data_5YIB
#
_model_server_result.job_id            sIeoXI8ADznz7m4KurbwmQ 
_model_server_result.datetime_utc      '2024-11-08 13:26:55' 
_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          5yib 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    5YIB 
#
_exptl.entry_id    5YIB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              731.944 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4R)-3-[(2S,3S)-3-[2-[4-[2-(dimethylamino)ethyl-methyl-amino]-2,6-dimethyl-phenoxy]ethanoylamino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-N-[(1S,2R)-2-oxidanyl-2,3-dihydro-1H-inden-1-yl]-1,3-thiazolidine-4-carboxamide 
_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            5YIB 
_cell.length_a            106.25 
_cell.length_b            106.25 
_cell.length_c            70.85 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YIB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4' 
#
_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,E,F,G,H,I,J,K 
_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 46 A CYS 49 1_555 A SG CYS 51 A CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf2 A SG CYS 248 A CYS 251 1_555 A SG CYS 284 A CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
#
_chem_comp.formula           'C40 H53 N5 O6 S' 
_chem_comp.formula_weight    731.944 
_chem_comp.id                8VC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4R)-3-[(2S,3S)-3-[2-[4-[2-(dimethylamino)ethyl-methyl-amino]-2,6-dimethyl-phenoxy]ethanoylamino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-N-[(1S,2R)-2-oxidanyl-2,3-dihydro-1H-inden-1-yl]-1,3-thiazolidine-4-carboxamide 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     5YIB 
_atom_sites.fract_transf_matrix[1][1]    0.009412 
_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]    0.009412 
_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]    0.014114 
_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 8VC A 1 401 2 8VC 743 . 
C 3 GOL A 1 402 1 GOL GOL . 
D 3 GOL A 1 403 3 GOL GOL . 
E 3 GOL A 1 404 4 GOL GOL . 
F 3 GOL A 1 405 6 GOL GOL . 
G 3 GOL A 1 406 7 GOL GOL . 
H 4 EDO A 1 407 1 EDO EDO . 
I 4 EDO A 1 408 2 EDO EDO . 
J 5 CPS A 1 409 1 CPS CPS . 
K 6 HOH A 1 501 101 HOH HOH . 
K 6 HOH A 2 502 31 HOH HOH . 
K 6 HOH A 3 503 45 HOH HOH . 
K 6 HOH A 4 504 55 HOH HOH . 
K 6 HOH A 5 505 100 HOH HOH . 
K 6 HOH A 6 506 98 HOH HOH . 
K 6 HOH A 7 507 120 HOH HOH . 
K 6 HOH A 8 508 103 HOH HOH . 
K 6 HOH A 9 509 8 HOH HOH . 
K 6 HOH A 10 510 20 HOH HOH . 
K 6 HOH A 11 511 67 HOH HOH . 
K 6 HOH A 12 512 51 HOH HOH . 
K 6 HOH A 13 513 113 HOH HOH . 
K 6 HOH A 14 514 35 HOH HOH . 
K 6 HOH A 15 515 48 HOH HOH . 
K 6 HOH A 16 516 6 HOH HOH . 
K 6 HOH A 17 517 34 HOH HOH . 
K 6 HOH A 18 518 66 HOH HOH . 
K 6 HOH A 19 519 96 HOH HOH . 
K 6 HOH A 20 520 26 HOH HOH . 
K 6 HOH A 21 521 30 HOH HOH . 
K 6 HOH A 22 522 15 HOH HOH . 
K 6 HOH A 23 523 33 HOH HOH . 
K 6 HOH A 24 524 52 HOH HOH . 
K 6 HOH A 25 525 11 HOH HOH . 
K 6 HOH A 26 526 105 HOH HOH . 
K 6 HOH A 27 527 12 HOH HOH . 
K 6 HOH A 28 528 54 HOH HOH . 
K 6 HOH A 29 529 97 HOH HOH . 
K 6 HOH A 30 530 102 HOH HOH . 
K 6 HOH A 31 531 64 HOH HOH . 
K 6 HOH A 32 532 17 HOH HOH . 
K 6 HOH A 33 533 43 HOH HOH . 
