data_5W84
#
_model_server_result.job_id            xasZSfciUIUyL6sRtYoFfw 
_model_server_result.datetime_utc      '2024-12-27 08:59:47' 
_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          5w84 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":4000}' 
#
_entry.id    5W84 
#
_exptl.entry_id    5W84 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              373.408 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-(benzylamino)-6-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]pyridine-3-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            5W84 
_cell.length_a            88.19 
_cell.length_b            125.2 
_cell.length_c            141.68 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5W84 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 2 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 C TPO 187 A TPO 342 1_555 A N VAL 188 A VAL 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? 
covale ? covale2 A C MET 189 A MET 344 1_555 A N TPO 190 A TPO 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? 
covale ? covale3 A C TPO 190 A TPO 345 1_555 A N SEP 191 A SEP 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? 
covale ? covale4 A C SEP 191 A SEP 346 1_555 A N ARG 192 A ARG 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? 
covale ? covale5 B C TPO 187 B TPO 342 1_555 B N VAL 188 B VAL 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale6 B C MET 189 B MET 344 1_555 B N TPO 190 B TPO 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? 
covale ? covale7 B C TPO 190 B TPO 345 1_555 B N SEP 191 B SEP 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? 
covale ? covale8 B C SEP 191 B SEP 346 1_555 B N ARG 192 B ARG 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? 
#
_chem_comp.formula           'C21 H19 N5 O2' 
_chem_comp.formula_weight    373.408 
_chem_comp.id                9YY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-(benzylamino)-6-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]pyridine-3-carboxamide 
_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
N3 C2 9YY doub 1 n y 
N3 C4 9YY sing 2 n y 
C2 C1 9YY sing 3 n y 
N10 C9 9YY sing 4 n n 
N8 C4 9YY sing 5 n n 
N8 C19 9YY sing 6 n n 
C4 C5 9YY doub 7 n y 
C9 C1 9YY sing 8 n n 
C9 O11 9YY doub 9 n n 
C1 C6 9YY doub 10 n y 
C24 C19 9YY doub 11 n y 
C24 C23 9YY sing 12 n y 
C19 C20 9YY sing 13 n y 
C5 C6 9YY sing 14 n y 
C6 N7 9YY sing 15 n n 
C23 C22 9YY doub 16 n y 
C20 C21 9YY doub 17 n y 
N7 C12 9YY sing 18 n n 
C22 C21 9YY sing 19 n y 
C22 N27 9YY sing 20 n n 
C21 C25 9YY sing 21 n n 
C12 C13 9YY sing 22 n n 
N27 C26 9YY sing 23 n n 
C18 C13 9YY doub 24 n y 
C18 C17 9YY sing 25 n y 
C25 C26 9YY sing 26 n n 
C13 C14 9YY sing 27 n y 
C17 C16 9YY doub 28 n y 
C26 O28 9YY doub 29 n n 
C14 C15 9YY doub 30 n y 
C16 C15 9YY sing 31 n y 
C18 H1 9YY sing 32 n n 
C17 H2 9YY sing 33 n n 
C16 H3 9YY sing 34 n n 
C15 H4 9YY sing 35 n n 
C20 H5 9YY sing 36 n n 
C23 H6 9YY sing 37 n n 
C24 H7 9YY sing 38 n n 
C12 H8 9YY sing 39 n n 
C12 H9 9YY sing 40 n n 
C2 H10 9YY sing 41 n n 
C5 H11 9YY sing 42 n n 
N7 H12 9YY sing 43 n n 
N8 H13 9YY sing 44 n n 
N10 H14 9YY sing 45 n n 
N10 H15 9YY sing 46 n n 
C14 H16 9YY sing 47 n n 
C25 H17 9YY sing 48 n n 
C25 H18 9YY sing 49 n n 
N27 H19 9YY sing 50 n n 
#
_atom_sites.entry_id                     5W84 
_atom_sites.fract_transf_matrix[1][1]    0.011339 
_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]    0.007987 
_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]    0.007058 
_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 9YY A 1 4000 4000 9YY LG1 . 
D 2 9YY B 1 4000 4000 9YY LG1 . 
E 3 HOH A 1 4101 26 HOH HOH . 
E 3 HOH A 2 4102 10 HOH HOH . 
E 3 HOH A 3 4103 4 HOH HOH . 
E 3 HOH A 4 4104 7 HOH HOH . 
E 3 HOH A 5 4105 9 HOH HOH . 
E 3 HOH A 6 4106 25 HOH HOH . 
E 3 HOH A 7 4107 21 HOH HOH . 
E 3 HOH A 8 4108 27 HOH HOH . 
E 3 HOH A 9 4109 3 HOH HOH . 
E 3 HOH A 10 4110 6 HOH HOH . 
E 3 HOH A 11 4111 8 HOH HOH . 
E 3 HOH A 12 4112 11 HOH HOH . 
E 3 HOH A 13 4113 2 HOH HOH . 
