data_8BOP
#
_model_server_result.job_id            5a9misoGgdzikWasiWcnSQ 
_model_server_result.datetime_utc      '2025-07-14 04:06:12' 
_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          8bop 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":901}' 
#
_entry.id    8BOP 
#
_exptl.entry_id    8BOP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              1071.917 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[7,8-dimethyl-2,4-bis(oxidanylidene)-5-[3-[4-(3-phenylphenyl)phenyl]propanoyl]-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate' 
_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            8BOP 
_cell.length_a            119.817 
_cell.length_b            177.601 
_cell.length_c            234.886 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8BOP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C 
_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                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C48 H51 N9 O16 P2' 
_chem_comp.formula_weight    1071.917 
_chem_comp.id                SV9 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[7,8-dimethyl-2,4-bis(oxidanylidene)-5-[3-[4-(3-phenylphenyl)phenyl]propanoyl]-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate' 
_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
C8 C7 SV9 sing 288 n n 
O1 C9 SV9 doub 289 n n 
C7 C6 SV9 doub 290 n y 
C7 C2 SV9 sing 291 n y 
C6 C5 SV9 sing 292 n y 
C9 C10 SV9 sing 293 n n 
C9 N1 SV9 sing 294 n n 
C10 C11 SV9 sing 295 n n 
C1 C2 SV9 sing 296 n n 
C2 C3 SV9 doub 297 n y 
C5 N1 SV9 sing 298 n n 
C5 C4 SV9 doub 299 n y 
N1 C30 SV9 sing 300 n n 
O3 C33 SV9 doub 301 n n 
C11 C12 SV9 sing 302 n n 
C3 C4 SV9 sing 303 n y 
C4 N4 SV9 sing 304 n n 
C30 C33 SV9 sing 305 n n 
C30 C31 SV9 doub 306 n n 
C12 C13 SV9 doub 307 n y 
C12 C29 SV9 sing 308 n y 
C33 N3 SV9 sing 309 n n 
C13 C14 SV9 sing 310 n y 
C29 C28 SV9 doub 311 n y 
N4 C31 SV9 sing 312 n n 
N4 C34 SV9 sing 313 n n 
C31 N2 SV9 sing 314 n n 
C14 C15 SV9 doub 315 n y 
C28 C15 SV9 sing 316 n y 
N3 C32 SV9 sing 317 n n 
C15 C16 SV9 sing 318 n n 
O4 C35 SV9 sing 319 n n 
C23 C22 SV9 doub 320 n y 
C23 C24 SV9 sing 321 n y 
C22 C21 SV9 sing 322 n y 
C34 C35 SV9 sing 323 n n 
C27 C16 SV9 doub 324 n y 
C27 C20 SV9 sing 325 n y 
C24 C25 SV9 doub 326 n y 
N2 C32 SV9 sing 327 n n 
C16 C17 SV9 sing 328 n y 
C32 O2 SV9 doub 329 n n 
C21 C20 SV9 sing 330 n n 
C21 C26 SV9 doub 331 n y 
C35 C36 SV9 sing 332 n n 
C20 C19 SV9 doub 333 n y 
C25 C26 SV9 sing 334 n y 
C17 C18 SV9 doub 335 n y 
O15 C47 SV9 sing 336 n n 
C36 O5 SV9 sing 337 n n 
C36 C37 SV9 sing 338 n n 
C19 C18 SV9 sing 339 n y 
C47 C48 SV9 sing 340 n n 
C47 C41 SV9 sing 341 n n 
O12 P2 SV9 doub 342 n n 
O6 C37 SV9 sing 343 n n 
C48 O16 SV9 sing 344 n n 
C48 C40 SV9 sing 345 n n 
C42 N6 SV9 doub 346 n y 