K 6 HOH A 34 534 42 HOH HOH . 
K 6 HOH A 35 535 108 HOH HOH . 
K 6 HOH A 36 536 19 HOH HOH . 
K 6 HOH A 37 537 7 HOH HOH . 
K 6 HOH A 38 538 111 HOH HOH . 
K 6 HOH A 39 539 13 HOH HOH . 
K 6 HOH A 40 540 122 HOH HOH . 
K 6 HOH A 41 541 53 HOH HOH . 
K 6 HOH A 42 542 121 HOH HOH . 
K 6 HOH A 43 543 41 HOH HOH . 
K 6 HOH A 44 544 4 HOH HOH . 
K 6 HOH A 45 545 65 HOH HOH . 
K 6 HOH A 46 546 78 HOH HOH . 
K 6 HOH A 47 547 5 HOH HOH . 
K 6 HOH A 48 548 24 HOH HOH . 
K 6 HOH A 49 549 18 HOH HOH . 
K 6 HOH A 50 550 29 HOH HOH . 
K 6 HOH A 51 551 73 HOH HOH . 
K 6 HOH A 52 552 124 HOH HOH . 
K 6 HOH A 53 553 36 HOH HOH . 
K 6 HOH A 54 554 10 HOH HOH . 
K 6 HOH A 55 555 2 HOH HOH . 
K 6 HOH A 56 556 14 HOH HOH . 
K 6 HOH A 57 557 123 HOH HOH . 
K 6 HOH A 58 558 115 HOH HOH . 
K 6 HOH A 59 559 86 HOH HOH . 
K 6 HOH A 60 560 38 HOH HOH . 
K 6 HOH A 61 561 25 HOH HOH . 
K 6 HOH A 62 562 79 HOH HOH . 
K 6 HOH A 63 563 77 HOH HOH . 
K 6 HOH A 64 564 47 HOH HOH . 
K 6 HOH A 65 565 40 HOH HOH . 
K 6 HOH A 66 566 21 HOH HOH . 
K 6 HOH A 67 567 99 HOH HOH . 
K 6 HOH A 68 568 9 HOH HOH . 
K 6 HOH A 69 569 137 HOH HOH . 
K 6 HOH A 70 570 60 HOH HOH . 
K 6 HOH A 71 571 95 HOH HOH . 
K 6 HOH A 72 572 39 HOH HOH . 
K 6 HOH A 73 573 82 HOH HOH . 
K 6 HOH A 74 574 76 HOH HOH . 
K 6 HOH A 75 575 118 HOH HOH . 
K 6 HOH A 76 576 125 HOH HOH . 
K 6 HOH A 77 577 112 HOH HOH . 
K 6 HOH A 78 578 16 HOH HOH . 
K 6 HOH A 79 579 50 HOH HOH . 
K 6 HOH A 80 580 136 HOH HOH . 
K 6 HOH A 81 581 68 HOH HOH . 
K 6 HOH A 82 582 28 HOH HOH . 
K 6 HOH A 83 583 27 HOH HOH . 
K 6 HOH A 84 584 72 HOH HOH . 
K 6 HOH A 85 585 22 HOH HOH . 
K 6 HOH A 86 586 32 HOH HOH . 
K 6 HOH A 87 587 109 HOH HOH . 
K 6 HOH A 88 588 135 HOH HOH . 
K 6 HOH A 89 589 114 HOH HOH . 
K 6 HOH A 90 590 37 HOH HOH . 
K 6 HOH A 91 591 107 HOH HOH . 
K 6 HOH A 92 592 88 HOH HOH . 
K 6 HOH A 93 593 69 HOH HOH . 
K 6 HOH A 94 594 44 HOH HOH . 
K 6 HOH A 95 595 133 HOH HOH . 
K 6 HOH A 96 596 58 HOH HOH . 
K 6 HOH A 97 597 62 HOH HOH . 
K 6 HOH A 98 598 74 HOH HOH . 
K 6 HOH A 99 599 23 HOH HOH . 
K 6 HOH A 100 600 132 HOH HOH . 
K 6 HOH A 101 601 1 HOH HOH . 
