data_6OYZ # _model_server_result.job_id H2r3IyKumenKDFs8iPDkvQ _model_server_result.datetime_utc '2025-08-31 14:58:53' _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 6oyz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 6OYZ # _exptl.entry_id 6OYZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 569.519 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2~{S},3~{S},4~{S})-2-[(1~{R})-2-azanyl-1-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-methoxy-4-oxidanyl-oxolan-2-yl]-2-oxidanylidene-ethoxy]-3,4-bis(oxidanyl)-~{N}-[(3~{S})-2-oxidanylideneazepan-3-yl]-3,4-dihydro-2~{H}-pyran-6-carboxamide _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 110.82 _cell.angle_gamma 90 _cell.entry_id 6OYZ _cell.length_a 93.759 _cell.length_b 128.067 _cell.length_c 129.516 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6OYZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 ? dimeric 2 author_defined_assembly 3 ? dimeric 2 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I 1 1 C,D 2 1 E,F 3 1 G,H 4 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 3 _struct_asym.id I _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 25 E CYS 22 1_555 A SG CYS 98 E CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 C SG CYS 25 G CYS 22 1_555 C SG CYS 98 G CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 E SG CYS 25 F CYS 22 1_555 E SG CYS 98 F CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 G SG CYS 25 H CYS 22 1_555 G SG CYS 98 H CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _chem_comp.formula 'C23 H31 N5 O12' _chem_comp.formula_weight 569.519 _chem_comp.id NKM _chem_comp.mon_nstd_flag . _chem_comp.name (2~{S},3~{S},4~{S})-2-[(1~{R})-2-azanyl-1-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-methoxy-4-oxidanyl-oxolan-2-yl]-2-oxidanylidene-ethoxy]-3,4-bis(oxidanyl)-~{N}-[(3~{S})-2-oxidanylideneazepan-3-yl]-3,4-dihydro-2~{H}-pyran-6-carboxamide _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 C01 O02 NKM sing 235 n n N11 C09 NKM sing 236 n n O02 C03 NKM sing 237 n n O29 C28 NKM doub 238 n n N27 C28 NKM sing 239 n n N27 C26 NKM sing 240 n n C07 C03 NKM sing 241 n n C07 C08 NKM sing 242 n n C07 O06 NKM sing 243 n n C09 C08 NKM sing 244 n n C09 O10 NKM doub 245 n n O40 C04 NKM sing 246 n n C03 C04 NKM sing 247 n n C28 C22 NKM sing 248 n n C08 O12 NKM sing 249 n n C26 C25 NKM sing 250 n n O06 C05 NKM sing 251 n n C04 C05 NKM sing 252 n n C05 N32 NKM sing 253 n n C24 C25 NKM sing 254 n n C24 C23 NKM sing 255 n n O39 C38 NKM doub 256 n n C22 N21 NKM sing 257 n n C22 C23 NKM sing 258 n n O12 C13 NKM sing 259 n n N21 C19 NKM sing 260 n n N32 C38 NKM sing 261 n n N32 C33 NKM sing 262 n n C13 O18 NKM sing 263 n n C13 C14 NKM sing 264 n n C38 N37 NKM sing 265 n n O18 C17 NKM sing 266 n n C33 C34 NKM doub 267 n n C19 C17 NKM sing 268 n n C19 O20 NKM doub 269 n n C17 C16 NKM doub 270 n n N37 C35 NKM sing 271 n n C14 O31 NKM sing 272 n n C14 C15 NKM sing 273 n n C34 C35 NKM sing 274 n n C35 O36 NKM doub 275 n n C16 C15 NKM sing 276 n n C15 O30 NKM sing 277 n n C13 H131 NKM sing 278 n n C15 H151 NKM sing 279 n n C22 H221 NKM sing 280 n n C24 H242 NKM sing 281 n n C24 H241 NKM sing 282 n n C26 H261 NKM sing 283 n n C26 H262 NKM sing 284 n n C01 H013 NKM sing 285 n n C01 H012 NKM sing 286 n n C01 H011 NKM sing 287 n n C03 H031 NKM sing 288 n n C04 H041 NKM sing 289 n n C05 H051 