C42 N5 SV9 sing 347 n y 
O11 P2 SV9 sing 348 n n 
N6 C43 SV9 sing 349 n y 
C37 C38 SV9 sing 350 n n 
P2 O13 SV9 sing 351 n n 
P2 O10 SV9 sing 352 n n 
N5 C41 SV9 sing 353 n n 
N5 C46 SV9 sing 354 n y 
C41 O14 SV9 sing 355 n n 
C38 O7 SV9 sing 356 n n 
C43 C46 SV9 doub 357 n y 
C43 C44 SV9 sing 358 n y 
O13 C39 SV9 sing 359 n n 
N7 C44 SV9 sing 360 n n 
C46 N9 SV9 sing 361 n y 
C40 O14 SV9 sing 362 n n 
C40 C39 SV9 sing 363 n n 
C44 N8 SV9 doub 364 n y 
O7 P1 SV9 sing 365 n n 
O10 P1 SV9 sing 366 n n 
N9 C45 SV9 doub 367 n y 
N8 C45 SV9 sing 368 n y 
P1 O9 SV9 doub 369 n n 
P1 O8 SV9 sing 370 n n 
C14 H1 SV9 sing 371 n n 
C6 H2 SV9 sing 372 n n 
C11 H3 SV9 sing 373 n n 
C11 H4 SV9 sing 374 n n 
C8 H5 SV9 sing 375 n n 
C8 H6 SV9 sing 376 n n 
C8 H7 SV9 sing 377 n n 
C10 H8 SV9 sing 378 n n 
C10 H9 SV9 sing 379 n n 
C13 H10 SV9 sing 380 n n 
N2 H11 SV9 sing 381 n n 
C3 H12 SV9 sing 382 n n 
N3 H13 SV9 sing 383 n n 
C1 H14 SV9 sing 384 n n 
C1 H15 SV9 sing 385 n n 
C1 H16 SV9 sing 386 n n 
C17 H17 SV9 sing 387 n n 
C18 H18 SV9 sing 388 n n 
C19 H19 SV9 sing 389 n n 
C22 H20 SV9 sing 390 n n 
C23 H21 SV9 sing 391 n n 
C24 H22 SV9 sing 392 n n 
C25 H23 SV9 sing 393 n n 
C26 H24 SV9 sing 394 n n 
C27 H25 SV9 sing 395 n n 
C28 H26 SV9 sing 396 n n 
C29 H27 SV9 sing 397 n n 
C34 H28 SV9 sing 398 n n 
C34 H29 SV9 sing 399 n n 
C35 H30 SV9 sing 400 n n 
C36 H31 SV9 sing 401 n n 
C37 H32 SV9 sing 402 n n 
C38 H33 SV9 sing 403 n n 
C38 H34 SV9 sing 404 n n 
C39 H35 SV9 sing 405 n n 
C39 H36 SV9 sing 406 n n 
C40 H37 SV9 sing 407 n n 
C41 H38 SV9 sing 408 n n 
C42 H39 SV9 sing 409 n n 
C45 H40 SV9 sing 410 n n 
C47 H41 SV9 sing 411 n n 
C48 H42 SV9 sing 412 n n 
N7 H43 SV9 sing 413 n n 
N7 H44 SV9 sing 414 n n 
O11 H45 SV9 sing 415 n n 
O15 H46 SV9 sing 416 n n 
O16 H47 SV9 sing 417 n n 
O4 H48 SV9 sing 418 n n 
O5 H49 SV9 sing 419 n n 
O6 H50 SV9 sing 420 n n 
O8 H51 SV9 sing 421 n n 
#
_atom_sites.entry_id                     8BOP 
_atom_sites.fract_transf_matrix[1][1]    0.008346 
_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]    0.005631 
_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]    0.004257 
_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          C 
_pdbx_nonpoly_scheme.entity_id        3 
_pdbx_nonpoly_scheme.mon_id           SV9 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      901 
_pdbx_nonpoly_scheme.auth_seq_num     901 
_pdbx_nonpoly_scheme.pdb_mon_id       SV9 
_pdbx_nonpoly_scheme.auth_mon_id      DRG 
_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 C4 SV9 . . . C 3 -7.085 59.164 83.429 1 80.79 ? C4 SV9 901 A 1 
HETATM 2 C C14 SV9 . . . C 3 -6.36 52.315 84.961 1 105.8 ? C14 SV9 901 A 1 
HETATM 3 C C5 SV9 . . . C 3 -7.62 58.536 82.339 1 77.97 ? C5 SV9 901 A 1 
HETATM 4 C C6 SV9 . . . C 3 -7.48 59.074 81.077 1 78.69 ? C6 SV9 901 A 1 
