data_8BDN
#
_model_server_result.job_id            42XQ_t7oXqXypTXqw6upCA 
_model_server_result.datetime_utc      '2024-11-08 15:35:47' 
_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          8bdn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":301}' 
#
_entry.id    8BDN 
#
_exptl.entry_id    8BDN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              509.62 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2~{R})-3-methyl-1-[(2~{S},4~{R})-2-[(5~{R})-5-methyl-5-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-4~{H}-1,2,4-oxadiazol-3-yl]-4-oxidanyl-pyrrolidin-1-yl]-2-(3-methyl-1,2-oxazol-5-yl)butan-1-one 
_entity.pdbx_number_of_molecules    4 
_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            8BDN 
_cell.length_a            93.173 
_cell.length_b            93.173 
_cell.length_c            358.85 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8BDN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        91 
_symmetry.space_group_name_Hall    'P 4w 2c' 
_symmetry.space_group_name_H-M     'P 41 2 2' 
#
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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_software_defined_assembly 2 
PISA trimeric 3 author_and_software_defined_assembly 3 
PISA trimeric 3 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,J,M,Q,R,S,Z 1 1 
C,D,E,K,M,S,T,U,AA 2 1 
F,G,L,N,P,V,W,BA 3 1 
H,I,L,O,P,X,Y,BA 4 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
? 4 M N N 
? 4 N N N 
? 4 O N N 
? 4 P 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 C LEU 88 A LEU 88 1_555 A N CAS 89 A CAS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? 
covale ? covale2 A C CAS 89 A CAS 89 1_555 A N ILE 90 A ILE 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale3 C C PHE 25 C PHE 76 1_555 C N CAS 26 C CAS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale4 C C CAS 26 C CAS 77 1_555 C N ASN 27 C ASN 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale5 D C LEU 88 D LEU 88 1_555 D N CAS 89 D CAS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale6 D C CAS 89 D CAS 89 1_555 D N ILE 90 D ILE 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale7 F C PHE 25 F PHE 76 1_555 F N CAS 26 F CAS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale8 F C CAS 26 F CAS 77 1_555 F N ASN 27 F ASN 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale9 G C LEU 88 G LEU 88 1_555 G N CAS 89 G CAS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale10 G C CAS 89 G CAS 89 1_555 G N ILE 90 G ILE 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale11 I C PHE 25 I PHE 76 1_555 I N CAS 26 I CAS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale12 I C CAS 26 I CAS 77 1_555 I N ASN 27 I ASN 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale13 J C LEU 88 J LEU 88 1_555 J N CAS 89 J CAS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale14 J C CAS 89 J CAS 89 1_555 J N ILE 90 J ILE 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale15 L C PHE 25 L PHE 76 1_555 L N CAS 26 L CAS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale16 L C CAS 26 L CAS 77 1_555 L N ASN 27 L ASN 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
#
_chem_comp.formula           'C26 H31 N5 O4 S' 
_chem_comp.formula_weight    509.62 
_chem_comp.id                QFR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2~{R})-3-methyl-1-[(2~{S},4~{R})-2-[(5~{R})-5-methyl-5-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-4~{H}-1,2,4-oxadiazol-3-yl]-4-oxidanyl-pyrrolidin-1-yl]-2-(3-methyl-1,2-oxazol-5-yl)butan-1-one 
