data_8ZPL
#
_model_server_result.job_id            grMKDZ6abiJ2F2yl02hiEw 
_model_server_result.datetime_utc      '2025-02-27 09:56:33' 
_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          8zpl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":403}' 
#
_entry.id    8ZPL 
#
_exptl.entry_id    8ZPL 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              522.729 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2S)-N-[[4-[[3-(cyclohexylamino)propylamino]methyl]phenyl]methyl]-5-(diaminomethylideneamino)-2-(pyridin-2-ylmethylamino)pentanamide 
_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            8ZPL 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8ZPL 
_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                      4 
_struct_asym.id                             E 
_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 62 N CYS 24 1_555 A SG CYS 135 N CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 B SG CYS 247 R CYS 109 1_555 B SG CYS 324 R CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
#
_chem_comp.formula           'C29 H46 N8 O' 
_chem_comp.formula_weight    522.729 
_chem_comp.id                A1D8K 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2S)-N-[[4-[[3-(cyclohexylamino)propylamino]methyl]phenyl]methyl]-5-(diaminomethylideneamino)-2-(pyridin-2-ylmethylamino)pentanamide 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     HF51116 
#
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
C5 C6 A1D8K sing 1 n n 
C5 C4 A1D8K sing 2 n n 
C6 C1 A1D8K sing 3 n n 
C1 C2 A1D8K sing 4 n n 
C28 C27 A1D8K doub 5 n y 
C28 C29 A1D8K sing 6 n y 
C4 N1 A1D8K sing 7 n n 
C4 C3 A1D8K sing 8 n n 
C27 C26 A1D8K sing 9 n y 
N1 C7 A1D8K sing 10 n n 
C29 N8 A1D8K doub 11 n y 
C2 C3 A1D8K sing 12 n n 
C26 C25 A1D8K doub 13 n y 
N8 C25 A1D8K sing 14 n y 
C25 C24 A1D8K sing 15 n n 
C7 C8 A1D8K sing 16 n n 
C8 C9 A1D8K sing 17 n n 
C24 N7 A1D8K sing 18 n n 
C9 N2 A1D8K sing 19 n n 
N7 C19 A1D8K sing 20 n n 
N2 C10 A1D8K sing 21 n n 
C21 C22 A1D8K sing 22 n n 
C21 C20 A1D8K sing 23 n n 
C10 C11 A1D8K sing 24 n n 
C19 C20 A1D8K sing 25 n n 
C19 C18 A1D8K sing 26 n n 
C22 N4 A1D8K sing 27 n n 
C16 C11 A1D8K doub 28 n y 
C16 C15 A1D8K sing 29 n y 
N5 C23 A1D8K sing 30 n n 
C11 C12 A1D8K sing 31 n y 
C15 C14 A1D8K doub 32 n y 
N4 C23 A1D8K doub 33 n n 
C23 N6 A1D8K sing 34 n n 
C18 O1 A1D8K doub 35 n n 
C18 N3 A1D8K sing 36 n n 
C12 C13 A1D8K doub 37 n y 
C14 C13 A1D8K sing 38 n y 
C14 C17 A1D8K sing 39 n n 
N3 C17 A1D8K sing 40 n n 
C1 H1 A1D8K sing 41 n n 
C1 H2 A1D8K sing 42 n n 
C10 H3 A1D8K sing 43 n n 
C10 H4 A1D8K sing 44 n n 
C12 H5 A1D8K sing 45 n n 
C13 H6 A1D8K sing 46 n n 
C15 H7 A1D8K sing 47 n n 
C16 H8 A1D8K sing 48 n n 
C17 H9 A1D8K sing 49 n n 
C17 H10 A1D8K sing 50 n n 
C19 H11 A1D8K sing 51 n n 
C2 H12 A1D8K sing 52 n n 
C2 H13 A1D8K sing 53 n n 
C20 H14 A1D8K sing 54 n n 
C20 H15 A1D8K sing 55 n n 
C21 H16 A1D8K sing 56 n n 
C21 H17 A1D8K sing 57 n n 
C22 H18 A1D8K sing 58 n n 
C22 H19 A1D8K sing 59 n n 
C24 H20 A1D8K sing 60 n n 
C24 H21 A1D8K sing 61 n n 
C26 H22 A1D8K sing 62 n n 
C27 H23 A1D8K sing 63 n n 
C28 H24 A1D8K sing 64 n n 
C29 H25 A1D8K sing 65 n n 
C3 H26 A1D8K sing 66 n n 
C3 H27 A1D8K sing 67 n n 
C4 H28 A1D8K sing 68 n n 
C5 H29 A1D8K sing 69 n n 
C5 H30 A1D8K sing 70 n n 
C6 H31 A1D8K sing 71 n n 
C6 H32 A1D8K sing 72 n n 
C7 H33 A1D8K sing 73 n n 
C7 H34 A1D8K sing 74 n n 
C8 H35 A1D8K sing 75 n n 
C8 H36 A1D8K sing 76 n n 
C9 H37 A1D8K sing 77 n n 
C9 H38 A1D8K sing 78 n n 
N1 H39 A1D8K sing 79 n n 
N2 H41 A1D8K sing 80 n n 
N3 H43 A1D8K sing 81 n n 
N5 H45 A1D8K sing 82 n n 
N6 H46 A1D8K sing 83 n n 
N6 H47 A1D8K sing 84 n n 
N7 H48 A1D8K sing 85 n n 
N5 H40 A1D8K sing 86 n n 
#
_atom_sites.entry_id                     8ZPL 
_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 CLR R 1 401 402 CLR CLR . 
D 3 CLR R 1 402 403 CLR CLR . 
