data_7VEK # _model_server_result.job_id Zdr2dZt74F-88MOqcUhPVQ _model_server_result.datetime_utc '2024-11-28 09:31:35' _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 7vek # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 7VEK # _exptl.entry_id 7VEK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 305.412 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide _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 7VEK _cell.length_a 94.276 _cell.length_b 103.022 _cell.length_c 109.648 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VEK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E 1 1 B,F,G 2 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 5 _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 metalc ? metalc1 A O GLU 258 A GLU 238 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc2 C OAM O4B . A O4B 501 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc3 C OAO O4B . A O4B 501 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? metalc ? metalc4 C OAQ O4B . A O4B 501 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.954 ? metalc ? metalc5 C OAR O4B . A O4B 501 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? metalc ? metalc6 C OAP O4B . A O4B 501 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc7 C OAN O4B . A O4B 501 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? metalc ? metalc8 D K K . A K 502 1_555 B O GLU 258 B GLU 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? # _chem_comp.formula 'C18 H27 N O3' _chem_comp.formula_weight 305.412 _chem_comp.id 4DY _chem_comp.mon_nstd_flag . _chem_comp.name (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Capsaicin;8-Methyl-N-vanillyl-trans-6-nonenamide;NGX-4010 # 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 C40 C38 4DY sing 1 n n C30 C33 4DY sing 2 n n C30 C27 4DY sing 3 n n C37 C38 4DY sing 4 n n C37 C36 4DY doub 5 e n C33 C36 4DY sing 6 n n C38 C44 4DY sing 7 n n C24 C27 4DY sing 8 n n C24 C22 4DY sing 9 n n C5 C6 4DY doub 10 n y C5 C4 4DY sing 11 n y C6 C1 4DY sing 12 n y N21 C22 4DY sing 13 n n N21 C17 4DY sing 14 n n C22 O23 4DY doub 15 n n O10 C4 4DY sing 16 n n C4 C3 4DY doub 17 n y C1 C17 4DY sing 18 n n C1 C2 4DY doub 19 n y C3 C2 4DY sing 20 n y C3 O12 4DY sing 21 n n O12 C13 4DY sing 22 n n C2 H2 4DY sing 23 n n C5 H5 4DY sing 24 n n C40 H40 4DY sing 25 n n C40 H6T 4DY sing 26 n n C40 H6S 4DY sing 27 n n C38 H38 4DY sing 28 n n C44 H6U 4DY sing 29 n n C44 H6V 4DY sing 30 n n C44 H44 4DY sing 31 n n C37 H37 4DY sing 32 n n C36 H36 4DY sing 33 n n C33 H33 4DY sing 34 n n C33 H6R 4DY sing 35 n n C30 H6Q 4DY sing 36 n n C30 H30 4DY sing 37 n n C27 H27 4DY sing 38 n n C27 H6P 4DY sing 39 n n C24 H6O 4DY sing 40 n n C24 H24 4DY sing 41 n n N21 H21 4DY sing 42 n n C17 H6N 4DY sing 43 n n C17 H17 4DY sing 44 n n C6 H6 4DY sing 45 n n O10 H10 4DY sing 46 n n C13 H6M 4DY sing 47 n n C13 H6L 4DY sing 48 n n C13 H13 4DY sing 49 n n # _atom_sites.entry_id 7VEK _atom_sites.fract_transf_matrix[1][1] 0.010607 _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] 0.009707 _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] 0.00912 _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 2 O4B A 1 501 1 O4B O4B . D 3 K A 1 502 1 K K . E 4 U2F A 1 503 1 U2F U2F . F 5 4DY B 1 501 501 4DY 4DY . G 4 U2F B 1 502 2 U2F U2F . # 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 4DY . . . F 5 27.2 6.744 -35.658 0.9 66.4 ? C1 4DY 501 B 1 HETATM 2 C C2 4DY . . . F 5 26.644 7.63 -34.744 0.9 66.05 ? C2 4DY 501 B 1 HETATM 3 C C3 4DY . . . F 5 27.097 7.653 -33.429 0.9 61.21 ? C3 4DY 501 B 1 HETATM 4 C C4 4DY . . . F 5 28.11 6.782 -33.039 0.9 67.98 ? C4 4DY 501 B 1 HETATM 5 C C5 4DY . . . F 5 28.661 5.898 -33.958 0.9 66.36 ? C5 4DY 501 B 1 HETATM 6 C C40 4DY . . . F 5 23.206 7.458 -45.468 0.9 43.41 ? C40 4DY 501 B 1 HETATM 7 C C38 4DY . . . F 5 23.918 7.977 -44.215 0.9 62.39 ? C38 4DY 501 B 1 HETATM 8 C C44 4DY . . . F 5 22.891 8.75 -43.388 0.9 53.96 ? C44 4DY 501 B 1 HETATM 9 C C37 4DY . . . F 5 25.039 8.923 -44.653 0.9 63.54 ? C37 4DY 501 B 1 HETATM 10 C C36 4DY . . . F 5 25.977 9.419 -43.857 0.9 69.74 ? C36 4DY 501 B 1 HETATM 11 C C33 4DY . . . F 5 26.13 9.129 -42.359 0.9 59.77 ? C33 4DY 501 B 1 HETATM 12 C C30 4DY . . . F 5 27.041 10.195 -41.749 0.9 40.04 ? C30 4DY 501 B 1 HETATM 13 C C27 4DY . . . F 5 27.361 9.842 -40.298 0.9 40.76 ? C27 4DY 501 B 1 HETATM 14 C C24 4DY . . . F 5 28.111 8.511 -40.259 0.9 53.05 ? C24 4DY 501 B 1 HETATM 15 C C22 4DY . . . F 5 27.35 7.536 -39.362 0.9 60.64 ? C22 4DY 501 B 1 HETATM 16 O O23 4DY . . . F 5 26.679 6.686 -39.849 0.9 70.56 ? O23 4DY 501 B 1 HETATM 17 N N21 4DY . . . F 5 27.443 7.646 -37.916 0.9 54.82 ? N21 4DY 501 B 1 HETATM 18 C C17 4DY . . . F 5 26.701 6.708 -37.098 0.9 69.31 ? C17 4DY 501 B 1 HETATM 19 C C6 4DY . . . F 5 28.207 5.88 -35.266 0.9 58.17 ? C6 4DY 501 B 1 HETATM 20 O O10 4DY . . . F 5 28.586 6.786 -31.719 0.9 67.93 ? O10 4DY 501 B 1 HETATM 21 O O12 4DY . . . F 5 26.534 8.555 -32.505 0.9 58.57 ? O12 4DY 501 B 1 HETATM 22 C C13 4DY . . . F 5 25.21 8.279 -32.134 0.9 47.74 ? C13 4DY 501 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #