data_5LM4 # _model_server_result.job_id '_MVRwWXHNlwWcFkYv8pcNg' _model_server_result.datetime_utc '2025-07-20 10:21:42' _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 5lm4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":603}' # _entry.id 5LM4 # _exptl.entry_id 5LM4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 422.475 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-Amino-5,6,7,8-tetrahydro-4-(4-methoxyphenyl)-7-(naphthalen-1-yl)-5-oxo-4H-chromene-3-carbonitrile _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 120 _cell.entry_id 5LM4 _cell.length_a 123.11 _cell.length_b 123.11 _cell.length_c 89.62 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LM4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 metalc ? metalc1 A O THR 376 A THR 376 1_555 B NA NA . A NA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc2 A O SER 417 A SER 417 1_555 B NA NA . A NA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc3 A O ILE 418 A ILE 418 1_555 B NA NA . A NA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.643 ? metalc ? metalc4 A O ALA 420 A ALA 420 1_555 B NA NA . A NA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? # _chem_comp.formula 'C27 H22 N2 O3' _chem_comp.formula_weight 422.475 _chem_comp.id 6Z6 _chem_comp.mon_nstd_flag . _chem_comp.name 2-Amino-5,6,7,8-tetrahydro-4-(4-methoxyphenyl)-7-(naphthalen-1-yl)-5-oxo-4H-chromene-3-carbonitrile _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 C O 6Z6 sing 1 n n O C1 6Z6 sing 2 n n C1 C2 6Z6 doub 3 n y C1 C6 6Z6 sing 4 n y C2 C3 6Z6 sing 5 n y C6 C5 6Z6 doub 6 n y C3 C4 6Z6 doub 7 n y C5 C4 6Z6 sing 8 n y C4 C7 6Z6 sing 9 n n N1 C16 6Z6 trip 10 n n C16 C15 6Z6 sing 11 n n C7 C15 6Z6 sing 12 n n C7 C8 6Z6 sing 13 n n O1 C9 6Z6 doub 14 n n C15 C14 6Z6 doub 15 n n C8 C9 6Z6 sing 16 n n C8 C13 6Z6 doub 17 n n C9 C10 6Z6 sing 18 n n C14 N 6Z6 sing 19 n n C14 O2 6Z6 sing 20 n n C24 C25 6Z6 doub 21 n y C24 C23 6Z6 sing 22 n y C13 O2 6Z6 sing 23 n n C13 C12 6Z6 sing 24 n n C10 C11 6Z6 sing 25 n n C25 C26 6Z6 sing 26 n y C23 C22 6Z6 doub 27 n y C12 C11 6Z6 sing 28 n n C11 C17 6Z6 sing 29 n n C26 C17 6Z6 doub 30 n y C26 C21 6Z6 sing 31 n y C17 C18 6Z6 sing 32 n y C22 C21 6Z6 sing 33 n y C21 C20 6Z6 doub 34 n y C18 C19 6Z6 doub 35 n y C20 C19 6Z6 sing 36 n y C2 H1 6Z6 sing 37 n n C5 H2 6Z6 sing 38 n n C6 H3 6Z6 sing 39 n n N H4 6Z6 sing 40 n n N H5 6Z6 sing 41 n n C3 H6 6Z6 sing 42 n n C H7 6Z6 sing 43 n n C H8 6Z6 sing 44 n n C H9 6Z6 sing 45 n n C10 H10 6Z6 sing 46 n n C10 H11 6Z6 sing 47 n n C11 H12 6Z6 sing 48 n n C12 H13 6Z6 sing 49 n n C12 H14 6Z6 sing 50 n n C18 H15 6Z6 sing 51 n n C19 H16 6Z6 sing 52 n n C20 H17 6Z6 sing 53 n n C22 H18 6Z6 sing 54 n n C23 H19 6Z6 sing 55 n n C24 H20 6Z6 sing 56 n n C25 H21 6Z6 sing 57 n n C7 H22 6Z6 sing 58 n n # _atom_sites.entry_id 5LM4 _atom_sites.fract_transf_matrix[1][1] 0.008123 _atom_sites.fract_transf_matrix[1][2] 