HETATM 5 C C11 SV9 . . . C 3 -6.275 55.61 83.07 1 85.13 ? C11 SV9 901 A 1 
HETATM 6 C C7 SV9 . . . C 3 -6.871 60.273 80.904 1 81.64 ? C7 SV9 901 A 1 
HETATM 7 C C8 SV9 . . . C 3 -6.752 60.851 79.527 1 74.07 ? C8 SV9 901 A 1 
HETATM 8 C C9 SV9 . . . C 3 -8.041 56.359 81.518 1 81.56 ? C9 SV9 901 A 1 
HETATM 9 C C10 SV9 . . . C 3 -6.936 55.369 81.74 1 81.69 ? C10 SV9 901 A 1 
HETATM 10 C C12 SV9 . . . C 3 -5.861 54.388 83.848 1 90.31 ? C12 SV9 901 A 1 
HETATM 11 C C13 SV9 . . . C 3 -6.764 53.418 84.229 1 95.13 ? C13 SV9 901 A 1 
HETATM 12 N N1 SV9 . . . C 3 -8.192 57.336 82.477 1 83.45 ? N1 SV9 901 A 1 
HETATM 13 N N2 SV9 . . . C 3 -8.522 57.169 86.105 1 75.2 ? N2 SV9 901 A 1 
HETATM 14 C C3 SV9 . . . C 3 -6.485 60.403 83.28 1 79.72 ? C3 SV9 901 A 1 
HETATM 15 N N3 SV9 . . . C 3 -9.945 55.618 85.14 1 85.33 ? N3 SV9 901 A 1 
HETATM 16 C C1 SV9 . . . C 3 -5.67 62.285 81.872 1 64.28 ? C1 SV9 901 A 1 
HETATM 17 C C15 SV9 . . . C 3 -5.039 52.157 85.369 1 106.74 ? C15 SV9 901 A 1 
HETATM 18 C C16 SV9 . . . C 3 -4.584 50.961 86.124 1 108.85 ? C16 SV9 901 A 1 
HETATM 19 C C17 SV9 . . . C 3 -3.465 51.002 86.946 1 109.32 ? C17 SV9 901 A 1 
HETATM 20 C C18 SV9 . . . C 3 -3.038 49.875 87.618 1 106.99 ? C18 SV9 901 A 1 
HETATM 21 C C19 SV9 . . . C 3 -3.708 48.679 87.457 1 107.88 ? C19 SV9 901 A 1 
HETATM 22 C C2 SV9 . . . C 3 -6.36 60.965 82.042 1 79.56 ? C2 SV9 901 A 1 
HETATM 23 C C20 SV9 . . . C 3 -4.822 48.59 86.632 1 114.48 ? C20 SV9 901 A 1 
HETATM 24 C C21 SV9 . . . C 3 -5.541 47.306 86.42 1 116.95 ? C21 SV9 901 A 1 
HETATM 25 C C22 SV9 . . . C 3 -4.953 46.269 85.705 1 115.23 ? C22 SV9 901 A 1 
HETATM 26 C C23 SV9 . . . C 3 -5.628 45.08 85.488 1 115.39 ? C23 SV9 901 A 1 
HETATM 27 C C24 SV9 . . . C 3 -6.906 44.912 85.967 1 113.6 ? C24 SV9 901 A 1 
HETATM 28 C C25 SV9 . . . C 3 -7.514 45.925 86.662 1 108.98 ? C25 SV9 901 A 1 
HETATM 29 C C26 SV9 . . . C 3 -6.839 47.115 86.882 1 116.24 ? C26 SV9 901 A 1 
HETATM 30 C C27 SV9 . . . C 3 -5.23 49.74 85.966 1 110.9 ? C27 SV9 901 A 1 
HETATM 31 C C28 SV9 . . . C 3 -4.139 53.141 84.996 1 96.44 ? C28 SV9 901 A 1 
HETATM 32 C C29 SV9 . . . C 3 -4.553 54.233 84.259 1 94.9 ? C29 SV9 901 A 1 
HETATM 33 C C30 SV9 . . . C 3 -8.684 56.975 83.753 1 81.72 ? C30 SV9 901 A 1 
HETATM 34 C C31 SV9 . . . C 3 -8.119 57.556 84.872 1 76.08 ? C31 SV9 901 A 1 
HETATM 35 C C32 SV9 . . . C 3 -9.449 56.187 86.266 1 76.39 ? C32 SV9 901 A 1 
HETATM 36 C C33 SV9 . . . C 3 -9.572 55.967 83.867 1 83.94 ? C33 SV9 901 A 1 
HETATM 37 C C34 SV9 . . . C 3 -6.623 59.293 85.845 1 79.85 ? C34 SV9 901 A 1 
HETATM 38 C C35 SV9 . . . C 3 -7.536 60.316 86.463 1 69.63 ? C35 SV9 901 A 1 
HETATM 39 C C36 SV9 . . . C 3 -6.763 61.338 87.285 1 72.67 ? C36 SV9 901 A 1 
HETATM 40 C C37 SV9 . . . C 3 -7.554 62.057 88.369 1 70.25 ? C37 SV9 901 A 1 
HETATM 41 C C38 SV9 . . . C 3 -6.741 63.175 88.966 1 68.56 ? C38 SV9 901 A 1 
