data_8U15
#
_model_server_result.job_id            wfEMZvxbgPcGw9aoNJqysg 
_model_server_result.datetime_utc      '2024-12-02 17:48:00' 
_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          8u15 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":502}' 
#
_entry.id    8U15 
#
_exptl.entry_id    8U15 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              449.499 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione 
_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          91.72 
_cell.angle_gamma         90 
_cell.entry_id            8U15 
_cell.length_a            110.729 
_cell.length_b            95.727 
_cell.length_c            150.947 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8U15 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,G,H,I,J,K,L,M,N,O,P,AA,BA,CA 1 1 
D,E,F,Q,R,S,T,U,V,W,X,Y,Z,DA,EA,FA 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
? 5 H N N 
? 5 R 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
disulf ? disulf1 B SG CYS 18 B CYS 18 1_555 B SG CYS 313 B CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf2 E SG CYS 18 E CYS 18 1_555 E SG CYS 313 E CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
metalc ? metalc1 A SG CYS 254 A CYS 323 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? 
metalc ? metalc2 A SG CYS 257 A CYS 326 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc3 A SG CYS 322 A CYS 391 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc4 A SG CYS 325 A CYS 394 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc5 C SG CYS 7 C CYS 384 1_555 N ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc6 C SG CYS 10 C CYS 387 1_555 N ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc7 C NE2 HIS 23 C HIS 400 1_555 N ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
metalc ? metalc8 C NE2 HIS 27 C HIS 404 1_555 N ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 
metalc ? metalc9 C SG CYS 35 C CYS 412 1_555 O ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc10 C SG CYS 38 C CYS 415 1_555 O ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc11 C NE2 HIS 51 C HIS 428 1_555 O ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc12 C NE2 HIS 55 C HIS 432 1_555 O ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc13 D SG CYS 254 D CYS 323 1_555 Q ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? 
metalc ? metalc14 D SG CYS 257 D CYS 326 1_555 Q ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc15 D SG CYS 322 D CYS 391 1_555 Q ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? 
metalc ? metalc16 D SG CYS 325 D CYS 394 1_555 Q ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc17 F SG CYS 7 F CYS 384 1_555 X ZN ZN . F ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc18 F SG CYS 10 F CYS 387 1_555 X ZN ZN . F ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? 
metalc ? metalc19 F NE2 HIS 27 F HIS 404 1_555 X ZN ZN . F ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc20 F SG CYS 35 F CYS 412 1_555 Y ZN ZN . F ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc21 F SG CYS 38 F CYS 415 1_555 Y ZN ZN . F ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
metalc ? metalc22 F NE2 HIS 51 F HIS 428 1_555 Y ZN ZN . F ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? 
