data_9CYD # _model_server_result.job_id NEPochQSWh2ndmI9ayXFrw _model_server_result.datetime_utc '2025-07-14 04:04:18' _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 9cyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 9CYD # _exptl.entry_id 9CYD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 396.522 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1S,4s)-4-{(3R)-3-[(E)-(methoxyimino)(6-methoxynaphthalen-2-yl)methyl]piperidin-1-yl}cyclohexan-1-ol _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 9CYD _cell.length_a 156.584 _cell.length_b 156.584 _cell.length_c 156.584 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9CYD _symmetry.cell_setting ? _symmetry.Int_Tables_number 212 _symmetry.space_group_name_Hall 'P 4acd 2ab 3' _symmetry.space_group_name_H-M 'P 43 3 2' # _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,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 2 _struct_asym.id B _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 SG CYS 192 A CYS 189 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc2 A SG CYS 195 A CYS 192 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc3 A SG CYS 227 A CYS 224 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc4 A SG CYS 229 A CYS 226 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc5 A SG CYS 273 A CYS 270 1_555 D ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc6 A SG CYS 273 A CYS 270 1_555 D ZN ZN . A ZN 403 12_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? # _chem_comp.formula 'C24 H32 N2 O3' _chem_comp.formula_weight 396.522 _chem_comp.id A1A0U _chem_comp.mon_nstd_flag . _chem_comp.name (1S,4s)-4-{(3R)-3-[(E)-(methoxyimino)(6-methoxynaphthalen-2-yl)methyl]piperidin-1-yl}cyclohexan-1-ol _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 O02 C01 A1A0U sing 1 n n C03 O02 A1A0U sing 2 n n C04 C03 A1A0U doub 3 n y C05 C04 A1A0U sing 4 n y C06 C05 A1A0U doub 5 n y C08 C07 A1A0U doub 6 n y C11 C10 A1A0U sing 7 n n N12 C11 A1A0U sing 8 n n C14 C13 A1A0U sing 9 n n C15 C14 A1A0U sing 10 n n C16 C15 A1A0U sing 11 n n O17 C16 A1A0U sing 12 n n C18 C16 A1A0U sing 13 n n C19 C18 A1A0U sing 14 n n C13 N12 A1A0U sing 15 n n C20 N12 A1A0U sing 16 n n C21 C20 A1A0U sing 17 n n C22 C21 A1A0U sing 18 n n C10 C09 A1A0U sing 19 n n N23 C09 A1A0U doub 20 e n O24 N23 A1A0U sing 21 n n C25 O24 A1A0U sing 22 n n C09 C08 A1A0U sing 23 n n C26 C08 A1A0U sing 24 n y C27 C26 A1A0U doub 25 n y C07 C06 A1A0U sing 26 n y C28 C06 A1A0U sing 27 n y C29 C28 A1A0U doub 28 n y C03 C29 A1A0U sing 29 n y C05 C27 A1A0U sing 30 n y C10 C22 A1A0U sing 31 n n C13 C19 A1A0U sing 32 n n C10 H101 A1A0U sing 33 n n C13 H131 A1A0U sing 34 n n C01 H012 A1A0U sing 35 n n C01 H011 A1A0U sing 36 n n C01 H013 A1A0U sing 37 n n C04 H041 A1A0U sing 38 n n C07 H071 A1A0U sing 39 n n C11 H112 A1A0U sing 40 n n C11 H111 A1A0U sing 41 n n C14 H141 A1A0U sing 42 n n C14 H142 A1A0U sing 43 n n C15 H151 A1A0U sing 44 n n C15 H152 A1A0U sing 45 n n C16 H161 A1A0U sing 46 n n C18 H182 A1A0U sing 47 n n