data_6W3A
#
_model_server_result.job_id            wF-lVV1-TEyVKgEkSPOKEg 
_model_server_result.datetime_utc      '2025-03-04 07:39:53' 
_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          6w3a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1001}' 
#
_entry.id    6W3A 
#
_exptl.entry_id    6W3A 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              492.572 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ~{N}-[6-methyl-5-[3-[2-[[(3~{S})-piperidin-3-yl]amino]pyrimidin-4-yl]pyridin-2-yl]oxy-naphthalen-1-yl]but-2-ynamide 
_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            6W3A 
_cell.length_a            77.114 
_cell.length_b            82.387 
_cell.length_c            164.027 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6W3A 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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 
#
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           'C29 H28 N6 O2' 
_chem_comp.formula_weight    492.572 
_chem_comp.id                SJM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              ~{N}-[6-methyl-5-[3-[2-[[(3~{S})-piperidin-3-yl]amino]pyrimidin-4-yl]pyridin-2-yl]oxy-naphthalen-1-yl]but-2-ynamide 
_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
C35 N36 SJM sing 290 n n 
C35 C34 SJM sing 291 n n 
N36 C37 SJM sing 292 n n 
C37 C31 SJM sing 293 n n 
C38 C15 SJM sing 294 n n 
C34 C33 SJM sing 295 n n 
C33 C31 SJM sing 296 n n 
N30 C31 SJM sing 297 n n 
N30 C28 SJM sing 298 n n 
C14 C15 SJM doub 299 n y 
C14 C13 SJM sing 300 n y 
N27 C28 SJM doub 301 n y 
N27 C26 SJM sing 302 n y 
C15 C16 SJM sing 303 n y 
C28 N29 SJM sing 304 n y 
O5 C4 SJM doub 305 n n 
C26 C25 SJM doub 306 n y 
C1 C2 SJM sing 307 n n 
N29 C24 SJM doub 308 n y 
C13 C12 SJM doub 309 n y 
C2 C3 SJM trip 310 n n 
C25 C24 SJM sing 311 n y 
C3 C4 SJM sing 312 n n 
C24 C19 SJM sing 313 n n 
C4 N6 SJM sing 314 n n 
C16 O17 SJM sing 315 n n 
C16 C11 SJM doub 316 n y 
C19 C20 SJM doub 317 n y 
C19 C18 SJM sing 318 n y 
C20 C21 SJM sing 319 n y 
O17 C18 SJM sing 320 n n 
C18 N23 SJM doub 321 n y 
C12 C11 SJM sing 322 n y 
C12 C7 SJM sing 323 n y 
C21 C22 SJM doub 324 n y 
C11 C10 SJM sing 325 n y 
N23 C22 SJM sing 326 n y 
N6 C7 SJM sing 327 n n 
C7 C8 SJM doub 328 n y 
C10 C9 SJM doub 329 n y 
C8 C9 SJM sing 330 n y 
C14 H1 SJM sing 331 n n 
C8 H2 SJM sing 332 n n 
C9 H3 SJM sing 333 n n 
C10 H4 SJM sing 334 n n 
C13 H5 SJM sing 335 n n 
C1 H6 SJM sing 336 n n 
C1 H7 SJM sing 337 n n 
C1 H8 SJM sing 338 n n 
C20 H9 SJM sing 339 n n 
C21 H10 SJM sing 340 n n 
C22 H11 SJM sing 341 n n 
C25 H12 SJM sing 342 n n 
C26 H13 SJM sing 343 n n 
C31 H32 SJM sing 344 n n 
C33 H14 SJM sing 345 n n 
C33 H15 SJM sing 346 n n 
C34 H16 SJM sing 347 n n 
C34 H17 SJM sing 348 n n 
C35 H18 SJM sing 349 n n 
C35 H19 SJM sing 350 n n 
C37 H20 SJM sing 351 n n 
C37 H21 SJM sing 352 n n 
C38 H22 SJM sing 353 n n 
C38 H23 SJM sing 354 n n 
C38 H24 SJM sing 355 n n 
N30 H25 SJM sing 356 n n 
N36 H26 SJM sing 357 n n 
N6 H28 SJM sing 358 n n 
#
_atom_sites.entry_id                     6W3A 
_atom_sites.fract_transf_matrix[1][1]    0.012968 
_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]    0.012138 
_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]    0.006097 
_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 SJM A 1 1001 2 SJM DRG . 