E 3 HOH A 14 4114 15 HOH HOH . 
E 3 HOH A 15 4115 16 HOH HOH . 
E 3 HOH A 16 4116 22 HOH HOH . 
E 3 HOH A 17 4117 5 HOH HOH . 
E 3 HOH A 18 4118 17 HOH HOH . 
F 3 HOH B 1 4101 20 HOH HOH . 
F 3 HOH B 2 4102 1 HOH HOH . 
F 3 HOH B 3 4103 13 HOH HOH . 
F 3 HOH B 4 4104 14 HOH HOH . 
F 3 HOH B 5 4105 23 HOH HOH . 
F 3 HOH B 6 4106 12 HOH HOH . 
F 3 HOH B 7 4107 18 HOH HOH . 
F 3 HOH B 8 4108 19 HOH HOH . 
F 3 HOH B 9 4109 24 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 C13 9YY . . . D 2 -23.323 19.121 12.425 1 115.62 ? C13 9YY 4000 B 1 
HETATM 2 C C18 9YY . . . D 2 -22.469 18.055 12.171 1 117.34 ? C18 9YY 4000 B 1 
HETATM 3 C C17 9YY . . . D 2 -22.699 16.812 12.742 1 118.37 ? C17 9YY 4000 B 1 
HETATM 4 C C16 9YY . . . D 2 -23.786 16.621 13.575 1 118.98 ? C16 9YY 4000 B 1 
HETATM 5 C C15 9YY . . . D 2 -24.644 17.675 13.834 1 118.97 ? C15 9YY 4000 B 1 
HETATM 6 C C19 9YY . . . D 2 -27.511 19.353 9.242 1 103.04 ? C19 9YY 4000 B 1 
HETATM 7 C C20 9YY . . . D 2 -27.328 18.451 10.294 1 101.99 ? C20 9YY 4000 B 1 
HETATM 8 C C21 9YY . . . D 2 -28.275 18.374 11.306 1 103.63 ? C21 9YY 4000 B 1 
HETATM 9 C C22 9YY . . . D 2 -29.399 19.197 11.276 1 104.39 ? C22 9YY 4000 B 1 
HETATM 10 C C23 9YY . . . D 2 -29.59 20.107 10.241 1 102.97 ? C23 9YY 4000 B 1 
HETATM 11 C C24 9YY . . . D 2 -28.641 20.18 9.227 1 102.39 ? C24 9YY 4000 B 1 
HETATM 12 C C12 9YY . . . D 2 -23.078 20.479 11.819 1 111.69 ? C12 9YY 4000 B 1 
HETATM 13 C C1 9YY . . . D 2 -22.502 20.109 8.1 1 106.25 ? C1 9YY 4000 B 1 
HETATM 14 C C2 9YY . . . D 2 -23.29 19.859 6.974 1 107.33 ? C2 9YY 4000 B 1 
HETATM 15 N N3 9YY . . . D 2 -24.612 19.647 7.009 1 108.73 ? N3 9YY 4000 B 1 
HETATM 16 C C4 9YY . . . D 2 -25.216 19.673 8.204 1 108.1 ? C4 9YY 4000 B 1 
HETATM 17 C C5 9YY . . . D 2 -24.529 19.927 9.401 1 108.49 ? C5 9YY 4000 B 1 
HETATM 18 C C6 9YY . . . D 2 -23.144 20.155 9.358 1 108.34 ? C6 9YY 4000 B 1 
HETATM 19 N N7 9YY . . . D 2 -22.421 20.426 10.524 1 108.94 ? N7 9YY 4000 B 1 
HETATM 20 N N8 9YY . . . D 2 -26.575 19.415 8.182 1 105.33 ? N8 9YY 4000 B 1 
HETATM 21 C C9 9YY . . . D 2 -21.026 20.301 7.96 1 103.26 ? C9 9YY 4000 B 1 
HETATM 22 N N10 9YY . . . D 2 -20.574 20.806 6.82 1 102.39 ? N10 9YY 4000 B 1 
HETATM 23 O O11 9YY . . . D 2 -20.27 19.987 8.891 1 102.46 ? O11 9YY 4000 B 1 
HETATM 24 C C14 9YY . . . D 2 -24.413 18.917 13.262 1 117.66 ? C14 9YY 4000 B 1 
HETATM 25 C C25 9YY . . . D 2 -28.358 17.512 12.533 1 106.14 ? C25 9YY 4000 B 1 
HETATM 26 C C26 9YY . . . D 2 -29.658 17.933 13.169 1 106.69 ? C26 9YY 4000 B 1 
HETATM 27 N N27 9YY . . . D 2 -30.204 18.921 12.382 1 106.33 ? N27 9YY 4000 B 1 
HETATM 28 O O28 9YY . . . D 2 -30.154 17.479 14.201 1 105.14 ? O28 9YY 4000 B 1 
#
_model_server_stats.io_time_ms              67 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           233 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#