metalc ? metalc23 F NE2 HIS 55 F HIS 432 1_555 Y ZN ZN . F ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
#
_chem_comp.formula           'C25 H27 N3 O5' 
_chem_comp.formula_weight    449.499 
_chem_comp.id                8W7 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione 
_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
C11 C10 8W7 sing 1 n n 
C11 C12 8W7 sing 2 n n 
C10 C9 8W7 sing 3 n n 
O3 C12 8W7 doub 4 n n 
C12 N2 8W7 sing 5 n n 
C9 N1 8W7 sing 6 n n 
C9 C13 8W7 sing 7 n n 
C7 N1 8W7 sing 8 n n 
C7 C6 8W7 sing 9 n n 
N1 C8 8W7 sing 10 n n 
O4 C3 8W7 sing 11 n n 
O4 C14 8W7 sing 12 n n 
C6 C3 8W7 doub 13 n y 
C6 C5 8W7 sing 14 n y 
C8 O1 8W7 doub 15 n n 
C8 C5 8W7 sing 16 n n 
C3 C2 8W7 sing 17 n y 
C5 C4 8W7 doub 18 n y 
C2 C1 8W7 doub 19 n y 
C14 C15 8W7 sing 20 n n 
N2 C13 8W7 sing 21 n n 
C4 C1 8W7 sing 22 n y 
C13 O2 8W7 doub 23 n n 
C15 C17 8W7 doub 24 n y 
C15 C16 8W7 sing 25 n y 
C17 C19 8W7 sing 26 n y 
C16 C18 8W7 doub 27 n y 
C19 C20 8W7 doub 28 n y 
C18 C20 8W7 sing 29 n y 
C20 C21 8W7 sing 30 n n 
C21 N3 8W7 sing 31 n n 
N3 C25 8W7 sing 32 n n 
N3 C22 8W7 sing 33 n n 
C25 C24 8W7 sing 34 n n 
C24 O5 8W7 sing 35 n n 
C22 C23 8W7 sing 36 n n 
C23 O5 8W7 sing 37 n n 
C1 H1 8W7 sing 38 n n 
C2 H2 8W7 sing 39 n n 
C4 H3 8W7 sing 40 n n 
N2 H4 8W7 sing 41 n n 
C7 H6 8W7 sing 42 n n 
C7 H7 8W7 sing 43 n n 
C9 H8 8W7 sing 44 n n 
C10 H9 8W7 sing 45 n n 
C10 H10 8W7 sing 46 n n 
C11 H11 8W7 sing 47 n n 
C11 H12 8W7 sing 48 n n 
C14 H13 8W7 sing 49 n n 
C14 H14 8W7 sing 50 n n 
C22 H15 8W7 sing 51 n n 
C22 H16 8W7 sing 52 n n 
C23 H17 8W7 sing 53 n n 
C23 H18 8W7 sing 54 n n 
C24 H19 8W7 sing 55 n n 
C24 H20 8W7 sing 56 n n 
C25 H21 8W7 sing 57 n n 
C25 H22 8W7 sing 58 n n 
C21 H23 8W7 sing 59 n n 
C21 H24 8W7 sing 60 n n 
C19 H25 8W7 sing 61 n n 
C17 H26 8W7 sing 62 n n 
C18 H27 8W7 sing 63 n n 
C16 H28 8W7 sing 64 n n 
#
_atom_sites.entry_id                     8U15 
_atom_sites.fract_transf_matrix[1][1]    0.009031 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000271 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010446 
_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]    0.006628 
_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
G 4 ZN A 1 501 501 ZN ZN . 
H 5 8W7 A 1 502 1 8W7 8W7 . 
I 6 SO4 A 1 503 5 SO4 SO4 . 
J 6 SO4 A 1 504 8 SO4 SO4 . 
K 6 SO4 A 1 505 10 SO4 SO4 . 
L 6 SO4 B 1 1201 6 SO4 SO4 . 
M 6 SO4 B 1 1202 12 SO4 SO4 . 
N 4 ZN C 1 501 501 ZN ZN . 
O 4 ZN C 1 502 502 ZN ZN . 
P 6 SO4 C 1 503 1 SO4 SO4 . 
Q 4 ZN D 1 501 501 ZN ZN . 
R 5 8W7 D 1 502 1 8W7 8W7 . 
S 6 SO4 D 1 503 3 SO4 SO4 . 
T 6 SO4 D 1 504 7 SO4 SO4 . 
U 6 SO4 E 1 1201 2 SO4 SO4 . 
V 6 SO4 E 1 1202 4 SO4 SO4 . 
W 6 SO4 E 1 1203 11 SO4 SO4 . 
X 4 ZN F 1 501 501 ZN ZN . 
Y 4 ZN F 1 502 502 ZN ZN . 
Z 6 SO4 F 1 503 9 SO4 SO4 . 
AA 7 HOH A 1 601 15 HOH HOH . 
AA 7 HOH A 2 602 17 HOH HOH . 
AA 7 HOH A 3 603 8 HOH HOH . 
AA 7 HOH A 4 604 10 HOH HOH . 
BA 7 HOH B 1 1301 3 HOH HOH . 
BA 7 HOH B 2 1302 19 HOH HOH . 
BA 7 HOH B 3 1303 18 HOH HOH . 
BA 7 HOH B 4 1304 7 HOH HOH . 
CA 7 HOH C 1 601 14 HOH HOH . 
DA 7 HOH D 1 601 12 HOH HOH . 
DA 7 HOH D 2 602 11 HOH HOH . 
EA 7 HOH E 1 1301 2 HOH HOH . 
