data_8ZPM
#
_model_server_result.job_id            nszxdV35cHEHxGtcgZBB4w 
_model_server_result.datetime_utc      '2025-04-04 03:00:09' 
_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          8zpm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    8ZPM 
#
_exptl.entry_id    8ZPM 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              349.473 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (S)-N1-((1H-Benzo[d]imidazol-2-yl)methyl)-N1-(5,6,7,8-tetrahydroquinolin-8-yl)butane-1,4-diamine 
_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            8ZPM 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8ZPM 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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 A SG CYS 247 R CYS 109 1_555 A SG CYS 324 R CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 B SG CYS 62 N CYS 24 1_555 B SG CYS 135 N CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
#
_chem_comp.formula           'C21 H27 N5' 
_chem_comp.formula_weight    349.473 
_chem_comp.id                A1D8L 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (S)-N1-((1H-Benzo[d]imidazol-2-yl)methyl)-N1-(5,6,7,8-tetrahydroquinolin-8-yl)butane-1,4-diamine 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     AMD-070 
#
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
N3 C13 A1D8L sing 1 n n 
C13 C12 A1D8L sing 2 n n 
C12 C11 A1D8L sing 3 n n 
C11 C10 A1D8L sing 4 n n 
C10 N2 A1D8L sing 5 n n 
C2 C1 A1D8L sing 6 n n 
C2 C3 A1D8L sing 7 n n 
N2 C14 A1D8L sing 8 n n 
N2 C3 A1D8L sing 9 n n 
C1 C6 A1D8L sing 10 n n 
C14 C15 A1D8L sing 11 n n 
C6 C5 A1D8L sing 12 n n 
C5 C7 A1D8L doub 13 n y 
C5 C4 A1D8L sing 14 n y 
C7 C8 A1D8L sing 15 n y 
C8 C9 A1D8L doub 16 n y 
C3 C4 A1D8L sing 17 n n 
C4 N1 A1D8L doub 18 n y 
C9 N1 A1D8L sing 19 n y 
N4 C15 A1D8L doub 20 n y 
N4 C16 A1D8L sing 21 n y 
C15 N5 A1D8L sing 22 n y 
C16 C17 A1D8L doub 23 n y 
C16 C21 A1D8L sing 24 n y 
N5 C21 A1D8L sing 25 n y 
C17 C18 A1D8L sing 26 n y 
C21 C20 A1D8L doub 27 n y 
C18 C19 A1D8L doub 28 n y 
C20 C19 A1D8L sing 29 n y 
C14 H1 A1D8L sing 30 n n 
C14 H2 A1D8L sing 31 n n 
C17 H3 A1D8L sing 32 n n 
C18 H4 A1D8L sing 33 n n 
C19 H5 A1D8L sing 34 n n 
C20 H6 A1D8L sing 35 n n 
C1 H8 A1D8L sing 36 n n 
C1 H9 A1D8L sing 37 n n 
C10 H10 A1D8L sing 38 n n 
C10 H11 A1D8L sing 39 n n 
C11 H12 A1D8L sing 40 n n 
C11 H13 A1D8L sing 41 n n 
C12 H14 A1D8L sing 42 n n 
C12 H15 A1D8L sing 43 n n 
C13 H16 A1D8L sing 44 n n 
C13 H17 A1D8L sing 45 n n 
C2 H18 A1D8L sing 46 n n 
C2 H19 A1D8L sing 47 n n 
C3 H20 A1D8L sing 48 n n 
C6 H21 A1D8L sing 49 n n 
C6 H22 A1D8L sing 50 n n 
C7 H23 A1D8L sing 51 n n 
C8 H24 A1D8L sing 52 n n 
C9 H25 A1D8L sing 53 n n 
N3 H26 A1D8L sing 54 n n 
N3 H27 A1D8L sing 55 n n 
N5 H30 A1D8L sing 56 n n 
#
_atom_sites.entry_id                     8ZPM 
_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 
#
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 3 A1D8L R 1 401 1 A1D8L 070 . 