D 2 SJM B 1 1001 1 SJM DRG . 
E 3 HOH A 1 1101 6 HOH HOH . 
E 3 HOH A 2 1102 28 HOH HOH . 
E 3 HOH A 3 1103 9 HOH HOH . 
E 3 HOH A 4 1104 1 HOH HOH . 
E 3 HOH A 5 1105 19 HOH HOH . 
E 3 HOH A 6 1106 37 HOH HOH . 
E 3 HOH A 7 1107 5 HOH HOH . 
E 3 HOH A 8 1108 26 HOH HOH . 
E 3 HOH A 9 1109 35 HOH HOH . 
E 3 HOH A 10 1110 47 HOH HOH . 
E 3 HOH A 11 1111 24 HOH HOH . 
E 3 HOH A 12 1112 2 HOH HOH . 
E 3 HOH A 13 1113 49 HOH HOH . 
E 3 HOH A 14 1114 10 HOH HOH . 
E 3 HOH A 15 1115 13 HOH HOH . 
E 3 HOH A 16 1116 43 HOH HOH . 
E 3 HOH A 17 1117 45 HOH HOH . 
E 3 HOH A 18 1118 20 HOH HOH . 
E 3 HOH A 19 1119 38 HOH HOH . 
F 3 HOH B 1 1101 25 HOH HOH . 
F 3 HOH B 2 1102 46 HOH HOH . 
F 3 HOH B 3 1103 3 HOH HOH . 
F 3 HOH B 4 1104 40 HOH HOH . 
F 3 HOH B 5 1105 44 HOH HOH . 
F 3 HOH B 6 1106 4 HOH HOH . 
F 3 HOH B 7 1107 27 HOH HOH . 
F 3 HOH B 8 1108 51 HOH HOH . 
F 3 HOH B 9 1109 8 HOH HOH . 
F 3 HOH B 10 1110 48 HOH HOH . 
F 3 HOH B 11 1111 18 HOH HOH . 
F 3 HOH B 12 1112 12 HOH HOH . 
F 3 HOH B 13 1113 32 HOH HOH . 
F 3 HOH B 14 1114 36 HOH HOH . 
F 3 HOH B 15 1115 23 HOH HOH . 
F 3 HOH B 16 1116 21 HOH HOH . 
F 3 HOH B 17 1117 39 HOH HOH . 
F 3 HOH B 18 1118 33 HOH HOH . 
F 3 HOH B 19 1119 41 HOH HOH . 
F 3 HOH B 20 1120 42 HOH HOH . 
F 3 HOH B 21 1121 16 HOH HOH . 
F 3 HOH B 22 1122 7 HOH HOH . 
F 3 HOH B 23 1123 31 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 C4 SJM . . . D 2 108.618 -15.613 51.891 1 24.54 ? C4 SJM 1001 B 1 
HETATM 2 C C14 SJM . . . D 2 108.547 -19.865 50.596 1 18.44 ? C14 SJM 1001 B 1 
HETATM 3 C C11 SJM . . . D 2 106.838 -19.58 52.755 1 22.56 ? C11 SJM 1001 B 1 
HETATM 4 C C7 SJM . . . D 2 107.808 -17.398 53.264 1 26.34 ? C7 SJM 1001 B 1 
HETATM 5 C C8 SJM . . . D 2 106.93 -17.298 54.324 1 24.8 ? C8 SJM 1001 B 1 
HETATM 6 C C9 SJM . . . D 2 106.023 -18.312 54.613 1 24.43 ? C9 SJM 1001 B 1 
HETATM 7 C C10 SJM . . . D 2 105.971 -19.437 53.85 1 21.61 ? C10 SJM 1001 B 1 
HETATM 8 C C12 SJM . . . D 2 107.77 -18.556 52.449 1 22.37 ? C12 SJM 1001 B 1 
HETATM 9 C C13 SJM . . . D 2 108.625 -18.73 51.348 1 20.07 ? C13 SJM 1001 B 1 
HETATM 10 C C3 SJM . . . D 2 109.499 -14.506 51.673 1 25.71 ? C3 SJM 1001 B 1 
HETATM 11 C C1 SJM . . . D 2 111.116 -12.456 51.241 1 27.75 ? C1 SJM 1001 B 1 
