63 463 37 HOH HOH . 
D 4 HOH A 64 464 53 HOH HOH . 
D 4 HOH A 65 465 54 HOH HOH . 
D 4 HOH A 66 466 17 HOH HOH . 
D 4 HOH A 67 467 52 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 8R3 . . . B 2 18.986 39.582 21.814 1 40.36 ? C1 8R3 301 A 1 
HETATM 2 O O2 8R3 . . . B 2 17.917 39.588 22.464 1 39.47 ? O2 8R3 301 A 1 
HETATM 3 O O32 8R3 . . . B 2 16.527 48.014 23.565 1 51.87 ? O32 8R3 301 A 1 
HETATM 4 C C31 8R3 . . . B 2 17.197 46.962 23.307 1 47.8 ? C31 8R3 301 A 1 
HETATM 5 O O33 8R3 . . . B 2 17.889 46.902 22.243 1 46.72 ? O33 8R3 301 A 1 
HETATM 6 C C26 8R3 . . . B 2 17.152 45.796 24.272 1 45.75 ? C26 8R3 301 A 1 
HETATM 7 C C25 8R3 . . . B 2 17.89 44.631 24.036 1 46.63 ? C25 8R3 301 A 1 
HETATM 8 C C27 8R3 . . . B 2 16.392 45.836 25.453 1 47.79 ? C27 8R3 301 A 1 
HETATM 9 C C28 8R3 . . . B 2 16.371 44.753 26.328 1 49.66 ? C28 8R3 301 A 1 
HETATM 10 C C29 8R3 . . . B 2 17.109 43.606 26.062 1 48.11 ? C29 8R3 301 A 1 
HETATM 11 C C21 8R3 . . . B 2 17.887 43.524 24.911 1 46.62 ? C21 8R3 301 A 1 
HETATM 12 N N20 8R3 . . . B 2 18.609 42.326 24.712 1 46.57 ? N20 8R3 301 A 1 
HETATM 13 C C19 8R3 . . . B 2 19.451 42.005 23.642 1 48.12 ? C19 8R3 301 A 1 
HETATM 14 O O30 8R3 . . . B 2 19.712 42.695 22.647 1 48.27 ? O30 8R3 301 A 1 
HETATM 15 C C17 8R3 . . . B 2 20.112 40.619 23.714 1 44.02 ? C17 8R3 301 A 1 
HETATM 16 N N16 8R3 . . . B 2 20.177 40.082 22.352 1 41.7 ? N16 8R3 301 A 1 
HETATM 17 C C15 8R3 . . . B 2 21.472 40.152 21.647 1 39.2 ? C15 8R3 301 A 1 
HETATM 18 C C13 8R3 . . . B 2 22.062 38.792 21.249 1 39.45 ? C13 8R3 301 A 1 
HETATM 19 N N14 8R3 . . . B 2 23.34 38.624 21.464 1 43.48 ? N14 8R3 301 A 1 
HETATM 20 N N62 8R3 . . . B 2 23.8 37.402 21.072 1 40.24 ? N62 8R3 301 A 1 
HETATM 21 C C68 8R3 . . . B 2 24.215 36.441 22.109 1 38.88 ? C68 8R3 301 A 1 
HETATM 22 C C63 8R3 . . . B 2 24.766 37.539 19.964 1 44.31 ? C63 8R3 301 A 1 
HETATM 23 N N12 8R3 . . . B 2 21.289 37.794 20.715 1 37.95 ? N12 8R3 301 A 1 
HETATM 24 C C11 8R3 . . . B 2 19.893 37.73 20.398 1 39.38 ? C11 8R3 301 A 1 
HETATM 25 C C3 8R3 . . . B 2 19.073 39.015 20.387 1 39.8 ? C3 8R3 301 A 1 
HETATM 26 C C4 8R3 . . . B 2 17.703 38.742 19.721 1 37.41 ? C4 8R3 301 A 1 
HETATM 27 C C5 8R3 . . . B 2 17.704 38 18.396 1 36.08 ? C5 8R3 301 A 1 
HETATM 28 C C10 8R3 . . . B 2 17.138 36.699 18.338 1 35.96 ? C10 8R3 301 A 1 
HETATM 29 C C6 8R3 . . . B 2 18.255 38.575 17.216 1 34.45 ? C6 8R3 301 A 1 
HETATM 30 O O23 8R3 . . . B 2 18.78 39.85 17.372 1 32.9 ? O23 8R3 301 A 1 
HETATM 31 C C24 8R3 . . . B 2 19.399 40.635 16.339 1 31.96 ? C24 8R3 301 A 1 
HETATM 32 C C7 8R3 . . . B 2 18.211 37.812 16.02 1 34.08 ? C7 8R3 301 A 1 
HETATM 33 C C8 8R3 . . . B 2 17.635 36.53 15.98 1 35.33 ? C8 8R3 301 A 1 
HETATM 34 C C9 8R3 . . . B 2 17.105 35.964 17.14 1 36.84 ? C9 8R3 301 A 1 
HETATM 35 CL CL2 8R3 . . . B 2 16.416 34.371 17.067 1 43.99 ? CL2 8R3 301 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           35 
#