NKM sing 290 n n C07 H071 NKM sing 291 n n C08 H081 NKM sing 292 n n C14 H141 NKM sing 293 n n C16 H2 NKM sing 294 n n C23 H232 NKM sing 295 n n C23 H231 NKM sing 296 n n C25 H251 NKM sing 297 n n C25 H252 NKM sing 298 n n C33 H331 NKM sing 299 n n C34 H341 NKM sing 300 n n N11 H112 NKM sing 301 n n N11 H111 NKM sing 302 n n N21 H211 NKM sing 303 n n N27 H271 NKM sing 304 n n N37 H371 NKM sing 305 n n O30 H301 NKM sing 306 n n O31 H311 NKM sing 307 n n O40 H401 NKM sing 308 n n # _atom_sites.entry_id 6OYZ _atom_sites.fract_transf_matrix[1][1] 0.010666 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004056 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007808 _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] 0.00826 _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 I _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id NKM _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 NKM _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 C13 NKM . . . I 3 -306.992 -3.059 277.889 1 136.95 ? C13 NKM 401 A 1 HETATM 2 C C15 NKM . . . I 3 -307.172 -3.049 280.426 1 123.04 ? C15 NKM 401 A 1 HETATM 3 C C17 NKM . . . I 3 -307.023 -1.17 278.987 1 137 ? C17 NKM 401 A 1 HETATM 4 C C22 NKM . . . I 3 -306.004 1.903 277.139 1 130.62 ? C22 NKM 401 A 1 HETATM 5 C C24 NKM . . . I 3 -303.819 3.158 276.812 1 130.13 ? C24 NKM 401 A 1 HETATM 6 C C26 NKM . . . I 3 -305.909 4.42 275.966 1 136.92 ? C26 NKM 401 A 1 HETATM 7 C C28 NKM . . . I 3 -306.058 2.092 275.751 1 133.75 ? C28 NKM 401 A 1 HETATM 8 C C01 NKM . . . I 3 -308.374 -0.896 273.725 1 155.16 ? C01 NKM 401 A 1 HETATM 9 C C03 NKM . . . I 3 -309.544 -1.993 275.599 1 133.08 ? C03 NKM 401 A 1 HETATM 10 C C04 NKM . . . I 3 -310.882 -1.933 276.339 1 122.29 ? C04 NKM 401 A 1 HETATM 11 C C05 NKM . . . I 3 -311.348 -3.403 276.407 1 124.23 ? C05 NKM 401 A 1 HETATM 12 C C07 NKM . . . I 3 -309.346 -3.496 275.379 1 133.95 ? C07 NKM 401 A 1 HETATM 13 C C08 NKM . . . I 3 -307.973 -3.946 275.91 1 136.62 ? C08 NKM 401 A 1 HETATM 14 C C09 NKM . . . I 3 -307.711 -5.383 275.429 1 139.79 ? C09 NKM 401 A 1 HETATM 15 C C14 NKM . . . I 3 -306.509 -3.71 279.205 1 132.18 ? C14 NKM 401 A 1 HETATM 16 C C16 NKM . . . I 3 -307.01 -1.671 280.29 1 124.72 ? C16 NKM 401 A 1 HETATM 17 C C19 NKM . . . I 3 -306.51 0.101 278.71 1 140.35 ? C19 NKM 401 A 1 HETATM 18 C C23 NKM . . . I 3 -304.537 2.038 277.594 1 131.49 ? C23 NKM 401 A 1 HETATM 19 C C25 NKM . . . I 3 -304.635 4.468 276.842 1 131.35 ? C25 NKM 401 A 1 HETATM 20 C C33 NKM . . . I 3 -310.86 -4.065 278.555 1 132.11 ? C33 NKM 401 A 1 HETATM 21 C C34 NKM . . . I 3 -311.245 -4.394 279.791 1 126.87 ? C34 NKM 401 A 1 HETATM 22 C C35 NKM . . . I 3 -312.601 -4.374 280.108 1 120.63 ? C35 NKM 401 A 1 HETATM 23 C C38 NKM . . . I 3 -313.074 -3.701 277.934 1 128.64 ? C38 NKM 401 A 1 HETATM 24 N N11 NKM . . . I 3 -306.794 -5.628 274.31 1 151.43 ? N11 NKM 401 A 1 HETATM 25 N N21 NKM . . . I 3 -306.532 0.567 277.451 1 138.68 ? N21 NKM 401 A 1 HETATM 26 N N27 NKM . . . I 3 -305.993 3.316 275.206 1 140.87 ? N27 NKM 401 A 1 HETATM 27 N N32 NKM . . . I 3 -311.764 -3.715 277.627 1 129.76 ? N32 NKM 401 A 1 HETATM 28 N N37 NKM . . . I 3 -313.491 -4.027 279.168 1 121.32 ? N37 NKM 401 A 1 HETATM 29 O O02 NKM . . . I 3 -309.596 -1.311 274.341 1 159.06 ? O02 NKM 401 A 1 HETATM 30 O O06 NKM . . . I 3 -310.386 -4.174 276.101 1 123.68 ? O06 NKM 401 A 1 HETATM 31 