data_7V6A
#
_model_server_result.job_id            EZyGzi1BBHp4UuvjC_0amg 
_model_server_result.datetime_utc      '2025-07-14 08:46:55' 
_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          7v6a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":601}' 
#
_entry.id    7V6A 
#
_exptl.entry_id    7V6A 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              372.461 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'methyl 4-[4-(3-methyl-2-oxidanylidene-benzimidazol-1-yl)piperidin-1-yl]piperidine-1-carboxylate' 
_entity.pdbx_number_of_molecules    1 
_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            7V6A 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7V6A 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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    ? 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             F 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 E SG CYS 105 R CYS 105 1_555 E SG CYS 185 R CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 E SG CYS 293 R CYS 426 1_555 E SG CYS 296 R CYS 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
#
_chem_comp.formula           'C20 H28 N4 O3' 
_chem_comp.formula_weight    372.461 
_chem_comp.id                5XI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'methyl 4-[4-(3-methyl-2-oxidanylidene-benzimidazol-1-yl)piperidin-1-yl]piperidine-1-carboxylate' 
_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
C8 N1 5XI sing 1 n n 
C4 C3 5XI doub 2 n y 
C4 C5 5XI sing 3 n y 
N1 C5 5XI sing 4 n n 
N1 C7 5XI sing 5 n n 
C3 C2 5XI sing 6 n y 
C5 C6 5XI doub 7 n y 
C7 O1 5XI doub 8 n n 
C7 N2 5XI sing 9 n n 
C2 C1 5XI doub 10 n y 
C6 N2 5XI sing 11 n n 
C6 C1 5XI sing 12 n y 
N2 C9 5XI sing 13 n n 
C9 C13 5XI sing 14 n n 
C9 C10 5XI sing 15 n n 
C13 C12 5XI sing 16 n n 
C10 C11 5XI sing 17 n n 
C12 N3 5XI sing 18 n n 
C11 N3 5XI sing 19 n n 
N3 C14 5XI sing 20 n n 
C18 C14 5XI sing 21 n n 
C18 C17 5XI sing 22 n n 
C14 C15 5XI sing 23 n n 
C15 C16 5XI sing 24 n n 
C17 N4 5XI sing 25 n n 
N4 C16 5XI sing 26 n n 
N4 C19 5XI sing 27 n n 
O3 C19 5XI sing 28 n n 
O3 C20 5XI sing 29 n n 
C19 O2 5XI doub 30 n n 
C14 H1 5XI sing 31 n n 
C13 H2 5XI sing 32 n n 
C13 H3 5XI sing 33 n n 
C12 H4 5XI sing 34 n n 
C12 H5 5XI sing 35 n n 
C16 H6 5XI sing 36 n n 
C16 H7 5XI sing 37 n n 
C17 H8 5XI sing 38 n n 
C17 H9 5XI sing 39 n n 
C20 H10 5XI sing 40 n n 
C20 H11 5XI sing 41 n n 
C20 H12 5XI sing 42 n n 
C11 H13 5XI sing 43 n n 
C11 H14 5XI sing 44 n n 
C8 H15 5XI sing 45 n n 
C8 H16 5XI sing 46 n n 
C8 H17 5XI sing 47 n n 
C2 H18 5XI sing 48 n n 
C4 H19 5XI sing 49 n n 
C3 H20 5XI sing 50 n n 
C1 H21 5XI sing 51 n n 
C10 H22 5XI sing 52 n n 
C10 H23 5XI sing 53 n n 
C15 H24 5XI sing 54 n n 
C15 H25 5XI sing 55 n n 
