data_6NM4
#
_model_server_result.job_id            ZxNgHm5SXS0JRPoy7p2Phw 
_model_server_result.datetime_utc      '2024-11-04 22:43:01' 
_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          6nm4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":403}' 
#
_entry.id    6NM4 
#
_exptl.entry_id    6NM4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              464.56 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-[3-(3,5-dimethoxyphenyl)-1,2,4-oxadiazol-5-yl]-1-methyl-9-(2-methylpyridin-4-yl)-1,4,9-triazaspiro[5.5]undecane 
_entity.pdbx_number_of_molecules    2 
_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            6NM4 
_cell.length_a            38.026 
_cell.length_b            74.8 
_cell.length_c            141.435 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6NM4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_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,F,G,L 1 1 
B,H,I,J,K,M 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 E N N 
? 4 J N 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 11 A CYS 205 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc2 A SG CYS 14 A CYS 208 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc3 A SG CYS 22 A CYS 216 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc4 A ND1 HIS 25 A HIS 219 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc5 B SG CYS 11 B CYS 205 1_555 H ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc6 B SG CYS 14 B CYS 208 1_555 H ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
metalc ? metalc7 B SG CYS 22 B CYS 216 1_555 H ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? 
metalc ? metalc8 B ND1 HIS 25 B HIS 219 1_555 H ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
#
_chem_comp.formula           'C25 H32 N6 O3' 
_chem_comp.formula_weight    464.56 
_chem_comp.id                KS7 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-[3-(3,5-dimethoxyphenyl)-1,2,4-oxadiazol-5-yl]-1-methyl-9-(2-methylpyridin-4-yl)-1,4,9-triazaspiro[5.5]undecane 
_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
C4 O1 KS7 sing 173 n n 
O1 C3 KS7 sing 174 n n 
C17 C18 KS7 doub 175 n y 
C17 N3 KS7 sing 176 n y 
C3 C2 KS7 doub 177 n y 
C3 C5 KS7 sing 178 n y 
C18 C13 KS7 sing 179 n y 
N3 C15 KS7 doub 180 n y 
C2 C1 KS7 sing 181 n y 
C5 C6 KS7 doub 182 n y 
C13 N2 KS7 sing 183 n n 
C13 C14 KS7 doub 184 n y 
C19 C20 KS7 sing 185 n n 
C19 N2 KS7 sing 186 n n 
C15 C14 KS7 sing 187 n y 
C15 C16 KS7 sing 188 n n 
C20 C10 KS7 sing 189 n n 
N2 C12 KS7 sing 190 n n 
