data_8U16
#
_model_server_result.job_id            V23o06jRzqTz9fuKMGYmlA 
_model_server_result.datetime_utc      '2024-12-03 12:04:14' 
_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          8u16 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":502}' 
#
_entry.id    8U16 
#
_exptl.entry_id    8U16 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              273.244 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-Pomalidomide 
_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            8U16 
_cell.length_a            95.536 
_cell.length_b            151.986 
_cell.length_c            218.46 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8U16 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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,P,Q,R 1 1 
D,E,F,K,L,M,N,O,S,T,U 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 L 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc1 A SG CYS 254 A CYS 323 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? 
metalc ? metalc2 A SG CYS 257 A CYS 326 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc3 A SG CYS 322 A CYS 391 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc4 A SG CYS 325 A CYS 394 1_555 G ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? 
metalc ? metalc5 C SG CYS 7 C CYS 384 1_555 I ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? 
metalc ? metalc6 C SG CYS 10 C CYS 387 1_555 I ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc7 C NE2 HIS 23 C HIS 400 1_555 I ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? 
metalc ? metalc8 C NE2 HIS 27 C HIS 404 1_555 I ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
metalc ? metalc9 C SG CYS 35 C CYS 412 1_555 J ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? 
metalc ? metalc10 C NE2 HIS 51 C HIS 428 1_555 J ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc11 C NE2 HIS 55 C HIS 432 1_555 J ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? 
metalc ? metalc12 D SG CYS 254 D CYS 323 1_555 K ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
metalc ? metalc13 D SG CYS 257 D CYS 326 1_555 K ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc14 D SG CYS 322 D CYS 391 1_555 K ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? 
metalc ? metalc15 D SG CYS 325 D CYS 394 1_555 K ZN ZN . D ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc16 F SG CYS 7 F CYS 384 1_555 N ZN ZN . F ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
metalc ? metalc17 F SG CYS 10 F CYS 387 1_555 N ZN ZN . F ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? 
metalc ? metalc18 F NE2 HIS 23 F HIS 400 1_555 N ZN ZN . F ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc19 F NE2 HIS 27 F HIS 404 1_555 N ZN ZN . F ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc20 F SG CYS 35 F CYS 412 1_555 O ZN ZN . F ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc21 F SG CYS 38 F CYS 415 1_555 O ZN ZN . F ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
metalc ? metalc22 F NE2 HIS 51 F HIS 428 1_555 O ZN ZN . F ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
metalc ? metalc23 F NE2 HIS 55 F HIS 432 1_555 O ZN ZN . F ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
#
_chem_comp.formula           'C13 H11 N3 O4' 
_chem_comp.formula_weight    273.244 
_chem_comp.id                Y70 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              S-Pomalidomide 
_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
C1 C2 Y70 sing 385 n y 
C1 C6 Y70 doub 386 n y 
C2 C3 Y70 doub 387 n y 
C3 C4 Y70 sing 388 n y 
C4 C5 Y70 doub 389 n y 
C4 C7 Y70 sing 390 n n 
C5 C6 Y70 sing 391 n y 
C5 C9 Y70 sing 392 n n 
C6 N10 Y70 sing 393 n n 
C7 N8 Y70 sing 394 n n 
C7 O13 Y70 doub 395 n n 
N8 C9 Y70 sing 396 n n 
N8 C12 Y70 sing 397 n n 
C9 O11 Y70 doub 398 n n 
C12 C14 Y70 sing 399 n n 
C12 C15 Y70 sing 400 n n 
C14 C18 Y70 sing 401 n n 
C15 N16 Y70 sing 402 n n 
C15 O19 Y70 doub 403 n n 
N16 C17 Y70 sing 404 n n 
C17 C18 Y70 sing 405 n n 
C17 O20 Y70 doub 406 n n 
C1 H1 Y70 sing 407 n n 
C2 H2 Y70 sing 408 n n 
C3 H3 Y70 sing 409 n n 
N10 H101 Y70 sing 410 n n 
N10 H102 Y70 sing 411 n n 
C12 H12 Y70 sing 412 n n 
C14 H141 Y70 sing 413 n n 
C14 H142 Y70 sing 414 n n 
C18 H181 Y70 sing 415 n n 
C18 H182 Y70 sing 416 n n 
N16 H16 Y70 sing 417 n n 
#
_atom_sites.entry_id                     8U16 
_atom_sites.fract_transf_matrix[1][1]    0.010467 
_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]    0.00658 
_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]    0.004577 
_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 Y70 A 1 502 601 Y70 Y70 . 
I 4 ZN C 1 501 501 ZN ZN . 
J 4 ZN C 1 502 502 ZN ZN . 
K 4 ZN D 1 501 501 ZN ZN . 
L 5 Y70 D 1 502 601 Y70 Y70 . 
M 6 EDO E 1 1201 1201 EDO EDO . 
N 4 ZN F 1 501 501 ZN ZN . 
O 4 ZN F 1 502 502 ZN ZN . 
P 7 HOH A 1 601 2 HOH HOH . 
