data_6XK9
#
_model_server_result.job_id            YeSuWQAnJs4TIAyBJnwtnA 
_model_server_result.datetime_utc      '2024-10-25 20:25:43' 
_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          6xk9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":501}' 
#
_entry.id    6XK9 
#
_exptl.entry_id    6XK9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              461.846 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide 
_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          95.791 
_cell.angle_gamma         90 
_cell.entry_id            6XK9 
_cell.length_a            157.616 
_cell.length_b            112.041 
_cell.length_c            176.582 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XK9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        3 
_symmetry.space_group_name_Hall    'P 2y' 
_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
PISA trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_software_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
? 4 G N N 
? 4 I 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
metalc ? metalc1 C SG CYS 287 Z CYS 323 1_555 H ZN ZN . Z ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? 
metalc ? metalc2 C SG CYS 290 Z CYS 326 1_555 H ZN ZN . Z ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? 
metalc ? metalc3 C SG CYS 355 Z CYS 391 1_555 H ZN ZN . Z ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? 
metalc ? metalc4 C SG CYS 358 Z CYS 394 1_555 H ZN ZN . Z ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? 
metalc ? metalc5 F SG CYS 287 C CYS 323 1_555 J ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? 
metalc ? metalc6 F SG CYS 290 C CYS 326 1_555 J ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? 
metalc ? metalc7 F SG CYS 355 C CYS 391 1_555 J ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? 
metalc ? metalc8 F SG CYS 358 C CYS 394 1_555 J ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? 
#
_chem_comp.formula           'C22 H18 Cl F2 N3 O4' 
_chem_comp.formula_weight    461.846 
_chem_comp.id                V4M 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide 
_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
CL1 C20 V4M sing 356 n n 
C20 C21 V4M doub 357 n y 
C20 C19 V4M sing 358 n y 
C21 C22 V4M sing 359 n y 
C19 C18 V4M doub 360 n y 
C22 C17 V4M doub 361 n y 
C18 C17 V4M sing 362 n y 
C17 C16 V4M sing 363 n n 
C16 F1 V4M sing 364 n n 
C16 F2 V4M sing 365 n n 
C16 C15 V4M sing 366 n n 
O4 C15 V4M doub 367 n n 
C15 N3 V4M sing 368 n n 
N3 C14 V4M sing 369 n n 
C14 C2 V4M sing 370 n n 
C2 C1 V4M doub 371 n y 
C2 C3 V4M sing 372 n y 
C1 C4 V4M sing 373 n y 
C3 C6 V4M doub 374 n y 
C4 C5 V4M doub 375 n y 
C6 C5 V4M sing 376 n y 
C6 C7 V4M sing 377 n n 
O2 C13 V4M doub 378 n n 
C5 C8 V4M sing 379 n n 
C7 N1 V4M sing 380 n n 
C13 N2 V4M sing 381 n n 
C13 C9 V4M sing 382 n n 
C8 N1 V4M sing 383 n n 
C8 O1 V4M doub 384 n n 
N1 C9 V4M sing 385 n n 
N2 C12 V4M sing 386 n n 
C9 C10 V4M sing 387 n n 
C12 O3 V4M doub 388 n n 
C12 C11 V4M sing 389 n n 
C10 C11 V4M sing 390 n n 
C1 H1 V4M sing 391 n n 
C3 H2 V4M sing 392 n n 
C4 H3 V4M sing 393 n n 
N2 H4 V4M sing 394 n n 
N3 H5 V4M sing 395 n n 
C7 H6 V4M sing 396 n n 
C7 H7 V4M sing 397 n n 
C9 H8 V4M sing 398 n n 
C10 H9 V4M sing 399 n n 
C10 H10 V4M sing 400 n n 
C11 H11 V4M sing 401 n n 
C11 H12 V4M sing 402 n n 
C14 H13 V4M sing 403 n n 
C14 H14 V4M sing 404 n n 
C18 H15 V4M sing 405 n n 
C19 H16 V4M sing 406 n n 
C21 H17 V4M sing 407 n n 
C22 H18 V4M sing 408 n n 
#
_atom_sites.entry_id                     6XK9 
_atom_sites.fract_transf_matrix[1][1]    0.006345 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000643 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008925 
_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]    0.005692 
_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 V4M Z 1 501 501 V4M MOL . 
H 5 ZN Z 1 502 2 ZN ZN . 
I 4 V4M C 1 501 502 V4M MOL . 
J 5 ZN C 1 502 1 ZN ZN . 
