data_5EBK
#
_model_server_result.job_id            vSo7MaoxeG_hG4JfniZ8ng 
_model_server_result.datetime_utc      '2024-12-15 03:42:25' 
_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          5ebk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    5EBK 
#
_exptl.entry_id    5EBK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              309.814 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            6-sec-Butoxy-2-[(3-chlorophenyl)sulfanyl]-4-pyrimidinamine 
_entity.pdbx_number_of_molecules    7 
_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            5EBK 
_cell.length_a            102.5 
_cell.length_b            102.5 
_cell.length_c            192 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5EBK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
_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,G,H,I,J,K,L 
_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
? 3 D N N 
? 3 E N N 
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 K N N 
? 3 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 A SG CYS 72 A CYS 52 1_555 A SG CYS 77 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 A SG CYS 109 A CYS 89 1_555 A SG CYS 233 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf3 B SG CYS 72 B CYS 52 1_555 B SG CYS 77 B CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf4 B SG CYS 109 B CYS 89 1_555 B SG CYS 233 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
#
_chem_comp.formula           'C14 H16 Cl N3 O S' 
_chem_comp.formula_weight    309.814 
_chem_comp.id                RDS 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              6-sec-Butoxy-2-[(3-chlorophenyl)sulfanyl]-4-pyrimidinamine 
_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
N C RDS sing 366 n n 
CL C13 RDS sing 367 n n 
C C1 RDS doub 368 n y 
C N2 RDS sing 369 n y 
C1 C2 RDS sing 370 n y 
N2 C7 RDS doub 371 n y 
C13 C12 RDS doub 372 n y 
C13 C11 RDS sing 373 n y 
C12 C8 RDS sing 374 n y 
C4 C3 RDS sing 375 n n 
C2 O RDS sing 376 n n 
C2 N1 RDS doub 377 n y 
C3 O RDS sing 378 n n 
C3 C5 RDS sing 379 n n 
C7 N1 RDS sing 380 n y 
C7 S RDS sing 381 n n 
C11 C10 RDS doub 382 n y 
C8 S RDS sing 383 n n 
C8 C9 RDS doub 384 n y 
C6 C5 RDS sing 385 n n 
C10 C9 RDS sing 386 n y 
C12 H1 RDS sing 387 n n 
C9 H2 RDS sing 388 n n 
C10 H3 RDS sing 389 n n 
C11 H4 RDS sing 390 n n 
C1 H5 RDS sing 391 n n 
N H6 RDS sing 392 n n 
N H7 RDS sing 393 n n 
C3 H8 RDS sing 394 n n 
C4 H9 RDS sing 395 n n 
C4 H10 RDS sing 396 n n 
C4 H11 RDS sing 397 n n 
C5 H12 RDS sing 398 n n 
C5 H13 RDS sing 399 n n 
C6 H14 RDS sing 400 n n 
C6 H15 RDS sing 401 n n 
C6 H16 RDS sing 402 n n 
#
_atom_sites.entry_id                     5EBK 
_atom_sites.fract_transf_matrix[1][1]    0.009756 
_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]    0.009756 
_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]    0.005208 
_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 FAD A 1 501 1486 FAD FAD . 
D 3 RDS A 1 502 2001 RDS RDS . 
E 3 RDS A 1 503 2002 RDS RDS . 
F 3 RDS A 1 504 2003 RDS RDS . 
G 4 SO4 A 1 505 3 SO4 SO4 . 
H 3 RDS B 1 501 2004 RDS RDS . 
I 2 FAD B 1 502 1486 FAD FAD . 
J 3 RDS B 1 503 2001 RDS RDS . 
K 3 RDS B 1 504 2002 RDS RDS . 
L 3 RDS B 1 505 2003 RDS RDS . 
#
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 CL CL RDS . . . D 3 1.551 24.815 9.034 0.8 148.23 ? CL RDS 502 A 1 
HETATM 2 C C13 RDS . . . D 3 2.155 25.229 10.666 0.8 139.39 ? C13 RDS 502 A 1 
HETATM 3 C C12 RDS . . . D 3 3.522 25.288 10.9 0.8 135.71 ? C12 RDS 502 A 1 
HETATM 4 C C8 RDS . . . D 3 3.996 25.598 12.166 0.8 134.14 ? C8 RDS 502 A 1 
HETATM 5 C C9 RDS . . . D 3 3.103 25.874 13.196 0.8 138.41 ? C9 RDS 502 A 1 
HETATM 6 C C10 RDS . . . D 3 1.732 25.815 12.961 0.8 139.82 ? C10 RDS 502 A 1 
HETATM 7 C C11 RDS . . . D 3 1.259 25.492 11.695 0.8 138.68 ? C11 RDS 502 A 1 
HETATM 8 S S RDS . . . D 3 5.664 25.686 12.433 0.8 128.13 ? S RDS 502 A 1 
HETATM 9 C C7 RDS . . . D 3 6.054 27.148 11.679 0.8 133.28 ? C7 RDS 502 A 1 
HETATM 10 N N1 RDS . . . D 3 5.485 28.293 12.131 0.8 137.31 ? N1 RDS 502 A 1 
HETATM 11 C C2 RDS . . . D 3 5.764 29.475 11.544 0.8 137.19 ? C2 RDS 502 A 1 
HETATM 12 C C1 RDS . . . D 3 6.628 29.512 10.459 0.8 131.29 ? C1 RDS 502 A 1 
HETATM 13 C C RDS . . . D 3 7.193 28.33 9.998 0.8 122.09 ? C RDS 502 A 1 
HETATM 14 N N RDS . . . D 3 8.042 28.347 8.941 0.8 110.44 ? N RDS 502 A 1 
HETATM 15 N N2 RDS . . . D 3 6.895 27.162 10.612 0.8 124.81 ? N2 RDS 502 A 1 
HETATM 16 O O RDS . . . D 3 5.189 30.628 12.014 0.8 132.26 ? O RDS 502 A 1 
HETATM 17 C C3 RDS . . . D 3 3.844 30.949 11.655 0.8 131.18 ? C3 RDS 502 A 1 
HETATM 18 C C4 RDS . . . D 3 3.769 32.404 11.206 0.8 126.42 ? C4 RDS 502 A 1 
HETATM 19 C C5 RDS . . . D 3 2.918 30.684 12.84 0.8 131.18 ? C5 RDS 502 A 1 
HETATM 20 C C6 RDS . . . D 3 1.463 30.798 12.434 0.8 131.13 ? C6 RDS 502 A 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#