data_6Z1Q
#
_model_server_result.job_id            JzT7cG0vJ9DLk37XI1NC2w 
_model_server_result.datetime_utc      '2025-07-31 06:48:09' 
_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          6z1q 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":701}' 
#
_entry.id    6Z1Q 
#
_exptl.entry_id    6Z1Q 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              490.554 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            DesF-3R/4076 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            6Z1Q 
_cell.length_a            84.77 
_cell.length_b            84.77 
_cell.length_c            118.52 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6Z1Q 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 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,C,E 1 1 
B,D,F 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 D N N 
#
_chem_comp.formula           'C26 H30 N6 O4' 
_chem_comp.formula_weight    490.554 
_chem_comp.id                Q58 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              DesF-3R/4076 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     4-[[4-[(3~{R})-3-(hydroxymethyl)-3-methyl-1,2-dihydropyrrolo[2,3-b]pyridin-5-yl]pyrimidin-2-yl]amino]-3-methoxy-~{N}-(oxan-4-yl)benzamide 
#
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
C7 N Q58 doub 277 n y 
C7 C6 Q58 sing 278 n y 
N C8 Q58 sing 279 n y 
C6 C5 Q58 doub 280 n y 
C8 N2 Q58 sing 281 n n 
C8 N1 Q58 doub 282 n y 
C5 N1 Q58 sing 283 n y 
C5 C4 Q58 sing 284 n n 
N2 C9 Q58 sing 285 n n 
C22 C4 Q58 doub 286 n y 
C22 N4 Q58 sing 287 n y 
O2 C21 Q58 sing 288 n n 
O2 C10 Q58 sing 289 n n 
C4 C3 Q58 sing 290 n y 
N4 C23 Q58 doub 291 n y 
C9 C10 Q58 doub 292 n y 
C9 C14 Q58 sing 293 n y 
C10 C11 Q58 sing 294 n y 
C3 C2 Q58 doub 295 n y 
C23 C2 Q58 sing 296 n y 
C23 N5 Q58 sing 297 n n 
C14 C13 Q58 doub 298 n y 
C2 C1 Q58 sing 299 n n 
C11 C12 Q58 doub 300 n y 
N5 C24 Q58 sing 301 n n 
C13 C12 Q58 sing 302 n y 
C25 C1 Q58 sing 303 n n 
C25 O3 Q58 sing 304 n n 
C12 C15 Q58 sing 305 n n 
C1 C24 Q58 sing 306 n n 
C1 C Q58 sing 307 n n 
O1 C15 Q58 doub 308 n n 
C15 N3 Q58 sing 309 n n 
N3 C16 Q58 sing 310 n n 
C16 C17 Q58 sing 311 n n 
C16 C20 Q58 sing 312 n n 
C17 C18 Q58 sing 313 n n 
C20 C19 Q58 sing 314 n n 
C18 O Q58 sing 315 n n 
C19 O Q58 sing 316 n n 
C13 H8 Q58 sing 317 n n 
C14 H9 Q58 sing 318 n n 
N5 H24 Q58 sing 319 n n 
C16 H11 Q58 sing 320 n n 
C17 H13 Q58 sing 321 n n 
C17 H12 Q58 sing 322 n n 
N3 H10 Q58 sing 323 n n 
N2 H6 Q58 sing 324 n n 
C11 H7 Q58 sing 325 n n 
C H Q58 sing 326 n n 
C H2 Q58 sing 327 n n 
C H1 Q58 sing 328 n n 
C3 H3 Q58 sing 329 n n 
C7 H5 Q58 sing 330 n n 
C6 H4 Q58 sing 331 n n 
C21 H20 Q58 sing 332 n n 
C21 H22 Q58 sing 333 n n 
C21 H21 Q58 sing 334 n n 
C20 H19 Q58 sing 335 n n 
C20 H18 Q58 sing 336 n n 
C19 H16 Q58 sing 337 n n 
C19 H17 Q58 sing 338 n n 
C18 H15 Q58 sing 339 n n 
C18 H14 Q58 sing 340 n n 
C22 H23 Q58 sing 341 n n 
C25 H27 Q58 sing 342 n n 
C25 H28 Q58 sing 343 n n 
O3 H29 Q58 sing 344 n n 
C24 H26 Q58 sing 345 n n 
C24 H25 Q58 sing 346 n n 
#
_atom_sites.entry_id                     6Z1Q 
_atom_sites.fract_transf_matrix[1][1]    0.011797 
_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]    0.011797 
_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]    0.008437 
_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 Q58 AAA 1 701 1 Q58 954 . 