K 6 HOH A 102 602 93 HOH HOH . 
K 6 HOH A 103 603 89 HOH HOH . 
K 6 HOH A 104 604 3 HOH HOH . 
K 6 HOH A 105 605 110 HOH HOH . 
K 6 HOH A 106 606 63 HOH HOH . 
K 6 HOH A 107 607 57 HOH HOH . 
K 6 HOH A 108 608 134 HOH HOH . 
K 6 HOH A 109 609 116 HOH HOH . 
K 6 HOH A 110 610 71 HOH HOH . 
K 6 HOH A 111 611 131 HOH HOH . 
K 6 HOH A 112 612 119 HOH HOH . 
K 6 HOH A 113 613 80 HOH HOH . 
K 6 HOH A 114 614 128 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 C10 8VC . . . B 2 20.122 -25.324 -25.018 1 39.06 ? C10 8VC 401 A 1 
HETATM 2 C C13 8VC . . . B 2 17.807 -26.267 -24.399 1 35.84 ? C13 8VC 401 A 1 
HETATM 3 C C16 8VC . . . B 2 16.692 -24.55 -27.02 1 37.23 ? C16 8VC 401 A 1 
HETATM 4 C C17 8VC . . . B 2 16.436 -23.297 -27.598 1 36.79 ? C17 8VC 401 A 1 
HETATM 5 C C18 8VC . . . B 2 15.648 -22.372 -26.923 1 36.46 ? C18 8VC 401 A 1 
HETATM 6 C C19 8VC . . . B 2 15.117 -22.685 -25.663 1 36.49 ? C19 8VC 401 A 1 
HETATM 7 C C20 8VC . . . B 2 15.364 -23.925 -25.091 1 36.2 ? C20 8VC 401 A 1 
HETATM 8 C C21 8VC . . . B 2 18 -27.586 -23.582 1 35.27 ? C21 8VC 401 A 1 
HETATM 9 C C22 8VC . . . B 2 17.183 -27.466 -22.277 1 34.45 ? C22 8VC 401 A 1 
HETATM 10 C C25 8VC . . . B 2 19.145 -25.89 -20.823 1 35.92 ? C25 8VC 401 A 1 
HETATM 11 C C27 8VC . . . B 2 17.997 -27.042 -18.803 1 35.4 ? C27 8VC 401 A 1 
HETATM 12 C C28 8VC . . . B 2 16.875 -26.563 -19.914 1 35.68 ? C28 8VC 401 A 1 
HETATM 13 C C01 8VC . . . B 2 23.378 -27.779 -26.096 1 69.57 ? C01 8VC 401 A 1 
HETATM 14 C C02 8VC . . . B 2 23.473 -26.931 -27.377 1 69.8 ? C02 8VC 401 A 1 
HETATM 15 C C03 8VC . . . B 2 24.678 -26.959 -28.1 1 75.5 ? C03 8VC 401 A 1 
HETATM 16 C C04 8VC . . . B 2 24.816 -26.219 -29.271 1 79.04 ? C04 8VC 401 A 1 
HETATM 17 C C05 8VC . . . B 2 23.734 -25.422 -29.715 1 76.76 ? C05 8VC 401 A 1 
HETATM 18 C C06 8VC . . . B 2 22.545 -25.38 -29.007 1 73.76 ? C06 8VC 401 A 1 
HETATM 19 C C07 8VC . . . B 2 22.401 -26.147 -27.823 1 67.69 ? C07 8VC 401 A 1 
HETATM 20 O O08 8VC . . . B 2 21.182 -26.089 -27.081 1 53.42 ? O08 8VC 401 A 1 
HETATM 21 C C09 8VC . . . B 2 21.286 -25.148 -26.027 1 43.59 ? C09 8VC 401 A 1 
HETATM 22 O O11 8VC . . . B 2 20.162 -24.82 -23.954 1 35.83 ? O11 8VC 401 A 1 
HETATM 23 N N12 8VC . . . B 2 18.941 -26.126 -25.398 1 35.75 ? N12 8VC 401 A 1 
HETATM 24 C C14 8VC . . . B 2 16.424 -26.241 -25.136 1 35.47 ? C14 8VC 401 A 1 
HETATM 25 C C15 8VC . . . B 2 16.158 -24.863 -25.772 1 36.16 ? C15 8VC 401 A 1 
HETATM 26 O O23 8VC . . . B 2 16.11 -27.947 -22.183 1 35.03 ? O23 8VC 401 A 1 
HETATM 27 N N24 8VC . . . B 2 17.68 -26.674 -21.146 1 34.36 ? N24 8VC 401 A 1 
HETATM 28 S S26 8VC . . . B 2 19.455 -26.283 -19.371 1 37.14 ? S26 8VC 401 A 1 
HETATM 29 C C29 8VC . . . B 2 16.338 -25.135 -19.694 1 36.27 ? C29 8VC 401 A 1 
HETATM 30 O O30 8VC . . . B 2 16.967 -24.158 -19.872 1 39.77 ? O30 8VC 401 A 1 
HETATM 31 N N31 8VC . . . B 2 14.952 -25.072 -19.166 1 35.78 ? N31 8VC 401 A 1 
HETATM 32 C C32 8VC . . . B 2 14.306 -23.79 -18.807 1 34.34 ? C32 8VC 401 A 1 
HETATM 33 C C33 8VC . . . B 2 13.301 -24.141 -17.71 1 33.15 ? C33 8VC 401 A 1 
HETATM 34 C C34 8VC . . . B 2 12.192 -23.13 -17.912 1 33.21 ? C34 8VC 401 A 1 
HETATM 35 C C35 8VC . . . B 2 12.261 -22.769 -19.419 1 32.39 ? C35 8VC 401 A 1 
HETATM 36 C C36 8VC . . . B 2 11.313 -22.159 -20.264 1 32.53 ? C36 8VC 401 A 1 
HETATM 37 C C37 8VC . . . B 2 11.613 -21.955 -21.635 1 32.19 ? C37 8VC 401 A 1 
HETATM 38 C C38 8VC . . . B 2 12.867 -22.344 -22.156 1 32.75 ? C38 8VC 401 A 1 
HETATM 39 C C39 8VC . . . B 2 13.82 -22.961 -21.315 1 33.05 ? C39 8VC 401 A 1 
HETATM 40 C C40 8VC . . . B 2 13.496 -23.17 -19.949 1 33.66 ? C40 8VC 401 A 1 
HETATM 41 O O41 8VC . . . B 2 12.8 -25.467 -17.896 1 32.53 ? O41 8VC 401 A 1 
HETATM 42 C C42 8VC . . . B 2 17.591 -26.61 -17.386 1 36.66 ? C42 8VC 401 A 1 
HETATM 43 C C43 8VC . . . B 2 18.075 -28.608 -18.94 1 34.67 ? C43 8VC 401 A 1 
HETATM 44 O O44 8VC . . . B 2 17.75 -28.747 -24.311 1 37.01 ? O44 8VC 401 A 1 
HETATM 45 C C45 8VC . . . B 2 21.393 -24.492 -29.548 1 74.64 ? C45 8VC 401 A 1 
HETATM 46 N N46 8VC . . . B 2 26.108 -26.239 -30.017 1 84.63 ? N46 8VC 401 A 1 
HETATM 47 C C47 8VC . . . B 2 26.703 -24.906 -30.38 1 85.68 ? C47 8VC 401 A 1 
HETATM 48 C C48 8VC . . . B 2 26.787 -27.531 -30.307 1 85.09 ? C48 8VC 401 A 1 
HETATM 49 C C49 8VC . . . B 2 27.936 -27.468 -31.367 1 87.84 ? C49 8VC 401 A 1 
HETATM 50 N N50 8VC . . . B 2 28.89 -28.586 -31.166 1 89.95 ? N50 8VC 401 A 1 
HETATM 51 C C51 8VC . . . B 2 29.966 -28.167 -30.291 1 89.67 ? C51 8VC 401 A 1 
HETATM 52 C C52 8VC . . . B 2 29.434 -29.155 -32.433 1 90.4 ? C52 8VC 401 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           52 
#