D 4 CLR R 1 402 402 CLR CLR . 
E 4 CLR R 1 403 403 CLR CLR . 
#
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 A1D8L . . . C 3 125.309 136.856 119.639 1 43.17 ? C14 A1D8L 401 R 1 
HETATM 2 C C15 A1D8L . . . C 3 124.032 137.541 119.989 1 44.8 ? C15 A1D8L 401 R 1 
HETATM 3 C C16 A1D8L . . . C 3 121.954 137.971 120.337 1 40.99 ? C16 A1D8L 401 R 1 
HETATM 4 C C17 A1D8L . . . C 3 120.571 137.951 120.466 1 43.36 ? C17 A1D8L 401 R 1 
HETATM 5 C C18 A1D8L . . . C 3 119.941 139.107 120.845 1 40.75 ? C18 A1D8L 401 R 1 
HETATM 6 C C19 A1D8L . . . C 3 120.658 140.261 121.108 1 37.88 ? C19 A1D8L 401 R 1 
HETATM 7 C C20 A1D8L . . . C 3 122.027 140.295 121.003 1 39.74 ? C20 A1D8L 401 R 1 
HETATM 8 C C21 A1D8L . . . C 3 122.659 139.133 120.608 1 39.68 ? C21 A1D8L 401 R 1 
HETATM 9 N N2 A1D8L . . . C 3 126.337 137.852 119.358 1 39.03 ? N2 A1D8L 401 R 1 
HETATM 10 C C1 A1D8L . . . C 3 129.537 135.867 119.582 1 35.75 ? C1 A1D8L 401 R 1 
HETATM 11 C C10 A1D8L . . . C 3 126.282 138.287 117.955 1 39.16 ? C10 A1D8L 401 R 1 
HETATM 12 C C11 A1D8L . . . C 3 125.711 137.376 116.894 1 38.03 ? C11 A1D8L 401 R 1 
HETATM 13 C C12 A1D8L . . . C 3 126.204 137.818 115.531 1 37.86 ? C12 A1D8L 401 R 1 
HETATM 14 C C13 A1D8L . . . C 3 125.289 138.799 114.854 1 38.9 ? C13 A1D8L 401 R 1 
HETATM 15 C C2 A1D8L . . . C 3 128.264 136.376 118.941 1 37.9 ? C2 A1D8L 401 R 1 
HETATM 16 C C3 A1D8L . . . C 3 127.659 137.454 119.776 1 35.82 ? C3 A1D8L 401 R 1 
HETATM 17 C C4 A1D8L . . . C 3 128.612 138.619 119.778 1 40.74 ? C4 A1D8L 401 R 1 
HETATM 18 C C5 A1D8L . . . C 3 129.977 138.363 119.759 1 44.13 ? C5 A1D8L 401 R 1 
HETATM 19 C C6 A1D8L . . . C 3 130.552 136.969 119.727 1 37.75 ? C6 A1D8L 401 R 1 
HETATM 20 C C7 A1D8L . . . C 3 130.831 139.459 119.763 1 41.85 ? C7 A1D8L 401 R 1 
HETATM 21 C C8 A1D8L . . . C 3 130.326 140.737 119.773 1 37.09 ? C8 A1D8L 401 R 1 
HETATM 22 C C9 A1D8L . . . C 3 128.959 140.884 119.79 1 36.47 ? C9 A1D8L 401 R 1 
HETATM 23 N N1 A1D8L . . . C 3 128.116 139.862 119.8 1 38.53 ? N1 A1D8L 401 R 1 
HETATM 24 N N3 A1D8L . . . C 3 126.004 139.598 113.872 1 36.1 ? N3 A1D8L 401 R 1 
HETATM 25 N N4 A1D8L . . . C 3 122.842 136.973 119.954 1 42 ? N4 A1D8L 401 R 1 
HETATM 26 N N5 A1D8L . . . C 3 123.98 138.826 120.386 1 40.41 ? N5 A1D8L 401 R 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           684 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#