P 7 HOH A 2 602 12 HOH HOH . 
P 7 HOH A 3 603 35 HOH HOH . 
P 7 HOH A 4 604 3 HOH HOH . 
Q 7 HOH B 1 1201 33 HOH HOH . 
Q 7 HOH B 2 1202 34 HOH HOH . 
Q 7 HOH B 3 1203 13 HOH HOH . 
Q 7 HOH B 4 1204 6 HOH HOH . 
Q 7 HOH B 5 1205 25 HOH HOH . 
Q 7 HOH B 6 1206 15 HOH HOH . 
Q 7 HOH B 7 1207 9 HOH HOH . 
Q 7 HOH B 8 1208 30 HOH HOH . 
Q 7 HOH B 9 1209 16 HOH HOH . 
Q 7 HOH B 10 1210 32 HOH HOH . 
R 7 HOH C 1 601 1 HOH HOH . 
R 7 HOH C 2 602 31 HOH HOH . 
S 7 HOH D 1 601 5 HOH HOH . 
S 7 HOH D 2 602 18 HOH HOH . 
S 7 HOH D 3 603 14 HOH HOH . 
S 7 HOH D 4 604 7 HOH HOH . 
T 7 HOH E 1 1301 24 HOH HOH . 
T 7 HOH E 2 1302 22 HOH HOH . 
T 7 HOH E 3 1303 20 HOH HOH . 
T 7 HOH E 4 1304 17 HOH HOH . 
T 7 HOH E 5 1305 23 HOH HOH . 
T 7 HOH E 6 1306 4 HOH HOH . 
T 7 HOH E 7 1307 19 HOH HOH . 
T 7 HOH E 8 1308 28 HOH HOH . 
T 7 HOH E 9 1309 26 HOH HOH . 
T 7 HOH E 10 1310 27 HOH HOH . 
T 7 HOH E 11 1311 8 HOH HOH . 
T 7 HOH E 12 1312 10 HOH HOH . 
T 7 HOH E 13 1313 29 HOH HOH . 
T 7 HOH E 14 1314 21 HOH HOH . 
U 7 HOH F 1 601 11 HOH HOH . 
U 7 HOH F 2 602 36 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 Y70 . . . L 5 8.47 -16.451 92.1 1 55.83 ? C1 Y70 502 D 1 
HETATM 2 C C2 Y70 . . . L 5 7.476 -16.06 91.225 1 54.42 ? C2 Y70 502 D 1 
HETATM 3 C C3 Y70 . . . L 5 6.915 -14.78 91.264 1 53.82 ? C3 Y70 502 D 1 
HETATM 4 C C4 Y70 . . . L 5 7.434 -13.957 92.228 1 54.11 ? C4 Y70 502 D 1 
HETATM 5 C C5 Y70 . . . L 5 8.436 -14.32 93.126 1 53.15 ? C5 Y70 502 D 1 
HETATM 6 C C6 Y70 . . . L 5 8.996 -15.583 93.101 1 56.53 ? C6 Y70 502 D 1 
HETATM 7 C C7 Y70 . . . L 5 7.072 -12.557 92.531 1 54.98 ? C7 Y70 502 D 1 
HETATM 8 N N8 Y70 . . . L 5 7.874 -12.164 93.609 1 55.95 ? N8 Y70 502 D 1 
HETATM 9 C C9 Y70 . . . L 5 8.733 -13.194 94.013 1 56.01 ? C9 Y70 502 D 1 
HETATM 10 N N10 Y70 . . . L 5 9.968 -15.961 93.956 1 62.2 ? N10 Y70 502 D 1 
HETATM 11 O O11 Y70 . . . L 5 9.534 -13.109 94.927 1 54.18 ? O11 Y70 502 D 1 
HETATM 12 C C12 Y70 . . . L 5 7.807 -10.832 94.176 1 52.84 ? C12 Y70 502 D 1 
HETATM 13 O O13 Y70 . . . L 5 6.245 -11.883 91.977 1 51.97 ? O13 Y70 502 D 1 
HETATM 14 C C14 Y70 . . . L 5 6.945 -10.664 95.417 1 54.29 ? C14 Y70 502 D 1 
HETATM 15 C C15 Y70 . . . L 5 9.198 -10.212 94.255 1 50.23 ? C15 Y70 502 D 1 
HETATM 16 N N16 Y70 . . . L 5 9.547 -9.49 95.358 1 47.5 ? N16 Y70 502 D 1 
HETATM 17 C C17 Y70 . . . L 5 8.797 -9.268 96.476 1 49.31 ? C17 Y70 502 D 1 
HETATM 18 C C18 Y70 . . . L 5 7.647 -10.195 96.673 1 54.16 ? C18 Y70 502 D 1 
HETATM 19 O O19 Y70 . . . L 5 9.957 -10.325 93.334 1 51.24 ? O19 Y70 502 D 1 
HETATM 20 O O20 Y70 . . . L 5 9.098 -8.4 97.245 1 50.2 ? O20 Y70 502 D 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           29 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#