O O10 NKM . . . I 3 -308.267 -6.309 275.972 1 134.23 ? O10 NKM 401 A 1 HETATM 32 O O12 NKM . . . I 3 -307.98 -3.933 277.337 1 129.62 ? O12 NKM 401 A 1 HETATM 33 O O18 NKM . . . I 3 -307.532 -1.888 278.042 1 138.29 ? O18 NKM 401 A 1 HETATM 34 O O20 NKM . . . I 3 -306.044 0.767 279.607 1 134.58 ? O20 NKM 401 A 1 HETATM 35 O O29 NKM . . . I 3 -306.134 1.132 275.021 1 128.82 ? O29 NKM 401 A 1 HETATM 36 O O30 NKM . . . I 3 -306.537 -3.511 281.62 1 121.28 ? O30 NKM 401 A 1 HETATM 37 O O31 NKM . . . I 3 -305.089 -3.562 279.303 1 132.25 ? O31 NKM 401 A 1 HETATM 38 O O36 NKM . . . I 3 -312.946 -4.663 281.205 1 120 ? O36 NKM 401 A 1 HETATM 39 O O39 NKM . . . I 3 -313.877 -3.397 277.119 1 130.86 ? O39 NKM 401 A 1 HETATM 40 O O40 NKM . . . I 3 -311.866 -1.11 275.581 1 135.35 ? O40 NKM 401 A 1 HETATM 41 H H131 NKM . . . I 3 -306.246 -2.99 277.273 1 164.34 ? H131 NKM 401 A 1 HETATM 42 H H151 NKM . . . I 3 -308.117 -3.269 280.448 1 147.65 ? H151 NKM 401 A 1 HETATM 43 H H221 NKM . . . I 3 -306.545 2.577 277.579 1 156.75 ? H221 NKM 401 A 1 HETATM 44 H H242 NKM . . . I 3 -302.948 3.316 277.209 1 156.16 ? H242 NKM 401 A 1 HETATM 45 H H241 NKM . . . I 3 -303.702 2.878 275.891 1 156.16 ? H241 NKM 401 A 1 HETATM 46 H H261 NKM . . . I 3 -306.686 4.457 276.545 1 164.3 ? H261 NKM 401 A 1 HETATM 47 H H262 NKM . . . I 3 -305.916 5.197 275.386 1 164.3 ? H262 NKM 401 A 1 HETATM 48 H H013 NKM . . . I 3 -308.572 -0.372 272.933 1 186.19 ? H013 NKM 401 A 1 HETATM 49 H H012 NKM . . . I 3 -307.856 -1.677 273.475 1 186.19 ? H012 NKM 401 A 1 HETATM 50 H H011 NKM . . . I 3 -307.864 -0.357 274.35 1 186.19 ? H011 NKM 401 A 1 HETATM 51 H H031 NKM . . . I 3 -308.833 -1.635 276.152 1 159.7 ? H031 NKM 401 A 1 HETATM 52 H H041 NKM . . . I 3 -310.758 -1.577 277.233 1 146.75 ? H041 NKM 401 A 1 HETATM 53 H H051 NKM . . . I 3 -312.075 -3.535 275.779 1 149.08 ? H051 NKM 401 A 1 HETATM 54 H H071 NKM . . . I 3 -309.416 -3.702 274.434 1 160.74 ? H071 NKM 401 A 1 HETATM 55 H H081 NKM . . . I 3 -307.277 -3.357 275.579 1 163.95 ? H081 NKM 401 A 1 HETATM 56 H H141 NKM . . . I 3 -306.732 -4.654 279.194 1 158.62 ? H141 NKM 401 A 1 HETATM 57 H H232 NKM . . . I 3 -304.515 2.246 278.541 1 157.79 ? H232 NKM 401 A 1 HETATM 58 H H231 NKM . . . I 3 -304.077 1.198 277.442 1 157.79 ? H231 NKM 401 A 1 HETATM 59 H H251 NKM . . . I 3 -304.895 4.651 277.758 1 157.62 ? H251 NKM 401 A 1 HETATM 60 H H252 NKM . . . I 3 -304.071 5.192 276.529 1 157.62 ? H252 NKM 401 A 1 HETATM 61 H H331 NKM . . . I 3 -309.917 -4.077 278.326 1 158.53 ? H331 NKM 401 A 1 HETATM 62 H H341 NKM . . . I 3 -310.588 -4.642 280.46 1 152.24 ? H341 NKM 401 A 1 HETATM 63 H H112 NKM . . . I 3 -306.4 -4.968 273.924 1 181.72 ? H112 NKM 401 A 1 HETATM 64 H H111 NKM . . . I 3 -306.649 -6.432 274.042 1 181.72 ? H111 NKM 401 A 1 HETATM 65 H H211 NKM . . . I 3 -306.871 0.086 276.824 1 166.41 ? H211 NKM 401 A 1 HETATM 66 H H271 NKM . . . I 3 -306.027 3.398 274.351 1 169.05 ? H271 NKM 401 A 1 HETATM 67 H H371 NKM . . . I 3 -314.33 -4.011 279.356 1 145.58 ? H371 NKM 401 A 1 HETATM 68 H H301 NKM . . . I 3 -307.127 -3.69 282.191 1 145.54 ? H301 NKM 401 A 1 HETATM 69 H H311 NKM . . . I 3 -304.881 -3.445 280.108 1 158.7 ? H311 NKM 401 A 1 HETATM 70 H H401 NKM . . . I 3 -311.505 -0.834 274.874 1 162.42 ? H401 NKM 401 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 424 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 70 #