data_6EKD
#
_model_server_result.job_id            vB9p-HattNN0hFDM8KeC5A 
_model_server_result.datetime_utc      '2024-11-27 17:09:40' 
_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          6ekd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":503}' 
#
_entry.id    6EKD 
#
_exptl.entry_id    6EKD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              381.495 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-(4-methyl-2-methylsulfanyl-1~{H}-imidazol-5-yl)-~{N}-(4-morpholin-4-ylphenyl)pyridin-2-amine 
_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            6EKD 
_cell.length_a            81.51 
_cell.length_b            124.82 
_cell.length_c            68.89 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6EKD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_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 
_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                      4 
_struct_asym.id                             D 
_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 248 A CYS 283 1_555 A SG CYS 248 A CYS 283 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? 
covale ? covale1 A SG CYS 166 A CYS 201 1_555 B S2 BME . A BME 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
#
_chem_comp.formula           'C20 H23 N5 O S' 
_chem_comp.formula_weight    381.495 
_chem_comp.id                B9K 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-(4-methyl-2-methylsulfanyl-1~{H}-imidazol-5-yl)-~{N}-(4-morpholin-4-ylphenyl)pyridin-2-amine 
_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
C02 C01 B9K doub 70 n y 
C02 N03 B9K sing 71 n y 
C01 C06 B9K sing 72 n y 
N03 C04 B9K doub 73 n y 
C12 C11 B9K sing 74 n n 
C06 C07 B9K sing 75 n n 
C06 C05 B9K doub 76 n y 
C11 C07 B9K doub 77 n y 
C11 N10 B9K sing 78 n y 
C04 C05 B9K sing 79 n y 
C04 N15 B9K sing 80 n n 
C07 N08 B9K sing 81 n y 
N10 C09 B9K doub 82 n y 
N15 C16 B9K sing 83 n n 
N08 C09 B9K sing 84 n y 
C09 S13 B9K sing 85 n n 
C16 C17 B9K doub 86 n y 
C16 C21 B9K sing 87 n y 
C14 S13 B9K sing 88 n n 
C17 C18 B9K sing 89 n y 
C21 C20 B9K doub 90 n y 
C18 C19 B9K doub 91 n y 
C20 C19 B9K sing 92 n y 
C19 N22 B9K sing 93 n n 
N22 C27 B9K sing 94 n n 
N22 C23 B9K sing 95 n n 
C27 C26 B9K sing 96 n n 
C23 C24 B9K sing 97 n n 
C26 O25 B9K sing 98 n n 
C24 O25 B9K sing 99 n n 
C17 H1 B9K sing 100 n n 
C20 H2 B9K sing 101 n n 
C21 H3 B9K sing 102 n n 
C24 H4 B9K sing 103 n n 
C24 H5 B9K sing 104 n n 
C26 H6 B9K sing 105 n n 
C26 H7 B9K sing 106 n n 
C01 H8 B9K sing 107 n n 
C02 H9 B9K sing 108 n n 
C05 H10 B9K sing 109 n n 
N08 H11 B9K sing 110 n n 
C12 H13 B9K sing 111 n n 
C12 H14 B9K sing 112 n n 
C12 H15 B9K sing 113 n n 
C14 H16 B9K sing 114 n n 
C14 H17 B9K sing 115 n n 
C14 H18 B9K sing 116 n n 
N15 H19 B9K sing 117 n n 
C18 H20 B9K sing 118 n n 
C23 H21 B9K sing 119 n n 
C23 H22 B9K sing 120 n n 
C27 H23 B9K sing 121 n n 
C27 H24 B9K sing 122 n n 
#
_atom_sites.entry_id                     6EKD 
_atom_sites.fract_transf_matrix[1][1]    0.012268 
_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]    0.008012 
_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]    0.014516 
_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 BME A 1 501 1 BME BME . 
C 3 EDO A 1 502 1 EDO EDO . 
D 4 B9K A 1 503 1 B9K LIG . 
E 5 HOH A 1 601 37 HOH HOH . 
E 5 HOH A 2 602 79 HOH HOH . 
E 5 HOH A 3 603 16 HOH HOH . 
E 5 HOH A 4 604 38 HOH HOH . 
E 5 HOH A 5 605 90 HOH HOH . 
E 5 HOH A 6 606 81 HOH HOH . 
E 5 HOH A 7 607 104 HOH HOH . 
E 5 HOH A 8 608 97 HOH HOH . 
E 5 HOH A 9 609 12 HOH HOH . 
E 5 HOH A 10 610 91 HOH HOH . 
E 5 HOH A 11 611 63 HOH HOH . 
E 5 HOH A 12 612 45 HOH HOH . 