D 2 Q58 BBB 1 701 1 Q58 954 . 
E 3 HOH AAA 1 801 71 HOH HOH . 
E 3 HOH AAA 2 802 5 HOH HOH . 
E 3 HOH AAA 3 803 32 HOH HOH . 
E 3 HOH AAA 4 804 27 HOH HOH . 
E 3 HOH AAA 5 805 79 HOH HOH . 
E 3 HOH AAA 6 806 3 HOH HOH . 
E 3 HOH AAA 7 807 72 HOH HOH . 
E 3 HOH AAA 8 808 58 HOH HOH . 
E 3 HOH AAA 9 809 16 HOH HOH . 
E 3 HOH AAA 10 810 55 HOH HOH . 
E 3 HOH AAA 11 811 46 HOH HOH . 
E 3 HOH AAA 12 812 43 HOH HOH . 
E 3 HOH AAA 13 813 44 HOH HOH . 
E 3 HOH AAA 14 814 61 HOH HOH . 
E 3 HOH AAA 15 815 13 HOH HOH . 
E 3 HOH AAA 16 816 51 HOH HOH . 
E 3 HOH AAA 17 817 11 HOH HOH . 
E 3 HOH AAA 18 818 17 HOH HOH . 
E 3 HOH AAA 19 819 60 HOH HOH . 
E 3 HOH AAA 20 820 47 HOH HOH . 
E 3 HOH AAA 21 821 67 HOH HOH . 
E 3 HOH AAA 22 822 48 HOH HOH . 
E 3 HOH AAA 23 823 22 HOH HOH . 
E 3 HOH AAA 24 824 20 HOH HOH . 
E 3 HOH AAA 25 825 50 HOH HOH . 
E 3 HOH AAA 26 826 8 HOH HOH . 
E 3 HOH AAA 27 827 9 HOH HOH . 
E 3 HOH AAA 28 828 75 HOH HOH . 
E 3 HOH AAA 29 829 10 HOH HOH . 
E 3 HOH AAA 30 830 40 HOH HOH . 
E 3 HOH AAA 31 831 4 HOH HOH . 
E 3 HOH AAA 32 832 56 HOH HOH . 
E 3 HOH AAA 33 833 42 HOH HOH . 
E 3 HOH AAA 34 834 2 HOH HOH . 
E 3 HOH AAA 35 835 7 HOH HOH . 
E 3 HOH AAA 36 836 25 HOH HOH . 
E 3 HOH AAA 37 837 19 HOH HOH . 
E 3 HOH AAA 38 838 64 HOH HOH . 
E 3 HOH AAA 39 839 39 HOH HOH . 
E 3 HOH AAA 40 840 49 HOH HOH . 
E 3 HOH AAA 41 841 62 HOH HOH . 
E 3 HOH AAA 42 842 41 HOH HOH . 
E 3 HOH AAA 43 843 57 HOH HOH . 
E 3 HOH AAA 44 844 63 HOH HOH . 
E 3 HOH AAA 45 845 6 HOH HOH . 
E 3 HOH AAA 46 846 59 HOH HOH . 
F 3 HOH BBB 1 801 53 HOH HOH . 
