data_5YHL # _model_server_result.job_id K8u3zqX1ZhXohcXcFRl4bA _model_server_result.datetime_utc '2024-11-23 10:35:52' _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 5yhl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 5YHL # _exptl.entry_id 5YHL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 465.339 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '4-[2-[[(2R)-2-(4-bromanylnaphthalen-1-yl)propanoyl]amino]-4-cyano-phenyl]butanoic acid' _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 5YHL _cell.length_a 101.97 _cell.length_b 392.23 _cell.length_c 81.08 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YHL _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 D _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 92 A CYS 92 1_555 A SG CYS 170 A CYS 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 B SG CYS 41 H CYS 41 1_555 B SG CYS 115 H CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 B SG CYS 155 H CYS 155 1_555 C SG CYS 236 L CYS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 B SG CYS 167 H CYS 167 1_555 B SG CYS 222 H CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 C SG CYS 45 L CYS 45 1_555 C SG CYS 110 L CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 C SG CYS 156 L CYS 156 1_555 C SG CYS 216 L CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? # _chem_comp.formula 'C24 H21 Br N2 O3' _chem_comp.formula_weight 465.339 _chem_comp.id 8VL _chem_comp.mon_nstd_flag . _chem_comp.name '4-[2-[[(2R)-2-(4-bromanylnaphthalen-1-yl)propanoyl]amino]-4-cyano-phenyl]butanoic acid' _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 BR1 C02 8VL sing 1 n n C28 C29 8VL doub 2 n y C28 C27 8VL sing 3 n y C29 C30 8VL sing 4 n y C27 C26 8VL doub 5 n y C30 C02 8VL doub 6 n y C30 C25 8VL sing 7 n y C02 C03 8VL sing 8 n y C26 C25 8VL sing 9 n y C25 C05 8VL doub 10 n y C03 C04 8VL doub 11 n y O22 C20 8VL doub 12 n n C05 C04 8VL sing 13 n y C05 C06 8VL sing 14 n n C20 C19 8VL sing 15 n n C20 O21 8VL sing 16 n n C19 C18 8VL sing 17 n n C06 C24 8VL sing 18 n n C06 C07 8VL sing 19 n n C18 C17 8VL sing 20 n n N08 C07 8VL sing 21 n n N08 C09 8VL sing 22 n n C07 O23 8VL doub 23 n n C09 C10 8VL doub 24 n y C09 C16 8VL sing 25 n y C17 C16 8VL sing 26 n n C10 C11 8VL sing 27 n y C16 C15 8VL doub 28 n y C11 C12 8VL sing 29 n n C11 C14 8VL doub 30 n y C15 C14 8VL sing 31 n y C12 N13 8VL trip 32 n n C10 H1 8VL sing 33 n n C15 H2 8VL sing 34 n n C17 H3 8VL sing 35 n n C17 H4 8VL sing 36 n n C24 H5 8VL sing 37 n n C24 H6 8VL sing 38 n n C24 H7 8VL sing 39 n n C26 H8 8VL sing 40 n n C28 H9 8VL sing 41 n n C03 H10 8VL sing 42 n n C04 H11 8VL sing 43 n n C06 H12 8VL sing 44 n n C14 H13 8VL sing 45 n n C18 H14 8VL sing 46 n n C18 H15 8VL sing 47 n n C19 H16 8VL sing 48 n n C19 H17 8VL sing 49 n n C27 H18 8VL sing 50 n n C29 H19 8VL sing 51 n n N08 H20 8VL sing 52 n n O21 H21 8VL sing 53 n n # _atom_sites.entry_id 5YHL _atom_sites.fract_transf_matrix[1][1] 0.009807 _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] 0.00255 _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] 0.012333 _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 D _pdbx_nonpoly_scheme.entity_id 4 _pdbx_nonpoly_scheme.mon_id 8VL _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 401 _pdbx_nonpoly_scheme.auth_seq_num 401 _pdbx_nonpoly_scheme.pdb_mon_id 8VL _pdbx_nonpoly_scheme.auth_mon_id LIG _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 C10 8VL . . . D 4 -46.624 -41.648 1.363 1 155.31 ? C10 8VL 401 A 1 HETATM 2 C C15 8VL . . . D 4 -47.134 -44.144 2.481 1 154.39 ? C15 8VL 401 A 1 HETATM 3 C C17 8VL . . . D 4 -45.198 -45.202 1.277 1 155.38 ? C17 8VL 401 A 1 HETATM 4 C C20 8VL . . . D 4 -43.627 -46.5 -1.071 1 159.91 ? C20 8VL 401 A 1 HETATM 5 C C24 8VL . . . D 4 -41.046 -41.672 0.292 1 164.21 ? C24 8VL 401 A 1 HETATM 6 C C26 8VL . . . D 4 -41.234 -42.834 -2.996 1 167.73 ? C26 8VL 401 A 1 HETATM 7 C C28 8VL . . . D 4 -40.919 -42.419 -5.318 1 171.25 ? C28 8VL 401 A 1 HETATM 8 C C02 8VL . . . D 4 -43.174 -39.794 -3.9 1 175.82 ? C02 8VL 401 A 1 HETATM 9 C C03 8VL . . . D 4 -43.724 -39.445 -2.711 1 171.58 ? C03 8VL 401 A 1 HETATM 10 C C04 8VL . . . D 4 -43.488 -40.211 -1.586 1 166.64 ? C04 8VL 401 A 1 HETATM 11 C C05 8VL . . . D 4 -42.681 -41.317 -1.624 1 169.26 ? C05 8VL 401 A 1 HETATM 12 C C06 8VL . . . D 4 -42.367 -42.103 -0.355 1 163.33 ? C06 8VL 401 A 1 HETATM 13 C C07 8VL . . . D 4 -43.525 -41.986 0.633 1 160.04 ? C07 8VL 401 A 1 HETATM 14 C C09 8VL . . . D 4 -45.807 -42.739 1.07 1 155.57 ? C09 8VL 401 A 1 HETATM 15 C C11 8VL . . . D 4 -47.698 -41.821 2.231 1 153.07 ? C11 8VL 401 A 1 HETATM 16 C C12 8VL . . . D 4 -48.545 -40.697 2.551 1 153.25 ? C12 8VL 401 A 1 HETATM 17 C C14 8VL . . . D 4 -47.948 -43.07 2.79 1 149.55 ? C14 8VL 401 A 1 HETATM 18 C C16 8VL . . . D 4 -46.056 -44.002 1.615 1 155.2 ? C16 8VL 401 A 1 HETATM 19 C C18 8VL . . . D 4 -45.792 -46.076 0.184 1 152.52 ? C18 8VL 401 A 1 HETATM 20 C C19 8VL . . . D 4 -44.84 -47.109 -0.397 1 154.31 ? C19 8VL 401 A 1 HETATM 21 C C25 8VL . . . D 4 -42.087 -41.702 -2.867 1 169.03 ? C25 8VL 401 A 1 HETATM 22 C C27 8VL . . . D 4 -40.667 -43.169 -4.191 1 171.96 ? C27 8VL 401 A 1 HETATM 23 C C29 8VL . . . D 4 -41.735 -41.324 -5.255 1 173.91 ? C29 8VL 401 A 1 HETATM 24 C C30 8VL . . . D 4 -42.337 -40.927 -4.035 1 172.2 ? C30 8VL 401 A 1 HETATM 25 N N08 8VL . . . D 4 -44.656 -42.619 0.258 1 158.66 ? N08 8VL 401 A 1 HETATM 26 N N13 8VL . . . D 4 -49.234 -39.828 2.827 1 149.34 ? N13 8VL 401 A 1 HETATM 27 O O21 8VL . . . D 4 -42.592 -46.354 -0.381 1 163.65 -1 O21 8VL 401 A 1 HETATM 28 O O22 8VL . . . D 4 -43.724 -46.171 -2.273 1 158.86 ? O22 8VL 401 A 1 HETATM 29 O O23 8VL . . . D 4 -43.392 -41.418 1.71 1 158.52 ? O23 8VL 401 A 1 HETATM 30 BR BR1 8VL . . . D 4 -43.615 -38.762 -5.426 1 247.65 ? BR1 8VL 401 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 72 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 30 #