0.00469 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009379 _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] 0.011158 _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 B 2 NA A 1 601 501 NA NA . C 3 ASP A 1 602 502 ASP ASP . D 4 6Z6 A 1 603 503 6Z6 UCP . # 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 N N1 6Z6 . . . D 4 -471.877 298.165 12.768 1 91.72 ? N1 6Z6 603 A 1 HETATM 2 C C2 6Z6 . . . D 4 -474.3 301.296 8.889 1 96.04 ? C2 6Z6 603 A 1 HETATM 3 O O2 6Z6 . . . D 4 -475.967 299.697 14.557 1 91.29 ? O2 6Z6 603 A 1 HETATM 4 C C4 6Z6 . . . D 4 -474.64 300.944 11.258 1 92.8 ? C4 6Z6 603 A 1 HETATM 5 C C5 6Z6 . . . D 4 -475.892 300.412 10.972 1 92.27 ? C5 6Z6 603 A 1 HETATM 6 C C6 6Z6 . . . D 4 -476.345 300.297 9.669 1 93.34 ? C6 6Z6 603 A 1 HETATM 7 O O1 6Z6 . . . D 4 -473.969 303.764 13.314 1 101.65 ? O1 6Z6 603 A 1 HETATM 8 C C9 6Z6 . . . D 4 -474.978 303.167 13.677 1 99.36 ? C9 6Z6 603 A 1 HETATM 9 C C8 6Z6 . . . D 4 -475.066 301.696 13.604 1 95.94 ? C8 6Z6 603 A 1 HETATM 10 C C13 6Z6 . . . D 4 -475.983 301.062 14.353 1 94.72 ? C13 6Z6 603 A 1 HETATM 11 C C14 6Z6 . . . D 4 -474.947 298.961 14.008 1 88.39 ? C14 6Z6 603 A 1 HETATM 12 N N 6Z6 . . . D 4 -474.976 297.716 14.492 1 85.39 ? N 6Z6 603 A 1 HETATM 13 C C15 6Z6 . . . D 4 -473.997 299.531 13.227 1 90.34 ? C15 6Z6 603 A 1 HETATM 14 C C16 6Z6 . . . D 4 -472.813 298.796 12.956 1 91.08 ? C16 6Z6 603 A 1 HETATM 15 C C7 6Z6 . . . D 4 -474.11 300.949 12.691 1 93.44 ? C7 6Z6 603 A 1 HETATM 16 C C3 6Z6 . . . D 4 -473.859 301.399 10.201 1 94.92 ? C3 6Z6 603 A 1 HETATM 17 C C1 6Z6 . . . D 4 -475.545 300.729 8.62 1 95.04 ? C1 6Z6 603 A 1 HETATM 18 O O 6Z6 . . . D 4 -476.204 300.468 7.441 1 93.76 ? O 6Z6 603 A 1 HETATM 19 C C 6Z6 . . . D 4 -475.579 300.828 6.214 1 95.56 ? C 6Z6 603 A 1 HETATM 20 C C10 6Z6 . . . D 4 -476.165 303.931 14.21 1 100.1 ? C10 6Z6 603 A 1 HETATM 21 C C11 6Z6 . . . D 4 -476.888 303.182 15.331 1 100.93 ? C11 6Z6 603 A 1 HETATM 22 C C12 6Z6 . . . D 4 -477.149 301.713 15.014 1 96.19 ? C12 6Z6 603 A 1 HETATM 23 C C17 6Z6 . . . D 4 -478.04 303.906 16.011 1 107.03 ? C17 6Z6 603 A 1 HETATM 24 C C18 6Z6 . . . D 4 -477.937 304.25 17.336 1 108.01 ? C18 6Z6 603 A 1 HETATM 25 C C19 6Z6 . . . D 4 -478.974 304.861 18.022 1 109.09 ? C19 6Z6 603 A 1 HETATM 26 C C20 6Z6 . . . D 4 -480.147 305.15 17.393 1 110.73 ? C20 6Z6 603 A 1 HETATM 27 C C21 6Z6 . . . D 4 -480.332 304.826 16.025 1 112.76 ? C21 6Z6 603 A 1 HETATM 28 C C26 6Z6 . . . D 4 -479.265 304.19 15.312 1 110.99 ? C26 6Z6 603 A 1 HETATM 29 C C22 6Z6 . . . D 4 -481.561 305.076 15.353 1 114.54 ? C22 6Z6 603 A 1 HETATM 30 C C23 6Z6 . . . D 4 -481.734 304.707 14.045 1 113.22 ? C23 6Z6 603 A 1 HETATM 31 C C24 6Z6 . . . D 4 -480.71 304.084 13.347 1 111.97 ? C24 6Z6 603 A 1 HETATM 32 C C25 6Z6 . . . D 4 -479.502 303.833 13.95 1 111.41 ? C25 6Z6 603 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 32 #