F 3 HOH BBB 2 802 78 HOH HOH . 
F 3 HOH BBB 3 803 34 HOH HOH . 
F 3 HOH BBB 4 804 68 HOH HOH . 
F 3 HOH BBB 5 805 38 HOH HOH . 
F 3 HOH BBB 6 806 70 HOH HOH . 
F 3 HOH BBB 7 807 37 HOH HOH . 
F 3 HOH BBB 8 808 28 HOH HOH . 
F 3 HOH BBB 9 809 66 HOH HOH . 
F 3 HOH BBB 10 810 12 HOH HOH . 
F 3 HOH BBB 11 811 26 HOH HOH . 
F 3 HOH BBB 12 812 76 HOH HOH . 
F 3 HOH BBB 13 813 23 HOH HOH . 
F 3 HOH BBB 14 814 69 HOH HOH . 
F 3 HOH BBB 15 815 74 HOH HOH . 
F 3 HOH BBB 16 816 52 HOH HOH . 
F 3 HOH BBB 17 817 31 HOH HOH . 
F 3 HOH BBB 18 818 73 HOH HOH . 
F 3 HOH BBB 19 819 29 HOH HOH . 
F 3 HOH BBB 20 820 24 HOH HOH . 
F 3 HOH BBB 21 821 14 HOH HOH . 
F 3 HOH BBB 22 822 77 HOH HOH . 
F 3 HOH BBB 23 823 1 HOH HOH . 
F 3 HOH BBB 24 824 15 HOH HOH . 
F 3 HOH BBB 25 825 45 HOH HOH . 
F 3 HOH BBB 26 826 21 HOH HOH . 
F 3 HOH BBB 27 827 36 HOH HOH . 
F 3 HOH BBB 28 828 18 HOH HOH . 
F 3 HOH BBB 29 829 65 HOH HOH . 
F 3 HOH BBB 30 830 35 HOH HOH . 
F 3 HOH BBB 31 831 54 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 C15 Q58 . . . D 2 44.813 -9.282 -2.001 1 68.39 ? C15 Q58 701 BBB 1 
HETATM 2 C C13 Q58 . . . D 2 42.828 -9.16 -0.402 1 62.66 ? C13 Q58 701 BBB 1 
HETATM 3 C C14 Q58 . . . D 2 42.307 -8.812 0.828 1 59.94 ? C14 Q58 701 BBB 1 
HETATM 4 N N5 Q58 . . . D 2 34.837 -8.667 0.221 1 46.93 ? N5 Q58 701 BBB 1 
HETATM 5 C C16 Q58 . . . D 2 44.548 -9.494 -4.445 1 81.71 ? C16 Q58 701 BBB 1 
HETATM 6 C C17 Q58 . . . D 2 44.18 -10.894 -4.905 1 84.07 ? C17 Q58 701 BBB 1 
HETATM 7 C C12 Q58 . . . D 2 44.174 -8.946 -0.688 1 67.22 ? C12 Q58 701 BBB 1 
HETATM 8 N N4 Q58 . . . D 2 35.581 -7.465 2.215 1 44.45 ? N4 Q58 701 BBB 1 
HETATM 9 C C10 Q58 . . . D 2 44.495 -8.013 1.506 1 64.23 ? C10 Q58 701 BBB 1 
HETATM 10 C C9 Q58 . . . D 2 43.136 -8.224 1.786 1 60.31 ? C9 Q58 701 BBB 1 
HETATM 11 O O Q58 . . . D 2 43.942 -10.095 -7.177 1 84.87 ? O Q58 701 BBB 1 
HETATM 12 N N3 Q58 . . . D 2 44.034 -9.248 -3.095 1 73.98 ? N3 Q58 701 BBB 1 
HETATM 13 N N2 Q58 . . . D 2 42.694 -7.832 3.072 1 55.2 ? N2 Q58 701 BBB 1 
HETATM 14 N N1 Q58 . . . D 2 40.366 -7.563 2.81 1 53.04 ? N1 Q58 701 BBB 1 