HETATM 42 C C39 SV9 . . . C 3 -6.43 69.095 89.484 1 69.63 ? C39 SV9 901 A 1 
HETATM 43 C C40 SV9 . . . C 3 -6.937 70.503 89.413 1 63.58 ? C40 SV9 901 A 1 
HETATM 44 C C41 SV9 . . . C 3 -6.217 72.558 88.918 1 68.38 ? C41 SV9 901 A 1 
HETATM 45 C C42 SV9 . . . C 3 -3.872 73.197 88.242 1 64.75 ? C42 SV9 901 A 1 
HETATM 46 C C43 SV9 . . . C 3 -3.741 75.12 89.084 1 60.72 ? C43 SV9 901 A 1 
HETATM 47 C C44 SV9 . . . C 3 -3.412 76.393 89.543 1 60.52 ? C44 SV9 901 A 1 
HETATM 48 C C45 SV9 . . . C 3 -5.522 76.487 90.453 1 61.2 ? C45 SV9 901 A 1 
HETATM 49 C C46 SV9 . . . C 3 -4.997 74.666 89.375 1 58.94 ? C46 SV9 901 A 1 
HETATM 50 C C47 SV9 . . . C 3 -6.84 72.112 87.624 1 67.37 ? C47 SV9 901 A 1 
HETATM 51 C C48 SV9 . . . C 3 -7.651 70.922 88.129 1 66.03 ? C48 SV9 901 A 1 
HETATM 52 N N4 SV9 . . . C 3 -7.248 58.604 84.698 1 81.8 ? N4 SV9 901 A 1 
HETATM 53 N N5 SV9 . . . C 3 -5.081 73.437 88.814 1 65.43 ? N5 SV9 901 A 1 
HETATM 54 N N6 SV9 . . . C 3 -3.04 74.187 88.36 1 60.98 ? N6 SV9 901 A 1 
HETATM 55 N N7 SV9 . . . C 3 -2.248 76.97 89.327 1 49.99 ? N7 SV9 901 A 1 
HETATM 56 N N8 SV9 . . . C 3 -4.344 77.062 90.236 1 56.52 ? N8 SV9 901 A 1 
HETATM 57 N N9 SV9 . . . C 3 -5.948 75.306 90.056 1 67.55 ? N9 SV9 901 A 1 
HETATM 58 O O1 SV9 . . . C 3 -8.837 56.244 80.62 1 85.44 ? O1 SV9 901 A 1 
HETATM 59 O O10 SV9 . . . C 3 -6.373 66.229 89.952 1 58.44 ? O10 SV9 901 A 1 
HETATM 60 O O11 SV9 . . . C 3 -8.238 66.087 88.349 1 66.17 ? O11 SV9 901 A 1 
HETATM 61 O O12 SV9 . . . C 3 -5.945 67.116 87.748 1 57.56 -1 O12 SV9 901 A 1 
HETATM 62 O O13 SV9 . . . C 3 -7.505 68.199 89.283 1 76.75 ? O13 SV9 901 A 1 
HETATM 63 O O14 SV9 . . . C 3 -5.796 71.363 89.477 1 69.57 ? O14 SV9 901 A 1 
HETATM 64 O O15 SV9 . . . C 3 -7.64 73.206 87.276 1 68.85 ? O15 SV9 901 A 1 
HETATM 65 O O16 SV9 . . . C 3 -8.97 71.294 88.469 1 64.74 ? O16 SV9 901 A 1 
HETATM 66 O O2 SV9 . . . C 3 -9.817 55.835 87.36 1 68.58 ? O2 SV9 901 A 1 
HETATM 67 O O3 SV9 . . . C 3 -10.09 55.398 82.921 1 84.51 ? O3 SV9 901 A 1 
HETATM 68 O O4 SV9 . . . C 3 -8.127 61.004 85.436 1 68.79 ? O4 SV9 901 A 1 
HETATM 69 O O5 SV9 . . . C 3 -5.729 60.684 87.911 1 71 ? O5 SV9 901 A 1 
HETATM 70 O O6 SV9 . . . C 3 -8.77 62.558 87.831 1 71.18 ? O6 SV9 901 A 1 
HETATM 71 O O7 SV9 . . . C 3 -7.477 64.115 89.771 1 71.08 ? O7 SV9 901 A 1 
HETATM 72 O O8 SV9 . . . C 3 -7.516 65.23 91.938 1 65.45 ? O8 SV9 901 A 1 
HETATM 73 O O9 SV9 . . . C 3 -5.368 64.306 91.01 1 63.39 -1 O9 SV9 901 A 1 
HETATM 74 P P1 SV9 . . . C 3 -6.651 64.952 90.793 1 64.04 ? P1 SV9 901 A 1 
HETATM 75 P P2 SV9 . . . C 3 -7.032 66.848 88.685 1 64.78 ? P2 SV9 901 A 1 
#
_model_server_stats.io_time_ms              55 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           224 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           75 
#