data_8F93
#
_model_server_result.job_id            rd8LhgPBy7qxM4xIvvi4tw 
_model_server_result.datetime_utc      '2024-10-19 12:44:27' 
_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          8f93 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    8F93 
#
_exptl.entry_id    8F93 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              560.639 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '3-ethynyl-5-{[(3R)-4-{1-[(2-methoxyphenyl)methyl]-1H-benzimidazole-5-carbonyl}-3-methylpiperazin-1-yl]methyl}benzene-1-sulfonyl fluoride' 
_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          101.545 
_cell.angle_gamma         90 
_cell.entry_id            8F93 
_cell.length_a            92.78 
_cell.length_b            103.022 
_cell.length_c            81.014 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8F93 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    'C 2y' 
_symmetry.space_group_name_H-M     'C 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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,D,E,F,G,H,I,J,K,L,M,N 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N 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 G 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 OH TYR 210 A TYR 228 1_555 C S1 XKN . A XKN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.596 ? 
covale ? covale2 B OH TYR 210 B TYR 228 1_555 G S1 XKN . B XKN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.587 ? 
#
_chem_comp.formula           'C30 H29 F N4 O4 S' 
_chem_comp.formula_weight    560.639 
_chem_comp.id                XKN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '3-ethynyl-5-{[(3R)-4-{1-[(2-methoxyphenyl)methyl]-1H-benzimidazole-5-carbonyl}-3-methylpiperazin-1-yl]methyl}benzene-1-sulfonyl fluoride' 
_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
C22 C23 XKN doub 374 n y 
C22 C21 XKN sing 375 n y 
C23 C24 XKN sing 376 n y 
C21 C19 XKN doub 377 n y 
C24 C18 XKN doub 378 n y 
C19 C18 XKN sing 379 n y 
C19 O3 XKN sing 380 n n 
C18 C17 XKN sing 381 n n 
C20 O3 XKN sing 382 n n 
C17 N4 XKN sing 383 n n 
N4 C25 XKN sing 384 n y 
N4 C16 XKN sing 385 n y 
C26 C25 XKN doub 386 n y 
C26 C27 XKN sing 387 n y 
C25 C15 XKN sing 388 n y 
C16 N3 XKN doub 389 n y 
C27 C13 XKN doub 390 n y 
C15 N3 XKN sing 391 n y 
C15 C14 XKN doub 392 n y 
C13 C14 XKN sing 393 n y 
C13 C12 XKN sing 394 n n 
C28 N2 XKN sing 395 n n 
C28 C29 XKN sing 396 n n 
C12 N2 XKN sing 397 n n 
C12 O4 XKN doub 398 n n 
N2 C10 XKN sing 399 n n 
C11 C10 XKN sing 400 n n 
C29 N1 XKN sing 401 n n 
C10 C9 XKN sing 402 n n 
C8 N1 XKN sing 403 n n 
C8 C7 XKN sing 404 n n 
N1 C9 XKN sing 405 n n 
C30 C7 XKN doub 406 n y 
C30 C3 XKN sing 407 n y 
C1 C2 XKN trip 408 n n 
C7 C6 XKN sing 409 n y 
C2 C3 XKN sing 410 n n 
C3 C4 XKN doub 411 n y 
C6 C5 XKN doub 412 n y 
C4 C5 XKN sing 413 n y 
C5 S1 XKN sing 414 n n 
S1 O2 XKN doub 415 n n 
S1 O1 XKN doub 416 n n 
S1 F1 XKN sing 417 n n 
C1 H1 XKN sing 418 n n 
C10 H2 XKN sing 419 n n 
C11 H3 XKN sing 420 n n 
C11 H4 XKN sing 421 n n 
C11 H5 XKN sing 422 n n 
C14 H6 XKN sing 423 n n 
C16 H7 XKN sing 424 n n 
C17 H8 XKN sing 425 n n 
C17 H9 XKN sing 426 n n 
C20 H10 XKN sing 427 n n 
C20 H11 XKN sing 428 n n 
C20 H12 XKN sing 429 n n 
C21 H13 XKN sing 430 n n 
C22 H14 XKN sing 431 n n 
C23 H15 XKN sing 432 n n 
C24 H16 XKN sing 433 n n 
C26 H17 XKN sing 434 n n 
C27 H18 XKN sing 435 n n 
C28 H19 XKN sing 436 n n 
C28 H20 XKN sing 437 n n 
C29 H21 XKN sing 438 n n 
C29 H22 XKN sing 439 n n 
C30 H23 XKN sing 440 n n 
C4 H24 XKN sing 441 n n 
C6 H25 XKN sing 442 n n 
C8 H26 XKN sing 443 n n 
C8 H27 XKN sing 444 n n 
C9 H28 XKN sing 445 n n 
C9 H29 XKN sing 446 n n 
#
_atom_sites.entry_id                     8F93 
_atom_sites.fract_transf_matrix[1][1]    0.010778 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002202 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009707 
_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]    0.012598 
_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 XKN A 1 401 401 XKN 2RS . 