E 5 HOH A 13 613 17 HOH HOH . 
E 5 HOH A 14 614 98 HOH HOH . 
E 5 HOH A 15 615 2 HOH HOH . 
E 5 HOH A 16 616 43 HOH HOH . 
E 5 HOH A 17 617 28 HOH HOH . 
E 5 HOH A 18 618 53 HOH HOH . 
E 5 HOH A 19 619 65 HOH HOH . 
E 5 HOH A 20 620 66 HOH HOH . 
E 5 HOH A 21 621 93 HOH HOH . 
E 5 HOH A 22 622 25 HOH HOH . 
E 5 HOH A 23 623 39 HOH HOH . 
E 5 HOH A 24 624 67 HOH HOH . 
E 5 HOH A 25 625 52 HOH HOH . 
E 5 HOH A 26 626 24 HOH HOH . 
E 5 HOH A 27 627 49 HOH HOH . 
E 5 HOH A 28 628 13 HOH HOH . 
E 5 HOH A 29 629 72 HOH HOH . 
E 5 HOH A 30 630 86 HOH HOH . 
E 5 HOH A 31 631 48 HOH HOH . 
E 5 HOH A 32 632 6 HOH HOH . 
E 5 HOH A 33 633 11 HOH HOH . 
E 5 HOH A 34 634 46 HOH HOH . 
E 5 HOH A 35 635 80 HOH HOH . 
E 5 HOH A 36 636 21 HOH HOH . 
E 5 HOH A 37 637 22 HOH HOH . 
E 5 HOH A 38 638 57 HOH HOH . 
E 5 HOH A 39 639 64 HOH HOH . 
E 5 HOH A 40 640 50 HOH HOH . 
E 5 HOH A 41 641 101 HOH HOH . 
E 5 HOH A 42 642 55 HOH HOH . 
E 5 HOH A 43 643 7 HOH HOH . 
E 5 HOH A 44 644 9 HOH HOH . 
E 5 HOH A 45 645 59 HOH HOH . 
E 5 HOH A 46 646 88 HOH HOH . 
E 5 HOH A 47 647 23 HOH HOH . 
E 5 HOH A 48 648 85 HOH HOH . 
E 5 HOH A 49 649 89 HOH HOH . 
E 5 HOH A 50 650 8 HOH HOH . 
E 5 HOH A 51 651 83 HOH HOH . 
E 5 HOH A 52 652 26 HOH HOH . 
E 5 HOH A 53 653 69 HOH HOH . 
E 5 HOH A 54 654 61 HOH HOH . 
E 5 HOH A 55 655 74 HOH HOH . 
E 5 HOH A 56 656 100 HOH HOH . 
E 5 HOH A 57 657 20 HOH HOH . 
E 5 HOH A 58 658 15 HOH HOH . 
E 5 HOH A 59 659 54 HOH HOH . 
E 5 HOH A 60 660 76 HOH HOH . 
E 5 HOH A 61 661 60 HOH HOH . 
E 5 HOH A 62 662 84 HOH HOH . 
E 5 HOH A 63 663 30 HOH HOH . 
E 5 HOH A 64 664 62 HOH HOH . 
E 5 HOH A 65 665 44 HOH HOH . 
E 5 HOH A 66 666 33 HOH HOH . 
E 5 HOH A 67 667 1 HOH HOH . 
E 5 HOH A 68 668 96 HOH HOH . 
E 5 HOH A 69 669 5 HOH HOH . 
E 5 HOH A 70 670 41 HOH HOH . 
E 5 HOH A 71 671 10 HOH HOH . 
E 5 HOH A 72 672 4 HOH HOH . 
E 5 HOH A 73 673 36 HOH HOH . 
E 5 HOH A 74 674 29 HOH HOH . 
E 5 HOH A 75 675 58 HOH HOH . 
E 5 HOH A 76 676 71 HOH HOH . 
E 5 HOH A 77 677 51 HOH HOH . 
E 5 HOH A 78 678 31 HOH HOH . 
E 5 HOH A 79 679 75 HOH HOH . 
E 5 HOH A 80 680 73 HOH HOH . 
E 5 HOH A 81 681 42 HOH HOH . 
E 5 HOH A 82 682 95 HOH HOH . 
E 5 HOH A 83 683 56 HOH HOH . 
E 5 HOH A 84 684 87 HOH HOH . 
E 5 HOH A 85 685 102 HOH HOH . 
E 5 HOH A 86 686 47 HOH HOH . 
E 5 HOH A 87 687 40 HOH HOH . 
E 5 HOH A 88 688 70 HOH HOH . 
E 5 HOH A 89 689 14 HOH HOH . 