FA 7 HOH F 1 601 4 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 8W7 . . . R 5 -16.453 56.655 -51.29 1 69.9 ? C1 8W7 502 D 1 
HETATM 2 C C2 8W7 . . . R 5 -15.39 57.344 -51.879 1 80.68 ? C2 8W7 502 D 1 
HETATM 3 C C3 8W7 . . . R 5 -14.288 57.74 -51.12 1 79.85 ? C3 8W7 502 D 1 
HETATM 4 C C4 8W7 . . . R 5 -16.455 56.334 -49.943 1 65.75 ? C4 8W7 502 D 1 
HETATM 5 C C5 8W7 . . . R 5 -15.35 56.732 -49.205 1 67.87 ? C5 8W7 502 D 1 
HETATM 6 C C6 8W7 . . . R 5 -14.292 57.413 -49.769 1 67.93 ? C6 8W7 502 D 1 
HETATM 7 N N1 8W7 . . . R 5 -13.85 57.116 -47.542 1 66.15 ? N1 8W7 502 D 1 
HETATM 8 N N2 8W7 . . . R 5 -12.18 58.924 -44.918 1 60.54 ? N2 8W7 502 D 1 
HETATM 9 N N3 8W7 . . . R 5 -17.174 63.593 -53.797 1 107.66 ? N3 8W7 502 D 1 
HETATM 10 O O1 8W7 . . . R 5 -15.754 55.983 -46.936 1 53.18 ? O1 8W7 502 D 1 
HETATM 11 C C7 8W7 . . . R 5 -13.263 57.704 -48.73 1 50.96 ? C7 8W7 502 D 1 
HETATM 12 C C8 8W7 . . . R 5 -15.064 56.54 -47.768 1 68.04 ? C8 8W7 502 D 1 
HETATM 13 C C9 8W7 . . . R 5 -13.24 57.122 -46.229 1 60.3 ? C9 8W7 502 D 1 
HETATM 14 C C10 8W7 . . . R 5 -11.855 56.489 -46.229 1 54.84 ? C10 8W7 502 D 1 
HETATM 15 C C11 8W7 . . . R 5 -11.053 56.745 -44.965 1 68.16 ? C11 8W7 502 D 1 
HETATM 16 C C12 8W7 . . . R 5 -11.104 58.167 -44.491 1 71.13 ? C12 8W7 502 D 1 
HETATM 17 C C13 8W7 . . . R 5 -13.229 58.555 -45.719 1 56.86 ? C13 8W7 502 D 1 
HETATM 18 C C14 8W7 . . . R 5 -13.14 58.716 -52.966 1 70.8 ? C14 8W7 502 D 1 
HETATM 19 C C15 8W7 . . . R 5 -13.813 60.039 -53.144 1 89.17 ? C15 8W7 502 D 1 
HETATM 20 O O2 8W7 . . . R 5 -14.1 59.344 -45.993 1 55.6 ? O2 8W7 502 D 1 
HETATM 21 C C22 8W7 . . . R 5 -17.961 63.914 -52.621 1 103.16 ? C22 8W7 502 D 1 
HETATM 22 C C23 8W7 . . . R 5 -19.371 63.399 -52.819 1 91.77 ? C23 8W7 502 D 1 
HETATM 23 O O5 8W7 . . . R 5 -19.937 63.899 -54.011 1 85.75 ? O5 8W7 502 D 1 
HETATM 24 C C24 8W7 . . . R 5 -19.151 63.596 -55.146 1 92.45 ? C24 8W7 502 D 1 
HETATM 25 C C25 8W7 . . . R 5 -17.749 64.153 -55.003 1 101.12 ? C25 8W7 502 D 1 
HETATM 26 C C21 8W7 . . . R 5 -15.762 63.833 -53.632 1 95.94 ? C21 8W7 502 D 1 
HETATM 27 C C20 8W7 . . . R 5 -15.078 62.51 -53.456 1 77.89 ? C20 8W7 502 D 1 
HETATM 28 C C19 8W7 . . . R 5 -14.211 62.296 -52.392 1 80.62 ? C19 8W7 502 D 1 
HETATM 29 C C17 8W7 . . . R 5 -13.592 61.067 -52.235 1 81.28 ? C17 8W7 502 D 1 
HETATM 30 C C18 8W7 . . . R 5 -15.306 61.478 -54.361 1 93.13 ? C18 8W7 502 D 1 
HETATM 31 C C16 8W7 . . . R 5 -14.682 60.25 -54.208 1 108.29 ? C16 8W7 502 D 1 
HETATM 32 O O4 8W7 . . . R 5 -13.206 58.396 -51.579 1 73.39 ? O4 8W7 502 D 1 
HETATM 33 O O3 8W7 . . . R 5 -10.268 58.673 -43.779 1 67.71 ? O3 8W7 502 D 1 
#
_model_server_stats.io_time_ms              244 
_model_server_stats.parse_time_ms           94 
_model_server_stats.create_model_time_ms    61 
_model_server_stats.query_time_ms           340 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           33 
#