D 3 GOL A 1 402 402 GOL GOL . 
E 4 SO4 A 1 403 1 SO4 SO4 . 
F 5 CL A 1 404 2 CL CL . 
G 2 XKN B 1 401 402 XKN 2RS . 
H 3 GOL B 1 402 404 GOL GOL . 
I 3 GOL B 1 403 406 GOL GOL . 
J 3 GOL B 1 404 407 GOL GOL . 
K 4 SO4 B 1 405 2 SO4 SO4 . 
L 5 CL B 1 406 1 CL CL . 
M 6 HOH A 1 501 35 HOH HOH . 
M 6 HOH A 2 502 3 HOH HOH . 
M 6 HOH A 3 503 10 HOH HOH . 
M 6 HOH A 4 504 52 HOH HOH . 
M 6 HOH A 5 505 18 HOH HOH . 
M 6 HOH A 6 506 45 HOH HOH . 
M 6 HOH A 7 507 96 HOH HOH . 
M 6 HOH A 8 508 1 HOH HOH . 
M 6 HOH A 9 509 64 HOH HOH . 
M 6 HOH A 10 510 92 HOH HOH . 
M 6 HOH A 11 511 28 HOH HOH . 
M 6 HOH A 12 512 72 HOH HOH . 
M 6 HOH A 13 513 25 HOH HOH . 
M 6 HOH A 14 514 95 HOH HOH . 
M 6 HOH A 15 515 32 HOH HOH . 
M 6 HOH A 16 516 73 HOH HOH . 
M 6 HOH A 17 517 87 HOH HOH . 
M 6 HOH A 18 518 97 HOH HOH . 
M 6 HOH A 19 519 75 HOH HOH . 
M 6 HOH A 20 520 53 HOH HOH . 
M 6 HOH A 21 521 48 HOH HOH . 
M 6 HOH A 22 522 34 HOH HOH . 
M 6 HOH A 23 523 12 HOH HOH . 
M 6 HOH A 24 524 44 HOH HOH . 
M 6 HOH A 25 525 19 HOH HOH . 
M 6 HOH A 26 526 47 HOH HOH . 
M 6 HOH A 27 527 14 HOH HOH . 
M 6 HOH A 28 528 23 HOH HOH . 
M 6 HOH A 29 529 24 HOH HOH . 
M 6 HOH A 30 530 30 HOH HOH . 
M 6 HOH A 31 531 17 HOH HOH . 
M 6 HOH A 32 532 67 HOH HOH . 
M 6 HOH A 33 533 33 HOH HOH . 
M 6 HOH A 34 534 50 HOH HOH . 
M 6 HOH A 35 535 89 HOH HOH . 
M 6 HOH A 36 536 22 HOH HOH . 
M 6 HOH A 37 537 71 HOH HOH . 
M 6 HOH A 38 538 31 HOH HOH . 
M 6 HOH A 39 539 29 HOH HOH . 
M 6 HOH A 40 540 74 HOH HOH . 
M 6 HOH A 41 541 90 HOH HOH . 
M 6 HOH A 42 542 9 HOH HOH . 
M 6 HOH A 43 543 78 HOH HOH . 
M 6 HOH A 44 544 46 HOH HOH . 
M 6 HOH A 45 545 21 HOH HOH . 
M 6 HOH A 46 546 26 HOH HOH . 
M 6 HOH A 47 547 16 HOH HOH . 