_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
N5 C24 QFR doub 298 n y 
N5 C25 QFR sing 299 n y 
C24 S1 QFR sing 300 n y 
C26 C25 QFR sing 301 n n 
C25 C15 QFR doub 302 n y 
S1 C15 QFR sing 303 n y 
C15 C12 QFR sing 304 n n 
C12 C11 QFR doub 305 n y 
C12 C13 QFR sing 306 n y 
C11 C10 QFR sing 307 n y 
C13 C14 QFR doub 308 n y 
C10 C9 QFR doub 309 n y 
C14 C9 QFR sing 310 n y 
C9 C8 QFR sing 311 n n 
C16 C8 QFR sing 312 n n 
C8 N2 QFR sing 313 n n 
C8 O3 QFR sing 314 n n 
N2 C7 QFR sing 315 n n 
O3 N3 QFR sing 316 n n 
C3 C2 QFR sing 317 n n 
C3 C4 QFR sing 318 n n 
C7 N3 QFR doub 319 n n 
C7 C2 QFR sing 320 n n 
C2 N1 QFR sing 321 n n 
C4 O2 QFR sing 322 n n 
C4 C1 QFR sing 323 n n 
N1 C1 QFR sing 324 n n 
N1 C5 QFR sing 325 n n 
O1 C5 QFR doub 326 n n 
C5 C6 QFR sing 327 n n 
C20 C18 QFR sing 328 n n 
C6 C18 QFR sing 329 n n 
C6 C17 QFR sing 330 n n 
C18 C19 QFR sing 331 n n 
C17 C21 QFR doub 332 n y 
C17 O4 QFR sing 333 n y 
C21 C22 QFR sing 334 n y 
O4 N4 QFR sing 335 n y 
C22 N4 QFR doub 336 n y 
C22 C23 QFR sing 337 n n 
C1 H1 QFR sing 338 n n 
C1 H2 QFR sing 339 n n 
C2 H3 QFR sing 340 n n 
C3 H4 QFR sing 341 n n 
C3 H5 QFR sing 342 n n 
C4 H6 QFR sing 343 n n 
C6 H7 QFR sing 344 n n 
C10 H11 QFR sing 345 n n 
C11 H12 QFR sing 346 n n 
C13 H13 QFR sing 347 n n 
C14 H14 QFR sing 348 n n 
O2 H16 QFR sing 349 n n 
C16 H18 QFR sing 350 n n 
C16 H19 QFR sing 351 n n 
C16 H20 QFR sing 352 n n 
C18 H21 QFR sing 353 n n 
C19 H22 QFR sing 354 n n 
C19 H23 QFR sing 355 n n 
C19 H24 QFR sing 356 n n 
C20 H25 QFR sing 357 n n 
C20 H26 QFR sing 358 n n 
C20 H27 QFR sing 359 n n 
C21 H28 QFR sing 360 n n 
C23 H29 QFR sing 361 n n 
C23 H30 QFR sing 362 n n 
C23 H31 QFR sing 363 n n 
N2 H8 QFR sing 364 n n 
C24 H9 QFR sing 365 n n 
C26 H10 QFR sing 366 n n 
C26 H15 QFR sing 367 n n 
C26 H17 QFR sing 368 n n 
#
_atom_sites.entry_id                     8BDN 
_atom_sites.fract_transf_matrix[1][1]    0.010733 
_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]    0.010733 
_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]    0.002787 
_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
M 4 QFR C 1 301 301 QFR UNL . 
N 4 QFR F 1 301 301 QFR UNL . 
O 4 QFR I 1 301 301 QFR UNL . 
P 4 QFR L 1 301 301 QFR UNL . 
Q 5 HOH A 1 201 26 HOH HOH . 
Q 5 HOH A 2 202 25 HOH HOH . 
Q 5 HOH A 3 203 4 HOH HOH . 
R 5 HOH B 1 201 1 HOH HOH . 
R 5 HOH B 2 202 38 HOH HOH . 
R 5 HOH B 3 203 18 HOH HOH . 
S 5 HOH C 1 401 10 HOH HOH . 
S 5 HOH C 2 402 16 HOH HOH . 
S 5 HOH C 3 403 19 HOH HOH . 
T 5 HOH D 1 201 15 HOH HOH . 
T 5 HOH D 2 202 7 HOH HOH . 
T 5 HOH D 3 203 8 HOH HOH . 
T 5 HOH D 4 204 30 HOH HOH . 
T 5 HOH D 5 205 41 HOH HOH . 
T 5 HOH D 6 206 32 HOH HOH . 
U 5 HOH E 1 201 35 HOH HOH . 
U 5 HOH E 2 202 5 HOH HOH . 
U 5 HOH E 3 203 39 HOH HOH . 
U 5 HOH E 4 204 36 HOH HOH . 
V 5 HOH F 1 401 11 HOH HOH . 
V 5 HOH F 2 402 13 HOH HOH . 
V 5 HOH F 3 403 21 HOH HOH . 
V 5 HOH F 4 404 2 HOH HOH . 
V 5 HOH F 5 405 14 HOH HOH . 
V 5 HOH F 6 406 40 HOH HOH . 
W 5 HOH G 1 201 20 HOH HOH . 
W 5 HOH G 2 202 22 HOH HOH . 
W 5 HOH G 3 203 24 HOH HOH . 
X 5 HOH H 1 201 3 HOH HOH . 
X 5 HOH H 2 202 12 HOH HOH . 
X 5 HOH H 3 203 37 HOH HOH . 
Y 5 HOH I 1 401 33 HOH HOH . 
Y 5 HOH I 2 402 27 HOH HOH . 
Y 5 HOH I 3 403 17 HOH HOH . 
Y 5 HOH I 4 404 6 HOH HOH . 
Y 5 HOH I 5 405 34 HOH HOH . 
Y 5 HOH I 6 406 23 HOH HOH . 
Z 5 HOH J 1 201 31 HOH HOH . 
AA 5 HOH K 1 201 28 HOH HOH . 
BA 5 HOH L 1 401 9 HOH HOH . 