HETATM 12 C C15 SJM . . . D 2 107.631 -20.871 50.892 1 20.31 ? C15 SJM 1001 B 1 
HETATM 13 C C16 SJM . . . D 2 106.784 -20.744 51.964 1 24.65 ? C16 SJM 1001 B 1 
HETATM 14 C C18 SJM . . . D 2 106.086 -23.006 52.404 1 38.4 ? C18 SJM 1001 B 1 
HETATM 15 C C19 SJM . . . D 2 105.061 -23.925 52.112 1 39.09 ? C19 SJM 1001 B 1 
HETATM 16 C C2 SJM . . . D 2 110.217 -13.596 51.482 1 26.73 ? C2 SJM 1001 B 1 
HETATM 17 C C20 SJM . . . D 2 105.345 -25.287 52.231 1 40.56 ? C20 SJM 1001 B 1 
HETATM 18 C C21 SJM . . . D 2 106.614 -25.677 52.627 1 43.07 ? C21 SJM 1001 B 1 
HETATM 19 C C22 SJM . . . D 2 107.565 -24.712 52.895 1 42.65 ? C22 SJM 1001 B 1 
HETATM 20 C C24 SJM . . . D 2 103.694 -23.52 51.683 1 39.4 ? C24 SJM 1001 B 1 
HETATM 21 C C25 SJM . . . D 2 103.266 -22.186 51.646 1 37.46 ? C25 SJM 1001 B 1 
HETATM 22 C C26 SJM . . . D 2 101.98 -21.899 51.233 1 38.08 ? C26 SJM 1001 B 1 
HETATM 23 C C28 SJM . . . D 2 101.601 -24.147 50.93 1 37.43 ? C28 SJM 1001 B 1 
HETATM 24 C C31 SJM . . . D 2 101.141 -26.56 50.645 1 22.92 ? C31 SJM 1001 B 1 
HETATM 25 C C33 SJM . . . D 2 99.895 -27.439 50.511 1 16.5 ? C33 SJM 1001 B 1 
HETATM 26 C C34 SJM . . . D 2 100.298 -28.913 50.433 1 15.6 ? C34 SJM 1001 B 1 
HETATM 27 C C35 SJM . . . D 2 101.269 -29.105 49.268 1 17.46 ? C35 SJM 1001 B 1 
HETATM 28 C C37 SJM . . . D 2 102.138 -26.868 49.522 1 20.35 ? C37 SJM 1001 B 1 
HETATM 29 C C38 SJM . . . D 2 107.605 -22.091 50.007 1 21.83 ? C38 SJM 1001 B 1 
HETATM 30 N N23 SJM . . . D 2 107.281 -23.43 52.779 1 41.67 ? N23 SJM 1001 B 1 
HETATM 31 N N27 SJM . . . D 2 101.181 -22.893 50.885 1 38.32 ? N27 SJM 1001 B 1 
HETATM 32 N N29 SJM . . . D 2 102.828 -24.462 51.318 1 40.73 ? N29 SJM 1001 B 1 
HETATM 33 N N30 SJM . . . D 2 100.731 -25.156 50.557 1 31 ? N30 SJM 1001 B 1 
HETATM 34 N N36 SJM . . . D 2 102.47 -28.298 49.512 1 18.53 ? N36 SJM 1001 B 1 
HETATM 35 N N6 SJM . . . D 2 108.679 -16.326 53.037 1 26.21 ? N6 SJM 1001 B 1 
HETATM 36 O O17 SJM . . . D 2 105.854 -21.674 52.305 1 34.09 ? O17 SJM 1001 B 1 
HETATM 37 O O5 SJM . . . D 2 107.813 -15.909 51.03 1 24.69 ? O5 SJM 1001 B 1 
HETATM 38 H H32 SJM . . . D 2 101.617 -26.741 51.61 1 27.51 ? H32 SJM 1001 B 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           324 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           38 
#