M 6 HOH A 48 548 84 HOH HOH . 
M 6 HOH A 49 549 7 HOH HOH . 
M 6 HOH A 50 550 70 HOH HOH . 
M 6 HOH A 51 551 58 HOH HOH . 
M 6 HOH A 52 552 94 HOH HOH . 
M 6 HOH A 53 553 40 HOH HOH . 
M 6 HOH A 54 554 55 HOH HOH . 
M 6 HOH A 55 555 20 HOH HOH . 
M 6 HOH A 56 556 88 HOH HOH . 
M 6 HOH A 57 557 63 HOH HOH . 
M 6 HOH A 58 558 69 HOH HOH . 
M 6 HOH A 59 559 59 HOH HOH . 
M 6 HOH A 60 560 93 HOH HOH . 
M 6 HOH A 61 561 66 HOH HOH . 
M 6 HOH A 62 562 61 HOH HOH . 
M 6 HOH A 63 563 81 HOH HOH . 
M 6 HOH A 64 564 82 HOH HOH . 
N 6 HOH B 1 501 42 HOH HOH . 
N 6 HOH B 2 502 49 HOH HOH . 
N 6 HOH B 3 503 15 HOH HOH . 
N 6 HOH B 4 504 8 HOH HOH . 
N 6 HOH B 5 505 27 HOH HOH . 
N 6 HOH B 6 506 41 HOH HOH . 
N 6 HOH B 7 507 5 HOH HOH . 
N 6 HOH B 8 508 79 HOH HOH . 
N 6 HOH B 9 509 60 HOH HOH . 
N 6 HOH B 10 510 56 HOH HOH . 
N 6 HOH B 11 511 85 HOH HOH . 
N 6 HOH B 12 512 68 HOH HOH . 
N 6 HOH B 13 513 4 HOH HOH . 
N 6 HOH B 14 514 62 HOH HOH . 
N 6 HOH B 15 515 91 HOH HOH . 
N 6 HOH B 16 516 11 HOH HOH . 
N 6 HOH B 17 517 54 HOH HOH . 
N 6 HOH B 18 518 2 HOH HOH . 
N 6 HOH B 19 519 51 HOH HOH . 
N 6 HOH B 20 520 38 HOH HOH . 
N 6 HOH B 21 521 65 HOH HOH . 
N 6 HOH B 22 522 13 HOH HOH . 
N 6 HOH B 23 523 76 HOH HOH . 
N 6 HOH B 24 524 6 HOH HOH . 
N 6 HOH B 25 525 83 HOH HOH . 
N 6 HOH B 26 526 57 HOH HOH . 
N 6 HOH B 27 527 39 HOH HOH . 
N 6 HOH B 28 528 80 HOH HOH . 
N 6 HOH B 29 529 37 HOH HOH . 
N 6 HOH B 30 530 36 HOH HOH . 
N 6 HOH B 31 531 43 HOH HOH . 
N 6 HOH B 32 532 86 HOH HOH . 