BA 5 HOH L 2 402 29 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 QFR . . . M 4 -7.822 18.593 -0.091 1 63.76 ? C1 QFR 301 C 1 
HETATM 2 N N1 QFR . . . M 4 -7.549 17.16 -0.258 1 69.91 ? N1 QFR 301 C 1 
HETATM 3 C C2 QFR . . . M 4 -7.774 16.719 -1.637 1 66.67 ? C2 QFR 301 C 1 
HETATM 4 C C3 QFR . . . M 4 -8.036 18.038 -2.367 1 62.85 ? C3 QFR 301 C 1 
HETATM 5 C C4 QFR . . . M 4 -8.706 18.877 -1.296 1 63.2 ? C4 QFR 301 C 1 
HETATM 6 C C5 QFR . . . M 4 -7.215 16.321 0.738 1 69.26 ? C5 QFR 301 C 1 
HETATM 7 C C6 QFR . . . M 4 -7.286 16.859 2.162 1 70.99 ? C6 QFR 301 C 1 
HETATM 8 O O1 QFR . . . M 4 -6.955 15.155 0.513 1 73.23 ? O1 QFR 301 C 1 
HETATM 9 C C7 QFR . . . M 4 -6.581 16.051 -2.239 1 65.29 ? C7 QFR 301 C 1 
HETATM 10 N N2 QFR . . . M 4 -6.657 15.111 -3.203 1 70.02 ? N2 QFR 301 C 1 
HETATM 11 C C8 QFR . . . M 4 -5.331 14.88 -3.754 1 70.08 ? C8 QFR 301 C 1 
HETATM 12 C C9 QFR . . . M 4 -5.097 15.656 -5.044 1 69.83 ? C9 QFR 301 C 1 
HETATM 13 C C10 QFR . . . M 4 -3.902 15.53 -5.732 1 61.25 ? C10 QFR 301 C 1 
HETATM 14 C C11 QFR . . . M 4 -3.679 16.247 -6.894 1 59.02 ? C11 QFR 301 C 1 
HETATM 15 C C12 QFR . . . M 4 -4.642 17.119 -7.395 1 61.17 ? C12 QFR 301 C 1 
HETATM 16 C C13 QFR . . . M 4 -5.843 17.238 -6.701 1 63.06 ? C13 QFR 301 C 1 
HETATM 17 C C14 QFR . . . M 4 -6.065 16.517 -5.54 1 68.8 ? C14 QFR 301 C 1 
HETATM 18 C C15 QFR . . . M 4 -4.406 17.891 -8.632 1 63.1 ? C15 QFR 301 C 1 
HETATM 19 O O2 QFR . . . M 4 -10.015 18.37 -1.088 1 62.29 ? O2 QFR 301 C 1 
HETATM 20 N N3 QFR . . . M 4 -5.366 16.301 -1.917 1 62.51 ? N3 QFR 301 C 1 
HETATM 21 O O3 QFR . . . M 4 -4.511 15.501 -2.72 1 72.34 ? O3 QFR 301 C 1 
HETATM 22 C C16 QFR . . . M 4 -4.958 13.413 -3.827 1 61.98 ? C16 QFR 301 C 1 
HETATM 23 C C17 QFR . . . M 4 -8.316 16.079 2.922 1 75.42 ? C17 QFR 301 C 1 
HETATM 24 C C18 QFR . . . M 4 -5.931 16.942 2.89 1 75.68 ? C18 QFR 301 C 1 
HETATM 25 C C19 QFR . . . M 4 -5.423 15.597 3.388 1 83.43 ? C19 QFR 301 C 1 
HETATM 26 C C20 QFR . . . M 4 -4.878 17.589 1.998 1 71.09 ? C20 QFR 301 C 1 
HETATM 27 C C21 QFR . . . M 4 -8.529 14.769 3.132 1 84.92 ? C21 QFR 301 C 1 
HETATM 28 C C22 QFR . . . M 4 -9.716 14.699 3.906 1 88.13 ? C22 QFR 301 C 1 
HETATM 29 N N4 QFR . . . M 4 -10.212 15.88 4.116 1 83.19 ? N4 QFR 301 C 1 
HETATM 30 O O4 QFR . . . M 4 -9.322 16.782 3.477 1 80.74 ? O4 QFR 301 C 1 
HETATM 31 C C23 QFR . . . M 4 -10.398 13.481 4.44 1 80.1 ? C23 QFR 301 C 1 
HETATM 32 S S1 QFR . . . M 4 -5.049 19.48 -8.822 1 59.92 ? S1 QFR 301 C 1 
HETATM 33 C C24 QFR . . . M 4 -4.144 19.637 -10.26 1 57.55 ? C24 QFR 301 C 1 
HETATM 34 N N5 QFR . . . M 4 -3.512 18.575 -10.651 1 63.44 ? N5 QFR 301 C 1 
HETATM 35 C C25 QFR . . . M 4 -3.747 17.536 -9.781 1 61.79 ? C25 QFR 301 C 1 
HETATM 36 C C26 QFR . . . M 4 -3.266 16.171 -10.161 1 59.39 ? C26 QFR 301 C 1 
#
_model_server_stats.io_time_ms              40 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    41 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           36 
#