E 4 A1D8K R 1 403 1 A1D8K HF5 . 
#
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 A1D8K . . . E 4 130.171 137.916 115.506 1 76.26 ? C1 A1D8K 403 R 1 
HETATM 2 C C10 A1D8K . . . E 4 122.443 141.168 120.226 1 79.61 ? C10 A1D8K 403 R 1 
HETATM 3 C C11 A1D8K . . . E 4 121.859 139.974 120.938 1 78.86 ? C11 A1D8K 403 R 1 
HETATM 4 C C12 A1D8K . . . E 4 122.61 139.244 121.842 1 71.33 ? C12 A1D8K 403 R 1 
HETATM 5 C C13 A1D8K . . . E 4 122.073 138.147 122.485 1 67.15 ? C13 A1D8K 403 R 1 
HETATM 6 C C14 A1D8K . . . E 4 120.771 137.756 122.239 1 73.2 ? C14 A1D8K 403 R 1 
HETATM 7 C C15 A1D8K . . . E 4 120.016 138.491 121.346 1 76.17 ? C15 A1D8K 403 R 1 
HETATM 8 C C16 A1D8K . . . E 4 120.553 139.586 120.7 1 76.07 ? C16 A1D8K 403 R 1 
HETATM 9 C C17 A1D8K . . . E 4 120.169 136.571 122.934 1 71.92 ? C17 A1D8K 403 R 1 
HETATM 10 C C18 A1D8K . . . E 4 118.605 135.178 121.761 1 70.44 ? C18 A1D8K 403 R 1 
HETATM 11 C C19 A1D8K . . . E 4 117.7 135.283 120.555 1 75.43 ? C19 A1D8K 403 R 1 
HETATM 12 C C2 A1D8K . . . E 4 129.345 137.378 116.642 1 75.31 ? C2 A1D8K 403 R 1 
HETATM 13 C C20 A1D8K . . . E 4 116.259 135.097 120.963 1 70.14 ? C20 A1D8K 403 R 1 
HETATM 14 C C21 A1D8K . . . E 4 115.479 134.287 119.949 1 71.07 ? C21 A1D8K 403 R 1 
HETATM 15 C C22 A1D8K . . . E 4 114.163 133.99 120.564 1 71.06 ? C22 A1D8K 403 R 1 
HETATM 16 C C23 A1D8K . . . E 4 112.638 135.39 121.583 1 75.78 ? C23 A1D8K 403 R 1 
HETATM 17 C C24 A1D8K . . . E 4 118.76 134.601 118.42 1 77.25 ? C24 A1D8K 403 R 1 
HETATM 18 C C25 A1D8K . . . E 4 118.911 133.448 117.459 1 75.42 ? C25 A1D8K 403 R 1 
HETATM 19 C C26 A1D8K . . . E 4 117.822 132.742 116.994 1 76.29 ? C26 A1D8K 403 R 1 
HETATM 20 C C27 A1D8K . . . E 4 118.025 131.692 116.122 1 79.99 ? C27 A1D8K 403 R 1 
HETATM 21 C C28 A1D8K . . . E 4 119.301 131.374 115.745 1 79.1 ? C28 A1D8K 403 R 1 
HETATM 22 C C29 A1D8K . . . E 4 120.33 132.113 116.261 1 76.99 ? C29 A1D8K 403 R 1 
HETATM 23 C C3 A1D8K . . . E 4 128.226 138.349 116.993 1 72.53 ? C3 A1D8K 403 R 1 
HETATM 24 C C4 A1D8K . . . E 4 127.44 138.723 115.762 1 70.3 ? C4 A1D8K 403 R 1 
HETATM 25 C C5 A1D8K . . . E 4 128.333 139.415 114.761 1 70.47 ? C5 A1D8K 403 R 1 
HETATM 26 C C6 A1D8K . . . E 4 129.783 139.342 115.213 1 76.12 ? C6 A1D8K 403 R 1 
HETATM 27 C C7 A1D8K . . . E 4 125.932 139.484 117.545 1 77.51 ? C7 A1D8K 403 R 1 
HETATM 28 C C8 A1D8K . . . E 4 125.56 140.84 118.109 1 77.67 ? C8 A1D8K 403 R 1 
HETATM 29 C C9 A1D8K . . . E 4 124.088 140.989 118.422 1 73.65 ? C9 A1D8K 403 R 1 
HETATM 30 N N1 A1D8K . . . E 4 126.304 139.559 116.135 1 76.59 ? N1 A1D8K 403 R 1 
HETATM 31 N N2 A1D8K . . . E 4 123.841 140.993 119.866 1 75.52 ? N2 A1D8K 403 R 1 
HETATM 32 N N3 A1D8K . . . E 4 118.853 136.288 122.44 1 67.71 ? N3 A1D8K 403 R 1 
HETATM 33 N N4 A1D8K . . . E 4 113.871 134.998 121.569 1 69.66 ? N4 A1D8K 403 R 1 
HETATM 34 N N5 A1D8K . . . E 4 111.659 134.761 120.934 1 77.23 ? N5 A1D8K 403 R 1 
HETATM 35 N N6 A1D8K . . . E 4 112.337 136.467 122.29 1 78.86 ? N6 A1D8K 403 R 1 
HETATM 36 N N7 A1D8K . . . E 4 117.966 134.236 119.591 1 81.25 ? N7 A1D8K 403 R 1 
HETATM 37 N N8 A1D8K . . . E 4 120.159 133.136 117.106 1 76.5 ? N8 A1D8K 403 R 1 
HETATM 38 O O1 A1D8K . . . E 4 119.097 134.104 122.066 1 73.12 ? O1 A1D8K 403 R 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           38 
#