data_8CRL # _model_server_result.job_id 4XXDEc-pSCRiJuugNi3WQA _model_server_result.datetime_utc '2025-06-29 06:08:53' _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 8crl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8CRL # _exptl.entry_id 8CRL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 437.583 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ~{N}-[3-[2-(6-aminopurin-9-yl)ethanoylamino]propyl]-5-[(3~{R})-1,2-dithiolan-3-yl]pentanamide _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 98.06 _cell.angle_gamma 90 _cell.entry_id 8CRL _cell.length_a 59.32 _cell.length_b 74.27 _cell.length_c 92.73 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CRL _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,H,I 1 1 B,J 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 2 _struct_asym.id C _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 OD2 ASP 9 A ASP 5 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc2 A OD1 ASP 157 A ASP 153 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? metalc ? metalc3 A OD1 ASP 244 A ASP 240 1_555 F NA NA . A NA 404 2_645 ? ? ? ? ? ? ? ? ? ? ? ? 3.023 ? metalc ? metalc4 A O TYR 335 A TYR 331 1_555 E CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc5 A OXT TYR 335 A TYR 331 1_555 E CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc6 E CA CA . A CA 403 2_555 B OXT TYR 335 B TYR 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? # _chem_comp.formula 'C18 H27 N7 O2 S2' _chem_comp.formula_weight 437.583 _chem_comp.id VK9 _chem_comp.mon_nstd_flag . _chem_comp.name ~{N}-[3-[2-(6-aminopurin-9-yl)ethanoylamino]propyl]-5-[(3~{R})-1,2-dithiolan-3-yl]pentanamide _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 C19 C17 VK9 sing 372 n n C19 N20 VK9 sing 373 n n N16 C17 VK9 sing 374 n n N16 C15 VK9 sing 375 n n C17 O18 VK9 doub 376 n n C15 C14 VK9 sing 377 n n C21 N20 VK9 sing 378 n y C21 N22 VK9 doub 379 n y N20 C24 VK9 sing 380 n y C14 C13 VK9 sing 381 n n N22 C23 VK9 sing 382 n y C13 N2 VK9 sing 383 n n C24 C23 VK9 doub 384 n y C24 N28 VK9 sing 385 n y C23 C25 VK9 sing 386 n y N28 C27 VK9 doub 387 n y N2 C1 VK9 sing 388 n n C25 N29 VK9 sing 389 n n C25 N26 VK9 doub 390 n y C27 N26 VK9 sing 391 n y C1 O2 VK9 doub 392 n n C1 C2 VK9 sing 393 n n C2 C3 VK9 sing 394 n n C3 C4 VK9 sing 395 n n C8 C7 VK9 sing 396 n n C8 S8 VK9 sing 397 n n C7 C6 VK9 sing 398 n n C4 C5 VK9 sing 399 n n C6 C5 VK9 sing 400 n n C6 S6 VK9 sing 401 n n S8 S6 VK9 sing 402 n n C4 H1 VK9 sing 403 n n C4 H2 VK9 sing 404 n n C5 H3 VK9 sing 405 n n C5 H4 VK9 sing 406 n n C6 H5 VK9 sing 407 n n C7 H6 VK9 sing 408 n n C7 H7 VK9 sing 409 n n C8 H8 VK9 sing 410 n n C8 H9 VK9 sing 411 n n C13 H10 VK9 sing 412 n n C13 H11 VK9 sing 413 n n C15 H12 VK9 sing 414 n n C15 H13 VK9 sing 415 n n C21 H14 VK9 sing 416 n n C3 H15 VK9 sing 417 n n C3 H16 VK9 sing 418 n n C2 H17 VK9 sing 419 n n C2 H18 VK9 sing 420 n n N2 H19 VK9 sing 421 n n C14 H20 VK9 sing 422 n n C14 H21 VK9 sing 423 n n N16 H22 VK9 sing 424 n n C19 H23 VK9 sing 425 n n C19 H24 VK9 sing 426 n n C27 H25 VK9 sing 427 n n N29 H26 VK9 sing 428 n n N29 H27 VK9 sing 429 n n # _atom_sites.entry_id 8CRL _atom_sites.fract_transf_matrix[1][1] 0.016858 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002387 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013464 _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] 0.010892 _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 VK9 A 1 401 991 VK9 LIG . D 3 CA A 1 402 1 CA CA . E 3 CA A 1 403 2 CA CA . F 4 NA A 1 404 3 NA NA . G 4 NA A 1 405 4 NA NA . H 5 EDO A 1 406 5 EDO EDO . I 6 HOH A 1 501 24 HOH HOH . I 6 HOH A 2 502 18 HOH HOH . I 6 HOH A 3 503 26 HOH HOH . I 6 HOH A 4 504 11 HOH HOH . I 6 HOH A 5 505 30 HOH HOH . I 6 HOH A 6 506 10 HOH HOH . I 6 HOH A 7 507 28 HOH HOH . I 6 HOH A 8 508 7 HOH HOH . I 6 HOH A 9 509 29 HOH HOH . I 6 HOH A 10 510 9 HOH HOH . I 6 HOH A 11 511 20 HOH HOH . I 6 HOH A 12 512 15 HOH HOH . I 6 HOH A 13 513 27 HOH HOH . J 6 HOH B 1 401 23 HOH HOH . J 6 HOH B 2 402 17 HOH HOH . J 6 HOH B 3 403 12 HOH HOH . J 6 HOH B 4 404 14 HOH HOH . J 6 HOH B 5 405 22 HOH HOH . J 6 HOH B 6 406 8 HOH HOH . J 6 HOH B 7 407 19 HOH HOH . J 6 HOH B 8 408 25 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 VK9 . . . C 2 16.651 -13.154 1.472 1 48.8 ? C4 VK9 401 A 1 HETATM 2 C C5 VK9 . . . C 2 17.242 -12.41 2.687 1 49.52 ? C5 VK9 401 A 1 HETATM 3 C C6 VK9 . . . C 2 18.601 -11.762 2.359 1 51.71 ? C6 VK9 401 A 1 HETATM 4 C C7 VK9 . . . C 2 19.396 -12.625 1.364 1 50.57 ? C7 VK9 401 A 1 HETATM 5 C C8 VK9 . . . C 2 20.59 -11.81 1.102 1 51.03 ? C8 VK9 401 A 1 HETATM 6 C C13 VK9 . . . C 2 14.875 -11.718 -3.78 1 50.29 ? C13 VK9 401 A 1 HETATM 7 C C15 VK9 . . . C 2 13.044 -11.544 -5.452 1 50.84 ? C15 VK9 401 A 1 HETATM 8 C C17 VK9 . . . C 2 13.477 -9.119 -5.511 1 53.77 ? C17 VK9 401 A 1 HETATM 9 C C21 VK9 . . . C 2 16.542 -7.173 -5.391 1 49.93 ? C21 VK9 401 A 1 HETATM 10 C C24 VK9 . . . C 2 15.19 -7.34 -3.758 1 52.74 ? C24 VK9 401 A 1 HETATM 11 S S8 VK9 . . . C 2 21.42 -11.835 2.667 1 55.01 ? S8 VK9 401 A 1 HETATM 12 S S6 VK9 . . . C 2 19.707 -11.636 3.76 1 59.94 ? S6 VK9 401 A 1 HETATM 13 C C3 VK9 . . . C 2 15.738 -12.259 0.629 1 47.3 ? C3 VK9 401 A 1 HETATM 14 C C2 VK9 . . . C 2 14.836 -13.145 -0.247 1 48.31 ? C2 VK9 401 A 1 HETATM 15 C C1 VK9 . . . C 2 14.396 -12.37 -1.49 1 50.22 ? C1 VK9 401 A 1 HETATM 16 O O2 VK9 . . . C 2 13.354 -11.725 -1.487 1 49.25 ? O2 VK9 401 A 1 HETATM 17 N N2 VK9 . . . C 2 15.181 -12.469 -2.567 1 51.27 ? N2 VK9 401 A 1 HETATM 18 C C14 VK9 . . . C 2 13.918 -12.497 -4.665 1 50.17 ? C14 VK9 401 A 1 HETATM 19 N N16 VK9 . . . C 2 13.823 -10.366 -5.876 1 53.49 ? N16 VK9 401 A 1 HETATM 20 O O18 VK9 . . . C 2 12.503 -8.859 -4.803 1 55.26 ? O18 VK9 401 A 1 HETATM 21 C C19 VK9 . . . C 2 14.369 -7.994 -6.055 1 54.99 ? C19 VK9 401 A 1 HETATM 22 N N20 VK9 . . . C 2 15.321 -7.52 -5.056 1 52.5 ? N20 VK9 401 A 1 HETATM 23 N N22 VK9 . . . C 2 17.162 -6.782 -4.299 1 48.67 ? N22 VK9 401 A 1 HETATM 24 C C23 VK9 . . . C 2 16.338 -6.885 -3.29 1 50.46 ? C23 VK9 401 A 1 HETATM 25 N N28 VK9 . . . C 2 14.164 -7.54 -2.942 1 53.49 ? N28 VK9 401 A 1 HETATM 26 C C27 VK9 . . . C 2 14.305 -7.271 -1.595 1 51.34 ? C27 VK9 401 A 1 HETATM 27 N N26 VK9 . . . C 2 15.505 -6.799 -1.134 1 50.75 ? N26 VK9 401 A 1 HETATM 28 C C25 VK9 . . . C 2 16.486 -6.624 -2.005 1 50.91 ? C25 VK9 401 A 1 HETATM 29 N N29 VK9 . . . C 2 17.648 -6.173 -1.607 1 50.68 ? N29 VK9 401 A 1 # _model_server_stats.io_time_ms 132 _model_server_stats.parse_time_ms 46 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 530 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 29 #