C18 H181 A1A0U sing 48 n n C19 H191 A1A0U sing 49 n n C19 H192 A1A0U sing 50 n n C20 H201 A1A0U sing 51 n n C20 H202 A1A0U sing 52 n n C21 H212 A1A0U sing 53 n n C21 H211 A1A0U sing 54 n n C22 H222 A1A0U sing 55 n n C22 H221 A1A0U sing 56 n n C25 H252 A1A0U sing 57 n n C25 H251 A1A0U sing 58 n n C25 H253 A1A0U sing 59 n n C26 H261 A1A0U sing 60 n n C27 H271 A1A0U sing 61 n n C28 H281 A1A0U sing 62 n n C29 H291 A1A0U sing 63 n n O17 H171 A1A0U sing 64 n n # _atom_sites.entry_id 9CYD _atom_sites.fract_transf_matrix[1][1] 0.006386 _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] 0.006386 _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] 0.006386 _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 A1A0U A 1 401 401 A1A0U 535 . C 3 ZN A 1 402 402 ZN ZN . D 3 ZN A 1 403 403 ZN ZN . E 4 CL A 1 404 404 CL CL . # 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 A1A0U . . . B 2 27.148 33.156 -35.236 1 69.28 ? C10 A1A0U 401 A 1 HETATM 2 C C13 A1A0U . . . B 2 29.905 32.844 -32.33 1 70.66 ? C13 A1A0U 401 A 1 HETATM 3 C C01 A1A0U . . . B 2 18.899 30.784 -38.667 1 70.75 ? C01 A1A0U 401 A 1 HETATM 4 C C03 A1A0U . . . B 2 20.701 31.191 -37.257 1 66.37 ? C03 A1A0U 401 A 1 HETATM 5 C C04 A1A0U . . . B 2 21.772 30.595 -37.843 1 64.6 ? C04 A1A0U 401 A 1 HETATM 6 C C05 A1A0U . . . B 2 23.044 31.078 -37.578 1 64.22 ? C05 A1A0U 401 A 1 HETATM 7 C C06 A1A0U . . . B 2 23.228 32.158 -36.707 1 63.87 ? C06 A1A0U 401 A 1 HETATM 8 C C07 A1A0U . . . B 2 24.515 32.637 -36.46 1 64.39 ? C07 A1A0U 401 A 1 HETATM 9 C C08 A1A0U . . . B 2 25.622 32.077 -37.013 1 65.33 ? C08 A1A0U 401 A 1 HETATM 10 C C09 A1A0U . . . B 2 26.899 32.658 -36.7 1 67.45 ? C09 A1A0U 401 A 1 HETATM 11 C C11 A1A0U . . . B 2 28.52 32.86 -34.588 1 70.24 ? C11 A1A0U 401 A 1 HETATM 12 C C14 A1A0U . . . B 2 29.791 31.333 -32.006 1 68.53 ? C14 A1A0U 401 A 1 HETATM 13 C C15 A1A0U . . . B 2 31.02 30.918 -31.202 1 68.64 ? C15 A1A0U 401 A 1 HETATM 14 C C16 A1A0U . . . B 2 32.347 31.216 -31.991 1 74.18 ? C16 A1A0U 401 A 1 HETATM 15 C C18 A1A0U . . . B 2 32.383 32.69 -32.468 1 66.13 ? C18 A1A0U 401 A 1 HETATM 16 C C19 A1A0U . . . B 2 31.123 33.103 -33.225 1 65.25 ? C19 A1A0U 401 A 1 HETATM 17 C C20 A1A0U . . . B 2 28.588 34.977 -33.128 1 65.23 ? C20 A1A0U 401 A 1 HETATM 18 C C21 A1A0U . . . B 2 28.1 35.446 -34.484 1 64.45 ? C21 A1A0U 401 A 1 HETATM 19 C C22 A1A0U . . . B 2 26.897 34.684 -35.066 1 65.13 ? C22 A1A0U 401 A 1 HETATM 20 C C25 A1A0U . . . B 2 30.155 33.093 -37.913 1 72.84 ? C25 A1A0U 401 A 1 HETATM 21 C C26 A1A0U . . . B 2 25.443 30.994 -37.893 1 68.17 ? C26 A1A0U 401 A 1 HETATM 22 C C27 A1A0U . . . B 2 24.191 30.515 -38.158 1 64.63 ? C27 A1A0U 401 A 1 HETATM 23 C C28 A1A0U . . . B 2 22.092 32.743 -36.117 1 65.51 ? C28 A1A0U 401 A 1 HETATM 24 C C29 A1A0U . . . B 2 20.838 32.281 -36.374 1 66.98 ? C29 A1A0U 401 A 1 HETATM 25 N N12 A1A0U . . . B 2 28.682 33.448 -33.116 1 70.58 ? N12 A1A0U 401 A 1 HETATM 26 N N23 A1A0U . . . B 2 27.855 32.784 -37.608 1 74.58 ? N23 A1A0U 401 A 1 HETATM 27 O O02 A1A0U . . . B 2 