E 5 HOH A 90 690 94 HOH HOH . 
E 5 HOH A 91 691 3 HOH HOH . 
E 5 HOH A 92 692 99 HOH HOH . 
E 5 HOH A 93 693 78 HOH HOH . 
E 5 HOH A 94 694 32 HOH HOH . 
E 5 HOH A 95 695 92 HOH HOH . 
E 5 HOH A 96 696 27 HOH HOH . 
E 5 HOH A 97 697 34 HOH HOH . 
E 5 HOH A 98 698 82 HOH HOH . 
E 5 HOH A 99 699 103 HOH HOH . 
E 5 HOH A 100 700 35 HOH HOH . 
E 5 HOH A 101 701 77 HOH HOH . 
E 5 HOH A 102 702 19 HOH HOH . 
E 5 HOH A 103 703 68 HOH HOH . 
E 5 HOH A 104 704 18 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 C17 B9K . . . D 4 8.692 32.401 13.214 1 45.76 ? C17 B9K 503 A 1 
HETATM 2 C C20 B9K . . . D 4 6.862 33.312 15.112 1 43.42 ? C20 B9K 503 A 1 
HETATM 3 C C21 B9K . . . D 4 6.954 33.937 13.88 1 45.09 ? C21 B9K 503 A 1 
HETATM 4 C C24 B9K . . . D 4 6.829 31.592 19.187 1 56.86 ? C24 B9K 503 A 1 
HETATM 5 C C26 B9K . . . D 4 8.772 30.425 18.728 1 59.45 ? C26 B9K 503 A 1 
HETATM 6 C C01 B9K . . . D 4 11.223 35.361 9.446 1 35.56 ? C01 B9K 503 A 1 
HETATM 7 C C02 B9K . . . D 4 9.935 35.435 8.994 1 39.48 ? C02 B9K 503 A 1 
HETATM 8 N N03 B9K . . . D 4 8.933 35.05 9.761 1 38.87 ? N03 B9K 503 A 1 
HETATM 9 C C04 B9K . . . D 4 9.108 34.574 10.972 1 40.83 ? C04 B9K 503 A 1 
HETATM 10 C C05 B9K . . . D 4 10.392 34.486 11.507 1 39.05 ? C05 B9K 503 A 1 
HETATM 11 C C06 B9K . . . D 4 11.479 34.902 10.726 1 39.35 ? C06 B9K 503 A 1 
HETATM 12 C C07 B9K . . . D 4 12.773 34.786 11.239 1 41.04 ? C07 B9K 503 A 1 
HETATM 13 N N08 B9K . . . D 4 13.12 33.911 12.179 1 42.61 ? N08 B9K 503 A 1 
HETATM 14 C C09 B9K . . . D 4 14.398 34.059 12.423 1 44.87 ? C09 B9K 503 A 1 
HETATM 15 N N10 B9K . . . D 4 14.912 34.98 11.652 1 42.26 ? N10 B9K 503 A 1 
HETATM 16 C C11 B9K . . . D 4 13.95 35.462 10.89 1 41.3 ? C11 B9K 503 A 1 
HETATM 17 C C12 B9K . . . D 4 14.177 36.573 9.873 1 41.7 ? C12 B9K 503 A 1 
HETATM 18 S S13 B9K . . . D 4 15.309 33.109 13.631 1 51.11 ? S13 B9K 503 A 1 
HETATM 19 C C14 B9K . . . D 4 17.06 33.181 13.168 1 57.28 ? C14 B9K 503 A 1 
HETATM 20 N N15 B9K . . . D 4 7.895 34.182 11.673 1 42.35 ? N15 B9K 503 A 1 
HETATM 21 C C16 B9K . . . D 4 7.87 33.491 12.936 1 44.04 ? C16 B9K 503 A 1 
HETATM 22 C C18 B9K . . . D 4 8.624 31.777 14.453 1 45.97 ? C18 B9K 503 A 1 
HETATM 23 C C19 B9K . . . D 4 7.698 32.225 15.422 1 47.99 ? C19 B9K 503 A 1 
HETATM 24 N N22 B9K . . . D 4 7.616 31.571 16.734 1 53.46 ? N22 B9K 503 A 1 
HETATM 25 C C23 B9K . . . D 4 6.805 32.228 17.806 1 57.57 ? C23 B9K 503 A 1 
HETATM 26 O O25 B9K . . . D 4 8.136 31.316 19.573 1 61.19 ? O25 B9K 503 A 1 
HETATM 27 C C27 B9K . . . D 4 8.845 30.943 17.285 1 56.41 ? C27 B9K 503 A 1 
#
_model_server_stats.io_time_ms              78 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#