C18 H26 5XI sing 56 n n 
C18 H27 5XI sing 57 n n 
C9 H28 5XI sing 58 n n 
#
_atom_sites.entry_id                     7V6A 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          F 
_pdbx_nonpoly_scheme.entity_id        6 
_pdbx_nonpoly_scheme.mon_id           5XI 
_pdbx_nonpoly_scheme.pdb_strand_id    R 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      601 
_pdbx_nonpoly_scheme.auth_seq_num     601 
_pdbx_nonpoly_scheme.pdb_mon_id       5XI 
_pdbx_nonpoly_scheme.auth_mon_id      L11 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 C14 5XI . . . F 6 130.608 133.537 153.421 1 85.68 ? C14 5XI 601 R 1 
HETATM 2 C C13 5XI . . . F 6 129.765 133.234 150.076 1 85.68 ? C13 5XI 601 R 1 
HETATM 3 C C12 5XI . . . F 6 129.773 132.399 151.384 1 85.68 ? C12 5XI 601 R 1 
HETATM 4 C C16 5XI . . . F 6 131.565 134.527 155.551 1 85.68 ? C16 5XI 601 R 1 
HETATM 5 C C17 5XI . . . F 6 130.223 135.944 154.124 1 85.68 ? C17 5XI 601 R 1 
HETATM 6 C C19 5XI . . . F 6 131.596 137.044 155.972 1 85.68 ? C19 5XI 601 R 1 
HETATM 7 C C20 5XI . . . F 6 131.047 139.34 156.385 1 85.68 ? C20 5XI 601 R 1 
HETATM 8 C C11 5XI . . . F 6 132.242 132.893 151.626 1 85.68 ? C11 5XI 601 R 1 
HETATM 9 C C8 5XI . . . F 6 129.179 135.117 145.092 1 85.68 ? C8 5XI 601 R 1 
HETATM 10 C C6 5XI . . . F 6 131.9 134.933 147.553 1 85.68 ? C6 5XI 601 R 1 
HETATM 11 C C7 5XI . . . F 6 129.886 133.984 147.259 1 85.68 ? C7 5XI 601 R 1 
HETATM 12 C C2 5XI . . . F 6 133.866 136.338 147.155 1 85.68 ? C2 5XI 601 R 1 
HETATM 13 C C5 5XI . . . F 6 131.341 135.447 146.377 1 85.68 ? C5 5XI 601 R 1 
HETATM 14 C C4 5XI . . . F 6 132.029 136.388 145.605 1 85.68 ? C4 5XI 601 R 1 
HETATM 15 C C3 5XI . . . F 6 133.291 136.84 145.991 1 85.68 ? C3 5XI 601 R 1 
HETATM 16 C C1 5XI . . . F 6 133.177 135.392 147.934 1 85.68 ? C1 5XI 601 R 1 
HETATM 17 C C10 5XI . . . F 6 132.191 133.72 150.31 1 85.68 ? C10 5XI 601 R 1 
HETATM 18 C C15 5XI . . . F 6 131.765 133.489 154.432 1 85.68 ? C15 5XI 601 R 1 
HETATM 19 C C18 5XI . . . F 6 130.358 134.974 152.936 1 85.68 ? C18 5XI 601 R 1 
HETATM 20 C C9 5XI . . . F 6 131.113 133.207 149.344 1 85.68 ? C9 5XI 601 R 1 
HETATM 21 N N1 5XI . . . F 6 130.111 134.857 146.212 1 85.68 ? N1 5XI 601 R 1 
HETATM 22 N N2 5XI . . . F 6 130.986 134.022 148.1 1 85.68 ? N2 5XI 601 R 1 
HETATM 23 N N3 5XI . . . F 6 130.927 132.66 152.272 1 85.68 ? N3 5XI 601 R 1 
HETATM 24 N N4 5XI . . . F 6 131.382 135.909 155.048 1 85.68 ? N4 5XI 601 R 1 
HETATM 25 O O1 5XI . . . F 6 128.885 133.314 147.389 1 85.68 ? O1 5XI 601 R 1 
HETATM 26 O O2 5XI . . . F 6 131.771 136.828 157.186 1 85.68 ? O2 5XI 601 R 1 
HETATM 27 O O3 5XI . . . F 6 131.601 138.383 155.475 1 85.68 ? O3 5XI 601 R 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           385 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#