HETATM 15 C C11 Q58 . . . D 2 44.998 -8.375 0.276 1 65.31 ? C11 Q58 701 BBB 1 
HETATM 16 C C5 Q58 . . . D 2 39.199 -7.12 3.311 1 46.8 ? C5 Q58 701 BBB 1 
HETATM 17 C C Q58 . . . D 2 37.377 -8.524 -1.845 1 50.95 ? C Q58 701 BBB 1 
HETATM 18 C C1 Q58 . . . D 2 36.925 -9.359 -0.647 1 49.14 ? C1 Q58 701 BBB 1 
HETATM 19 C C2 Q58 . . . D 2 37.023 -8.547 0.627 1 46.4 ? C2 Q58 701 BBB 1 
HETATM 20 C C3 Q58 . . . D 2 38.147 -8.189 1.33 1 46.33 ? C3 Q58 701 BBB 1 
HETATM 21 C C4 Q58 . . . D 2 37.996 -7.42 2.488 1 46.67 ? C4 Q58 701 BBB 1 
HETATM 22 N N Q58 . . . D 2 41.496 -6.886 4.793 1 50.78 ? N Q58 701 BBB 1 
HETATM 23 C C8 Q58 . . . D 2 41.479 -7.414 3.547 1 49.59 ? C8 Q58 701 BBB 1 
HETATM 24 C C7 Q58 . . . D 2 40.317 -6.505 5.284 1 47.25 ? C7 Q58 701 BBB 1 
HETATM 25 C C6 Q58 . . . D 2 39.127 -6.616 4.598 1 45.94 ? C6 Q58 701 BBB 1 
HETATM 26 C C21 Q58 . . . D 2 46.502 -6.848 2.137 1 67.66 ? C21 Q58 701 BBB 1 
HETATM 27 O O2 Q58 . . . D 2 45.267 -7.467 2.496 1 67.45 ? O2 Q58 701 BBB 1 
HETATM 28 O O1 Q58 . . . D 2 46.016 -9.521 -2.07 1 68.08 ? O1 Q58 701 BBB 1 
HETATM 29 C C20 Q58 . . . D 2 44.035 -8.445 -5.417 1 83.34 ? C20 Q58 701 BBB 1 
HETATM 30 C C19 Q58 . . . D 2 44.414 -8.796 -6.835 1 83.57 ? C19 Q58 701 BBB 1 
HETATM 31 C C18 Q58 . . . D 2 44.546 -11.09 -6.356 1 86.6 ? C18 Q58 701 BBB 1 
HETATM 32 C C22 Q58 . . . D 2 36.678 -7.111 2.914 1 44.89 ? C22 Q58 701 BBB 1 
HETATM 33 C C23 Q58 . . . D 2 35.774 -8.19 1.099 1 46.14 ? C23 Q58 701 BBB 1 
HETATM 34 C C25 Q58 . . . D 2 37.801 -10.594 -0.53 1 50.11 ? C25 Q58 701 BBB 1 
HETATM 35 O O3 Q58 . . . D 2 37.448 -11.583 -1.489 1 54.03 ? O3 Q58 701 BBB 1 
HETATM 36 C C24 Q58 . . . D 2 35.418 -9.67 -0.693 1 48 ? C24 Q58 701 BBB 1 
HETATM 37 H H8 Q58 . . . D 2 42.263 -9.537 -1.052 1 63.1 ? H8 Q58 701 BBB 1 
HETATM 38 H H9 Q58 . . . D 2 41.396 -8.947 1.017 1 60.93 ? H9 Q58 701 BBB 1 
HETATM 39 H H24 Q58 . . . D 2 34.001 -8.408 0.2 1 47.02 ? H24 Q58 701 BBB 1 
HETATM 40 H H11 Q58 . . . D 2 45.535 -9.431 -4.427 1 80.86 ? H11 Q58 701 BBB 1 