C O KS7 sing 191 n n 
C1 O KS7 sing 192 n n 
C1 C24 KS7 doub 193 n y 
C6 C24 KS7 sing 194 n y 
C6 C7 KS7 sing 195 n n 
C9 C10 KS7 sing 196 n n 
C9 N1 KS7 sing 197 n n 
N5 C7 KS7 sing 198 n y 
N5 C8 KS7 doub 199 n y 
C12 C11 KS7 sing 200 n n 
C10 C11 KS7 sing 201 n n 
C10 N4 KS7 sing 202 n n 
C7 N KS7 doub 203 n y 
C8 N1 KS7 sing 204 n n 
C8 O2 KS7 sing 205 n y 
N1 C23 KS7 sing 206 n n 
N4 C21 KS7 sing 207 n n 
N4 C22 KS7 sing 208 n n 
N O2 KS7 sing 209 n y 
C22 C23 KS7 sing 210 n n 
C4 H1 KS7 sing 211 n n 
C4 H2 KS7 sing 212 n n 
C4 H3 KS7 sing 213 n n 
C5 H4 KS7 sing 214 n n 
C9 H5 KS7 sing 215 n n 
C9 H6 KS7 sing 216 n n 
C11 H7 KS7 sing 217 n n 
C11 H8 KS7 sing 218 n n 
C12 H9 KS7 sing 219 n n 
C12 H10 KS7 sing 220 n n 
C14 H11 KS7 sing 221 n n 
C21 H13 KS7 sing 222 n n 
C21 H14 KS7 sing 223 n n 
C21 H15 KS7 sing 224 n n 
C20 H16 KS7 sing 225 n n 
C20 H17 KS7 sing 226 n n 
C19 H18 KS7 sing 227 n n 
C19 H19 KS7 sing 228 n n 
C18 H20 KS7 sing 229 n n 
C17 H21 KS7 sing 230 n n 
C16 H22 KS7 sing 231 n n 
C16 H23 KS7 sing 232 n n 
C16 H24 KS7 sing 233 n n 
C22 H25 KS7 sing 234 n n 
C22 H26 KS7 sing 235 n n 
C23 H27 KS7 sing 236 n n 
C23 H28 KS7 sing 237 n n 
C2 H29 KS7 sing 238 n n 
C24 H30 KS7 sing 239 n n 
C H31 KS7 sing 240 n n 
C H32 KS7 sing 241 n n 
C H33 KS7 sing 242 n n 
#
_atom_sites.entry_id                     6NM4 
_atom_sites.fract_transf_matrix[1][1]    0.026298 
_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]    0.013369 
_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]    0.00707 
_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 ZN A 1 401 400 ZN ZN . 
D 3 SAM A 1 402 401 SAM SAM . 
E 4 KS7 A 1 403 402 KS7 XXX . 
F 5 UNX A 1 404 1 UNX UNX . 
G 5 UNX A 1 405 5 UNX UNX . 
H 2 ZN B 1 401 400 ZN ZN . 
I 3 SAM B 1 402 401 SAM SAM . 
J 4 KS7 B 1 403 402 KS7 XXX . 
K 5 UNX B 1 404 21 UNX UNX . 
L 6 HOH A 1 501 173 HOH HOH . 
L 6 HOH A 2 502 7 HOH HOH . 
L 6 HOH A 3 503 180 HOH HOH . 
L 6 HOH A 4 504 16 HOH HOH . 
L 6 HOH A 5 505 17 HOH HOH . 
L 6 HOH A 6 506 11 HOH HOH . 
L 6 HOH A 7 507 172 HOH HOH . 
L 6 HOH A 8 508 6 HOH HOH . 
L 6 HOH A 9 509 174 HOH HOH . 
L 6 HOH A 10 510 43 HOH HOH . 
L 6 HOH A 11 511 186 HOH HOH . 
L 6 HOH A 12 512 3 HOH HOH . 
L 6 HOH A 13 513 183 HOH HOH . 
L 6 HOH A 14 514 18 HOH HOH . 
L 6 HOH A 15 515 196 HOH HOH . 
M 6 HOH B 1 501 170 HOH HOH . 
M 6 HOH B 2 502 187 HOH HOH . 
M 6 HOH B 3 503 13 HOH HOH . 
M 6 HOH B 4 504 14 HOH HOH . 
M 6 HOH B 5 505 193 HOH HOH . 
M 6 HOH B 6 506 9 HOH HOH . 
M 6 HOH B 7 507 8 HOH HOH . 
M 6 HOH B 8 508 10 HOH HOH . 