19.464 30.639 -37.502 1 69.31 ? O02 A1A0U 401 A 1 HETATM 28 O O17 A1A0U . . . B 2 32.413 30.313 -33.097 1 74.86 ? O17 A1A0U 401 A 1 HETATM 29 O O24 A1A0U . . . B 2 29.008 33.37 -37.265 1 79.02 ? O24 A1A0U 401 A 1 HETATM 30 H H101 A1A0U . . . B 2 26.383 32.544 -34.692 1 83.13 ? H101 A1A0U 401 A 1 HETATM 31 H H131 A1A0U . . . B 2 29.962 33.394 -31.355 1 84.79 ? H131 A1A0U 401 A 1 HETATM 32 H H012 A1A0U . . . B 2 17.97 30.195 -38.569 1 84.9 ? H012 A1A0U 401 A 1 HETATM 33 H H011 A1A0U . . . B 2 19.647 30.364 -39.362 1 84.9 ? H011 A1A0U 401 A 1 HETATM 34 H H013 A1A0U . . . B 2 18.754 31.876 -38.741 1 84.9 ? H013 A1A0U 401 A 1 HETATM 35 H H041 A1A0U . . . B 2 21.636 29.742 -38.519 1 77.52 ? H041 A1A0U 401 A 1 HETATM 36 H H071 A1A0U . . . B 2 24.605 33.498 -35.792 1 77.27 ? H071 A1A0U 401 A 1 HETATM 37 H H112 A1A0U . . . B 2 29.35 33.275 -35.206 1 84.29 ? H112 A1A0U 401 A 1 HETATM 38 H H111 A1A0U . . . B 2 28.704 31.762 -34.531 1 84.29 ? H111 A1A0U 401 A 1 HETATM 39 H H141 A1A0U . . . B 2 29.728 30.711 -32.922 1 82.23 ? H141 A1A0U 401 A 1 HETATM 40 H H142 A1A0U . . . B 2 28.877 31.097 -31.423 1 82.23 ? H142 A1A0U 401 A 1 HETATM 41 H H151 A1A0U . . . B 2 30.963 29.839 -30.942 1 82.36 ? H151 A1A0U 401 A 1 HETATM 42 H H152 A1A0U . . . B 2 31.032 31.44 -30.221 1 82.36 ? H152 A1A0U 401 A 1 HETATM 43 H H161 A1A0U . . . B 2 33.226 31.064 -31.307 1 89.02 ? H161 A1A0U 401 A 1 HETATM 44 H H182 A1A0U . . . B 2 33.27 32.85 -33.106 1 79.36 ? H182 A1A0U 401 A 1 HETATM 45 H H181 A1A0U . . . B 2 32.53 33.355 -31.599 1 79.36 ? H181 A1A0U 401 A 1 HETATM 46 H H191 A1A0U . . . B 2 31.053 32.539 -34.182 1 78.3 ? H191 A1A0U 401 A 1 HETATM 47 H H192 A1A0U . . . B 2 31.191 34.174 -33.521 1 78.3 ? H192 A1A0U 401 A 1 HETATM 48 H H201 A1A0U . . . B 2 29.569 35.446 -32.865 1 78.28 ? H201 A1A0U 401 A 1 HETATM 49 H H202 A1A0U . . . B 2 27.927 35.35 -32.307 1 78.28 ? H202 A1A0U 401 A 1 HETATM 50 H H212 A1A0U . . . B 2 28.954 35.405 -35.195 1 77.34 ? H212 A1A0U 401 A 1 HETATM 51 H H211 A1A0U . . . B 2 27.864 36.53 -34.414 1 77.34 ? H211 A1A0U 401 A 1 HETATM 52 H H222 A1A0U . . . B 2 26.619 35.121 -36.046 1 78.16 ? H222 A1A0U 401 A 1 HETATM 53 H H221 A1A0U . . . B 2 26.011 34.839 -34.418 1 78.16 ? H221 A1A0U 401 A 1 HETATM 54 H H252 A1A0U . . . B 2 30.464 34.08 -38.292 1 87.4 ? H252 A1A0U 401 A 1 HETATM 55 H H251 A1A0U . . . B 2 29.832 32.374 -38.683 1 87.4 ? H251 A1A0U 401 A 1 HETATM 56 H H253 A1A0U . . . B 2 30.79 32.674 -37.116 1 87.4 ? H253 A1A0U 401 A 1 HETATM 57 H H261 A1A0U . . . B 2 26.295 30.521 -38.376 1 81.8 ? H261 A1A0U 401 A 1 HETATM 58 H H271 A1A0U . . . B 2 24.036 29.67 -38.836 1 77.55 ? H271 A1A0U 401 A 1 HETATM 59 H H281 A1A0U . . . B 2 22.237 33.589 -35.438 1 78.62 ? H281 A1A0U 401 A 1 HETATM 60 H H291 A1A0U . . . B 2 19.961 32.736 -35.913 1 80.38 ? H291 A1A0U 401 A 1 HETATM 61 H H171 A1A0U . . . B 2 33.336 30.208 -33.323 1 89.83 ? H171 A1A0U 401 A 1 HETATM 62 H H121 A1A0U . . . B 2 27.828 33.143 -32.579 1 84.7 ? H121 A1A0U 401 A 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 62 #