#
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 V4M . . . I 4 -15.429 130.01 26.717 1 61.43 ? C1 V4M 501 C 1 
HETATM 2 C C2 V4M . . . I 4 -16.172 131.108 26.329 1 57.8 ? C2 V4M 501 C 1 
HETATM 3 C C3 V4M . . . I 4 -17.469 131.279 26.737 1 60.17 ? C3 V4M 501 C 1 
HETATM 4 C C4 V4M . . . I 4 -16.034 129.071 27.556 1 67.78 ? C4 V4M 501 C 1 
HETATM 5 C C5 V4M . . . I 4 -17.356 129.265 27.964 1 68.47 ? C5 V4M 501 C 1 
HETATM 6 C C6 V4M . . . I 4 -18.048 130.348 27.559 1 64.29 ? C6 V4M 501 C 1 
HETATM 7 N N1 V4M . . . I 4 -19.474 129.058 28.949 1 62.94 ? N1 V4M 501 C 1 
HETATM 8 N N2 V4M . . . I 4 -23.149 128.712 29.155 1 70.63 ? N2 V4M 501 C 1 
HETATM 9 N N3 V4M . . . I 4 -16.56 132.656 24.536 1 75.15 ? N3 V4M 501 C 1 
HETATM 10 O O1 V4M . . . I 4 -17.842 127.402 29.337 1 68.29 ? O1 V4M 501 C 1 
HETATM 11 C C7 V4M . . . I 4 -19.493 130.339 28.146 1 64.73 ? C7 V4M 501 C 1 
HETATM 12 C C8 V4M . . . I 4 -18.179 128.418 28.829 1 66.38 ? C8 V4M 501 C 1 
HETATM 13 C C9 V4M . . . I 4 -20.657 128.646 29.677 1 57.93 ? C9 V4M 501 C 1 
HETATM 14 C C10 V4M . . . I 4 -21.023 129.68 30.755 1 60.78 ? C10 V4M 501 C 1 
HETATM 15 C C11 V4M . . . I 4 -22.242 129.132 31.532 1 63.59 ? C11 V4M 501 C 1 
HETATM 16 C C12 V4M . . . I 4 -23.399 129.027 30.531 1 67.85 ? C12 V4M 501 C 1 
HETATM 17 C C13 V4M . . . I 4 -21.813 128.474 28.707 1 65.96 ? C13 V4M 501 C 1 
HETATM 18 C C14 V4M . . . I 4 -15.53 132.14 25.411 1 66.14 ? C14 V4M 501 C 1 
HETATM 19 C C15 V4M . . . I 4 -16.447 132.521 23.098 1 83.46 ? C15 V4M 501 C 1 
HETATM 20 O O2 V4M . . . I 4 -21.616 128.123 27.593 1 69.15 ? O2 V4M 501 C 1 
HETATM 21 C C16 V4M . . . I 4 -17.57 133.086 22.231 1 96.34 ? C16 V4M 501 C 1 
HETATM 22 C C17 V4M . . . I 4 -17.133 133.273 20.777 1 98.88 ? C17 V4M 501 C 1 
HETATM 23 C C18 V4M . . . I 4 -15.982 133.984 20.466 1 93.15 ? C18 V4M 501 C 1 
HETATM 24 C C19 V4M . . . I 4 -15.603 134.147 19.144 1 86.2 ? C19 V4M 501 C 1 
HETATM 25 C C20 V4M . . . I 4 -16.379 133.608 18.131 1 94.06 ? C20 V4M 501 C 1 
HETATM 26 C C21 V4M . . . I 4 -17.532 132.903 18.437 1 96.34 ? C21 V4M 501 C 1 
HETATM 27 C C22 V4M . . . I 4 -17.909 132.738 19.76 1 96.95 ? C22 V4M 501 C 1 
HETATM 28 F F1 V4M . . . I 4 -18.638 132.237 22.27 1 98.9 ? F1 V4M 501 C 1 
HETATM 29 F F2 V4M . . . I 4 -17.951 134.292 22.745 1 103.51 ? F2 V4M 501 C 1 
HETATM 30 O O3 V4M . . . I 4 -24.51 129.218 30.894 1 69.94 ? O3 V4M 501 C 1 
HETATM 31 O O4 V4M . . . I 4 -15.511 131.973 22.62 1 79.3 ? O4 V4M 501 C 1 
HETATM 32 CL CL1 V4M . . . I 4 -15.891 133.823 16.428 1 122.14 ? CL1 V4M 501 C 1 
#
_model_server_stats.io_time_ms              37 
_model_server_stats.parse_time_ms           34 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           260 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           32 
#