#
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 C4 KS7 . . . J 4 -10.514 -0.166 15.17 1 62.54 ? C4 KS7 403 B 1 
HETATM 2 C C5 KS7 . . . J 4 -10.627 0.223 18.719 1 64.24 ? C5 KS7 403 B 1 
HETATM 3 C C6 KS7 . . . J 4 -10.101 0.894 19.818 1 64.02 ? C6 KS7 403 B 1 
HETATM 4 N N1 KS7 . . . J 4 -12.798 -0.753 23.363 1 56.85 ? N1 KS7 403 B 1 
HETATM 5 C C7 KS7 . . . J 4 -10.54 0.528 21.184 1 62.77 ? C7 KS7 403 B 1 
HETATM 6 C C8 KS7 . . . J 4 -11.789 -0.204 22.708 1 61.87 ? C8 KS7 403 B 1 
HETATM 7 N N2 KS7 . . . J 4 -17.168 -1.089 20.848 1 54.53 ? N2 KS7 403 B 1 
HETATM 8 C C9 KS7 . . . J 4 -13.743 -1.566 22.607 1 56.23 ? C9 KS7 403 B 1 
HETATM 9 C C10 KS7 . . . J 4 -15.196 -1.563 23.111 1 55.37 ? C10 KS7 403 B 1 
HETATM 10 C C11 KS7 . . . J 4 -15.872 -0.221 22.786 1 54.29 ? C11 KS7 403 B 1 
HETATM 11 C C12 KS7 . . . J 4 -16.229 -0.058 21.314 1 54.07 ? C12 KS7 403 B 1 
HETATM 12 N N3 KS7 . . . J 4 -20.944 -0.233 19.185 1 55.75 ? N3 KS7 403 B 1 
HETATM 13 C C13 KS7 . . . J 4 -18.429 -0.791 20.285 1 53.78 ? C13 KS7 403 B 1 
HETATM 14 C C14 KS7 . . . J 4 -19.005 0.478 20.385 1 53 ? C14 KS7 403 B 1 
HETATM 15 C C15 KS7 . . . J 4 -20.246 0.728 19.803 1 53.04 ? C15 KS7 403 B 1 
HETATM 16 N N4 KS7 . . . J 4 -15.154 -2.056 24.555 1 57.59 ? N4 KS7 403 B 1 
HETATM 17 C C21 KS7 . . . J 4 -16.25 -1.814 25.515 1 58.77 ? C21 KS7 403 B 1 
HETATM 18 C C20 KS7 . . . J 4 -15.804 -2.653 22.22 1 55.35 ? C20 KS7 403 B 1 
HETATM 19 C C19 KS7 . . . J 4 -17.182 -2.271 21.716 1 56.49 ? C19 KS7 403 B 1 
HETATM 20 C C18 KS7 . . . J 4 -19.156 -1.763 19.619 1 55.76 ? C18 KS7 403 B 1 
HETATM 21 C C17 KS7 . . . J 4 -20.395 -1.448 19.107 1 56.29 ? C17 KS7 403 B 1 
HETATM 22 C C16 KS7 . . . J 4 -20.816 2.103 19.745 1 53.13 ? C16 KS7 403 B 1 
HETATM 23 C C22 KS7 . . . J 4 -13.861 -1.905 25.24 1 58.32 ? C22 KS7 403 B 1 
HETATM 24 C C23 KS7 . . . J 4 -13.138 -0.64 24.782 1 58.2 ? C23 KS7 403 B 1 
HETATM 25 O O2 KS7 . . . J 4 -10.838 0.519 23.32 1 65.89 ? O2 KS7 403 B 1 
HETATM 26 N N KS7 . . . J 4 -9.994 1.016 22.267 1 68.09 ? N KS7 403 B 1 
HETATM 27 N N5 KS7 . . . J 4 -11.644 -0.248 21.402 1 62.36 ? N5 KS7 403 B 1 
HETATM 28 C C3 KS7 . . . J 4 -10.199 0.544 17.443 1 61.98 ? C3 KS7 403 B 1 
HETATM 29 O O1 KS7 . . . J 4 -10.832 -0.283 16.552 1 63.2 ? O1 KS7 403 B 1 
HETATM 30 C C2 KS7 . . . J 4 -9.264 1.542 17.227 1 62.16 ? C2 KS7 403 B 1 
HETATM 31 C C24 KS7 . . . J 4 -9.146 1.888 19.621 1 66 ? C24 KS7 403 B 1 
HETATM 32 C C1 KS7 . . . J 4 -8.747 2.211 18.327 1 66.02 ? C1 KS7 403 B 1 
HETATM 33 O O KS7 . . . J 4 -7.843 3.244 18.251 1 68.14 ? O KS7 403 B 1 
HETATM 34 C C KS7 . . . J 4 -7.406 3.69 16.967 1 68.03 ? C KS7 403 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           34 
#