data_5HXB
#
_model_server_result.job_id            Tp-dAvEGes9nJxSaBMa6gw 
_model_server_result.datetime_utc      '2024-11-14 21:57:40' 
_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          5hxb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":502}' 
#
_entry.id    5HXB 
#
_exptl.entry_id    5HXB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              440.88 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea 
_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          95.81 
_cell.angle_gamma         90 
_cell.entry_id            5HXB 
_cell.length_a            156.747 
_cell.length_b            111.522 
_cell.length_c            175.057 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5HXB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        3 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? trimeric 3 author_defined_assembly 1 
? trimeric 3 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,B,C,G,H 1 1 
D,E,F,I,J 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
? 5 H N N 
? 5 J 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
disulf ? disulf1 A SG CYS 84 X CYS 519 1_555 A SG CYS 90 X CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
disulf ? disulf2 B SG CYS 18 Y CYS 18 1_555 B SG CYS 313 Y CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
disulf ? disulf3 D SG CYS 18 B CYS 18 1_555 D SG CYS 313 B CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
covale ? covale1 B CA LEU 569 Y LEU 569 1_555 B CB LEU 576 Y LEU 576 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.521 ? 
metalc ? metalc1 C SG CYS 287 Z CYS 323 1_555 G ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? 
metalc ? metalc2 C SG CYS 290 Z CYS 326 1_555 G ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
metalc ? metalc3 C SG CYS 355 Z CYS 391 1_555 G ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? 
metalc ? metalc4 C SG CYS 358 Z CYS 394 1_555 G ZN ZN . Z ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? 
metalc ? metalc5 E SG CYS 287 C CYS 323 1_555 I ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc6 E SG CYS 290 C CYS 326 1_555 I ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
metalc ? metalc7 E SG CYS 355 C CYS 391 1_555 I ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? 
#
_chem_comp.formula           'C22 H21 Cl N4 O4' 
_chem_comp.formula_weight    440.88 
_chem_comp.id                85C 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea 
_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
C11 C10 85C sing 1 n n 
C11 C12 85C sing 2 n n 
C10 C9 85C sing 3 n n 
O3 C12 85C doub 4 n n 
C12 N2 85C sing 5 n n 
C9 N1 85C sing 6 n n 
C9 C13 85C sing 7 n n 
O1 C8 85C doub 8 n n 
N2 C13 85C sing 9 n n 
N1 C8 85C sing 10 n n 
N1 C7 85C sing 11 n n 
C13 O2 85C doub 12 n n 
C8 C5 85C sing 13 n n 
C7 C6 85C sing 14 n n 
C5 C6 85C doub 15 n y 
C5 C4 85C sing 16 n y 
C6 C3 85C sing 17 n y 
C4 C1 85C doub 18 n y 
C3 C2 85C doub 19 n y 
C1 C2 85C sing 20 n y 
C2 C14 85C sing 21 n n 
C14 N3 85C sing 22 n n 
N3 C15 85C sing 23 n n 
C15 O4 85C doub 24 n n 
C15 N4 85C sing 25 n n 
N4 C16 85C sing 26 n n 
C16 C17 85C doub 27 n y 
C16 C21 85C sing 28 n y 
C17 C18 85C sing 29 n y 
C21 C20 85C doub 30 n y 
C18 CL1 85C sing 31 n n 
C18 C19 85C doub 32 n y 
C20 C19 85C sing 33 n y 
C19 C22 85C sing 34 n n 
C1 H1 85C sing 35 n n 
C3 H2 85C sing 36 n n 
C4 H3 85C sing 37 n n 
N2 H4 85C sing 38 n n 
N3 H5 85C sing 39 n n 
C7 H6 85C sing 40 n n 
C7 H7 85C sing 41 n n 
C9 H8 85C sing 42 n n 
C10 H9 85C sing 43 n n 
C10 H10 85C sing 44 n n 
C11 H11 85C sing 45 n n 
C11 H12 85C sing 46 n n 
C14 H13 85C sing 47 n n 
C14 H14 85C sing 48 n n 
C17 H15 85C sing 49 n n 
C22 H16 85C sing 50 n n 
C22 H17 85C sing 51 n n 
C22 H18 85C sing 52 n n 
C20 H19 85C sing 53 n n 
C21 H20 85C sing 54 n n 
N4 H21 85C sing 55 n n 
#
_atom_sites.entry_id                     5HXB 
_atom_sites.fract_transf_matrix[1][1]    0.00638 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000649 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008967 
_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]    0.005742 
_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
G 4 ZN Z 1 501 501 ZN ZN . 