HETATM 41 H H13 Q58 . . . D 2 43.227 -11.032 -4.787 1 84.08 ? H13 Q58 701 BBB 1 
HETATM 42 H H12 Q58 . . . D 2 44.649 -11.544 -4.359 1 84.03 ? H12 Q58 701 BBB 1 
HETATM 43 H H10 Q58 . . . D 2 43.191 -9.065 -3.001 1 74.26 ? H10 Q58 701 BBB 1 
HETATM 44 H H6 Q58 . . . D 2 43.317 -7.867 3.685 1 54.97 ? H6 Q58 701 BBB 1 
HETATM 45 H H7 Q58 . . . D 2 45.912 -8.229 0.084 1 65.24 ? H7 Q58 701 BBB 1 
HETATM 46 H H Q58 . . . D 2 37.75 -9.109 -2.526 1 50.39 ? H Q58 701 BBB 1 
HETATM 47 H H2 Q58 . . . D 2 38.055 -7.888 -1.558 1 50.37 ? H2 Q58 701 BBB 1 
HETATM 48 H H1 Q58 . . . D 2 36.619 -8.04 -2.21 1 50.37 ? H1 Q58 701 BBB 1 
HETATM 49 H H3 Q58 . . . D 2 39.017 -8.461 1.032 1 46.43 ? H3 Q58 701 BBB 1 
HETATM 50 H H5 Q58 . . . D 2 40.3 -6.108 6.146 1 47.85 ? H5 Q58 701 BBB 1 
HETATM 51 H H4 Q58 . . . D 2 38.319 -6.329 4.97 1 46.68 ? H4 Q58 701 BBB 1 
HETATM 52 H H20 Q58 . . . D 2 46.844 -6.349 2.896 1 67.59 ? H20 Q58 701 BBB 1 
HETATM 53 H H22 Q58 . . . D 2 46.357 -6.243 1.391 1 67.59 ? H22 Q58 701 BBB 1 
HETATM 54 H H21 Q58 . . . D 2 47.145 -7.53 1.883 1 67.59 ? H21 Q58 701 BBB 1 
HETATM 55 H H19 Q58 . . . D 2 44.407 -7.58 -5.185 1 82.99 ? H19 Q58 701 BBB 1 
HETATM 56 H H18 Q58 . . . D 2 43.069 -8.385 -5.347 1 82.91 ? H18 Q58 701 BBB 1 
HETATM 57 H H16 Q58 . . . D 2 45.39 -8.771 -6.933 1 83.83 ? H16 Q58 701 BBB 1 
HETATM 58 H H17 Q58 . . . D 2 44.028 -8.14 -7.453 1 83.82 ? H17 Q58 701 BBB 1 
HETATM 59 H H15 Q58 . . . D 2 44.247 -11.975 -6.655 1 85.55 ? H15 Q58 701 BBB 1 
HETATM 60 H H14 Q58 . . . D 2 45.52 -11.046 -6.461 1 85.57 ? H14 Q58 701 BBB 1 
HETATM 61 H H23 Q58 . . . D 2 36.568 -6.616 3.704 1 45.32 ? H23 Q58 701 BBB 1 
HETATM 62 H H27 Q58 . . . D 2 37.708 -10.972 0.371 1 50.76 ? H27 Q58 701 BBB 1 
HETATM 63 H H28 Q58 . . . D 2 38.739 -10.338 -0.661 1 50.77 ? H28 Q58 701 BBB 1 
HETATM 64 H H26 Q58 . . . D 2 35.066 -9.568 -1.6 1 48.02 ? H26 Q58 701 BBB 1 
HETATM 65 H H25 Q58 . . . D 2 35.238 -10.579 -0.378 1 48.03 ? H25 Q58 701 BBB 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           343 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           65 
#