N 6 HOH B 33 533 77 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 XKN . . . C 2 32.144 7.753 26.855 1 64.58 ? C1 XKN 401 A 1 
HETATM 2 C C10 XKN . . . C 2 25.753 3.65 25.53 1 39.35 ? C10 XKN 401 A 1 
HETATM 3 C C11 XKN . . . C 2 26.506 4.762 24.827 1 38.79 ? C11 XKN 401 A 1 
HETATM 4 C C12 XKN . . . C 2 24.067 2.315 24.473 1 40.04 ? C12 XKN 401 A 1 
HETATM 5 C C13 XKN . . . C 2 23.557 1.318 23.471 1 35.4 ? C13 XKN 401 A 1 
HETATM 6 C C14 XKN . . . C 2 23.028 0.096 23.886 1 44.11 ? C14 XKN 401 A 1 
HETATM 7 C C15 XKN . . . C 2 22.481 -0.762 22.934 1 41.77 ? C15 XKN 401 A 1 
HETATM 8 C C16 XKN . . . C 2 21.548 -2.358 21.867 1 41.61 ? C16 XKN 401 A 1 
HETATM 9 C C17 XKN . . . C 2 21.476 -1.5 19.483 1 53.66 ? C17 XKN 401 A 1 
HETATM 10 C C18 XKN . . . C 2 22.574 -1.973 18.559 1 49.3 ? C18 XKN 401 A 1 
HETATM 11 C C19 XKN . . . C 2 22.836 -3.34 18.465 1 51.23 ? C19 XKN 401 A 1 
HETATM 12 C C2 XKN . . . C 2 31.504 6.819 27.182 1 61.64 ? C2 XKN 401 A 1 
HETATM 13 C C20 XKN . . . C 2 22.143 -5.524 19.108 1 50.1 ? C20 XKN 401 A 1 
HETATM 14 C C21 XKN . . . C 2 23.836 -3.818 17.635 1 45.56 ? C21 XKN 401 A 1 
HETATM 15 C C22 XKN . . . C 2 24.575 -2.933 16.878 1 40.02 ? C22 XKN 401 A 1 
HETATM 16 C C23 XKN . . . C 2 24.318 -1.584 16.937 1 49.71 ? C23 XKN 401 A 1 
HETATM 17 C C24 XKN . . . C 2 23.316 -1.104 17.763 1 46.12 ? C24 XKN 401 A 1 
HETATM 18 C C25 XKN . . . C 2 22.418 -0.371 21.594 1 42.83 ? C25 XKN 401 A 1 
HETATM 19 C C26 XKN . . . C 2 22.902 0.859 21.161 1 43.77 ? C26 XKN 401 A 1 
HETATM 20 C C27 XKN . . . C 2 23.451 1.69 22.123 1 46.56 ? C27 XKN 401 A 1 
HETATM 21 C C28 XKN . . . C 2 26.498 1.884 24.001 1 40.23 ? C28 XKN 401 A 1 
HETATM 22 C C29 XKN . . . C 2 27.247 1.218 25.136 1 48.74 ? C29 XKN 401 A 1 
HETATM 23 C C3 XKN . . . C 2 30.741 5.669 27.574 1 61.51 ? C3 XKN 401 A 1 
HETATM 24 C C30 XKN . . . C 2 30.187 4.855 26.591 1 67.62 ? C30 XKN 401 A 1 
HETATM 25 C C4 XKN . . . C 2 30.558 5.331 28.911 1 66.27 ? C4 XKN 401 A 1 
HETATM 26 C C5 XKN . . . C 2 29.82 4.206 29.246 1 69 ? C5 XKN 401 A 1 
HETATM 27 C C6 XKN . . . C 2 29.269 3.412 28.249 1 57.27 ? C6 XKN 401 A 1 
HETATM 28 C C7 XKN . . . C 2 29.445 3.734 26.911 1 64.08 ? C7 XKN 401 A 1 
HETATM 29 C C8 XKN . . . C 2 28.849 2.912 25.795 1 54.56 ? C8 XKN 401 A 1 
HETATM 30 C C9 XKN . . . C 2 26.55 3.016 26.646 1 43.85 ? C9 XKN 401 A 1 
HETATM 31 N N1 XKN . . . C 2 27.656 2.159 26.19 1 53.32 ? N1 XKN 401 A 1 
HETATM 32 N N2 XKN . . . C 2 25.367 2.579 24.597 1 44.3 ? N2 XKN 401 A 1 
HETATM 33 N N3 XKN . . . C 2 21.92 -2.026 23.079 1 48.69 ? N3 XKN 401 A 1 
HETATM 34 N N4 XKN . . . C 2 21.816 -1.422 20.914 1 49.87 ? N4 XKN 401 A 1 
HETATM 35 O O1 XKN . . . C 2 30.407 4.712 31.699 1 75.2 ? O1 XKN 401 A 1 
HETATM 36 O O2 XKN . . . C 2 29.991 2.448 31.097 1 100.52 ? O2 XKN 401 A 1 
HETATM 37 O O3 XKN . . . C 2 22.058 -4.111 19.274 1 52.71 ? O3 XKN 401 A 1 
HETATM 38 O O4 XKN . . . C 2 23.245 2.938 25.148 1 40.92 ? O4 XKN 401 A 1 
HETATM 39 S S1 XKN . . . C 2 29.553 3.817 30.947 1 95.68 ? S1 XKN 401 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           39 
#