H 5 85C Z 1 502 502 85C 85C . 
I 4 ZN C 1 501 501 ZN ZN . 
J 5 85C C 1 502 502 85C 85C . 
#
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 85C . . . H 5 9.886 -103.549 28.476 1 74.72 ? C1 85C 502 Z 1 
HETATM 2 C C2 85C . . . H 5 10.543 -104.775 28.443 1 92.33 ? C2 85C 502 Z 1 
HETATM 3 C C3 85C . . . H 5 11.648 -104.98 29.26 1 91.86 ? C3 85C 502 Z 1 
HETATM 4 C C4 85C . . . H 5 10.333 -102.541 29.325 1 70.69 ? C4 85C 502 Z 1 
HETATM 5 C C5 85C . . . H 5 11.427 -102.754 30.154 1 85.14 ? C5 85C 502 Z 1 
HETATM 6 C C6 85C . . . H 5 12.087 -103.976 30.113 1 85.29 ? C6 85C 502 Z 1 
HETATM 7 N N1 85C . . . H 5 13.057 -102.583 31.701 1 95.36 ? N1 85C 502 Z 1 
HETATM 8 N N2 85C . . . H 5 16.572 -101.967 32.424 1 91.63 ? N2 85C 502 Z 1 
HETATM 9 N N3 85C . . . H 5 11.197 -106.224 26.583 1 132.79 ? N3 85C 502 Z 1 
HETATM 10 O O1 85C . . . H 5 11.754 -100.777 31.331 1 76.58 ? O1 85C 502 Z 1 
HETATM 11 C C7 85C . . . H 5 13.234 -103.912 31.114 1 94.04 ? C7 85C 502 Z 1 
HETATM 12 C C8 85C . . . H 5 12.083 -101.934 31.075 1 90.57 ? C8 85C 502 Z 1 
HETATM 13 C C9 85C . . . H 5 14.022 -101.96 32.611 1 92.73 ? C9 85C 502 Z 1 
HETATM 14 C C10 85C . . . H 5 14.261 -102.888 33.8 1 108.48 ? C10 85C 502 Z 1 
HETATM 15 C C11 85C . . . H 5 15.44 -102.404 34.641 1 109.24 ? C11 85C 502 Z 1 
HETATM 16 C C12 85C . . . H 5 16.69 -102.249 33.781 1 94.39 ? C12 85C 502 Z 1 
HETATM 17 C C13 85C . . . H 5 15.317 -101.781 31.832 1 88.11 ? C13 85C 502 Z 1 
HETATM 18 C C14 85C . . . H 5 10.078 -105.894 27.488 1 115.09 ? C14 85C 502 Z 1 
HETATM 19 C C15 85C . . . H 5 11.121 -106.136 25.254 1 133.93 ? C15 85C 502 Z 1 
HETATM 20 O O2 85C . . . H 5 15.246 -101.548 30.63 1 116.95 ? O2 85C 502 Z 1 
HETATM 21 C C17 85C . . . H 5 12.641 -107.462 22.54 1 160.22 ? C17 85C 502 Z 1 
HETATM 22 C C18 85C . . . H 5 12.676 -107.407 21.154 1 185.44 ? C18 85C 502 Z 1 
HETATM 23 CL CL1 85C . . . H 5 13.128 -108.797 20.235 1 235.51 ? CL1 85C 502 Z 1 
HETATM 24 C C19 85C . . . H 5 12.347 -106.232 20.492 1 210.86 ? C19 85C 502 Z 1 
HETATM 25 C C22 85C . . . H 5 12.392 -106.19 18.964 1 211.92 ? C22 85C 502 Z 1 
HETATM 26 C C20 85C . . . H 5 11.983 -105.102 21.218 1 178.84 ? C20 85C 502 Z 1 
HETATM 27 C C21 85C . . . H 5 11.945 -105.155 22.606 1 149.64 ? C21 85C 502 Z 1 
HETATM 28 C C16 85C . . . H 5 12.265 -106.34 23.266 1 144.9 ? C16 85C 502 Z 1 
HETATM 29 N N4 85C . . . H 5 12.246 -106.397 24.591 1 131.01 ? N4 85C 502 Z 1 
HETATM 30 O O4 85C . . . H 5 10.078 -105.842 24.672 1 130.08 ? O4 85C 502 Z 1 
HETATM 31 O O3 85C . . . H 5 17.805 -102.382 34.278 1 91.61 ? O3 85C 502 Z 1 
#
_model_server_stats.io_time_ms              43 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    38 
_model_server_stats.query_time_ms           221 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#