data_4IO8 # _model_server_result.job_id ce3gRh2nEBVAPM8aiJ6u7g _model_server_result.datetime_utc '2024-10-19 03:46:07' _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 4io8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4IO8 # _exptl.entry_id 4IO8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 556.401 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile _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 101.07 _cell.angle_gamma 90 _cell.entry_id 4IO8 _cell.length_a 58.68 _cell.length_b 53.973 _cell.length_c 70.796 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4IO8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C25 H23 Cl2 N7 O4' _chem_comp.formula_weight 556.401 _chem_comp.id 3FD _chem_comp.mon_nstd_flag . _chem_comp.name 4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile _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 C18 C17 3FD doub 1 n y C18 C13 3FD sing 2 n y C17 C16 3FD sing 3 n y C16 CL20 3FD sing 4 n n C16 C15 3FD doub 5 n y C15 C14 3FD sing 6 n y C15 CL21 3FD sing 7 n n C14 C13 3FD doub 8 n y C13 C12 3FD sing 9 n n C12 N11 3FD sing 10 n n N11 C6 3FD sing 11 n n C6 N7 3FD doub 12 n y C6 N5 3FD sing 13 n y N7 C8 3FD sing 14 n y C8 C4 3FD doub 15 n y C8 C9 3FD sing 16 n y C4 N10 3FD sing 17 n n C4 N1 3FD sing 18 n y N1 C2 3FD doub 19 n y C2 N3 3FD sing 20 n y N3 C9 3FD doub 21 n y C9 N5 3FD sing 22 n y N5 C21 3FD sing 23 n n C21 O22 3FD sing 24 n n C21 C24 3FD sing 25 n n O22 C23 3FD sing 26 n n C24 O26 3FD sing 27 n n C24 C25 3FD sing 28 n n C25 O27 3FD sing 29 n n C25 C23 3FD sing 30 n n C23 C28 3FD sing 31 n n C28 O29 3FD sing 32 n n O29 C30 3FD sing 33 n n C30 C31 3FD sing 34 n n C31 C32 3FD doub 35 n y C31 C36 3FD sing 36 n y C32 C33 3FD sing 37 n y C33 C34 3FD doub 38 n y C34 C37 3FD sing 39 n n C34 C35 3FD sing 40 n y C37 N38 3FD trip 41 n n C35 C36 3FD doub 42 n y C18 H18 3FD sing 43 n n C17 H17 3FD sing 44 n n C14 H14 3FD sing 45 n n C12 H12 3FD sing 46 n n C12 H12A 3FD sing 47 n n N11 HN11 3FD sing 48 n n N10 HN10 3FD sing 49 n n N10 HN1A 3FD sing 50 n n C2 H2 3FD sing 51 n n C21 H21 3FD sing 52 n n C24 H24 3FD sing 53 n n O26 HO26 3FD sing 54 n n C25 H25 3FD sing 55 n n O27 HO27 3FD sing 56 n n C23 H23 3FD sing 57 n n C28 H28 3FD sing 58 n n C28 H28A 3FD sing 59 n n C30 H30 3FD sing 60 n n C30 H30A 3FD sing 61 n n C32 H32 3FD sing 62 n n C33 H33 3FD sing 63 n n C35 H35 3FD sing 64 n n C36 H36 3FD sing 65 n n # _atom_sites.entry_id 4IO8 _atom_sites.fract_transf_matrix[1][1] 0.017042 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003334 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018528 _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] 0.014393 _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 3FD A 1 401 1 3FD INH . C 3 HOH A 1 501 1 HOH HOH . C 3 HOH A 2 502 2 HOH HOH . C 3 HOH A 3 503 3 HOH HOH . C 3 HOH A 4 504 4 HOH HOH . C 3 HOH A 5 505 5 HOH HOH . C 3 HOH A 6 506 6 HOH HOH . C 3 HOH A 7 507 7 HOH HOH . C 3 HOH A 8 508 8 HOH HOH . C 3 HOH A 9 509 9 HOH HOH . C 3 HOH A 10 510 10 HOH HOH . C 3 HOH A 11 511 11 HOH HOH . C 3 HOH A 12 512 12 HOH HOH . C 3 HOH A 13 513 13 HOH HOH . C 3 HOH A 14 514 14 HOH HOH . C 3 HOH A 15 515 15 HOH HOH . C 3 HOH A 16 516 16 HOH HOH . C 3 HOH A 17 517 17 HOH HOH . C 3 HOH A 18 518 18 HOH HOH . C 3 HOH A 19 519 19 HOH HOH . C 3 HOH A 20 520 20 HOH HOH . C 3 HOH A 21 521 21 HOH HOH . C 3 HOH A 22 522 22 HOH HOH . C 3 HOH A 23 523 23 HOH HOH . C 3 HOH A 24 524 24 HOH HOH . C 3 HOH A 25 525 25 HOH HOH . C 3 HOH A 26 526 26 HOH HOH . C 3 HOH A 27 527 27 HOH HOH . C 3 HOH A 28 528 28 HOH HOH . C 3 HOH A 29 529 29 HOH HOH . C 3 HOH A 30 530 30 HOH HOH . C 3 HOH A 31 531 31 HOH HOH . C 3 HOH A 32 532 32 HOH HOH . C 3 HOH A 33 533 33 HOH HOH . C 3 HOH A 34 534 34 HOH HOH . C 3 HOH A 35 535 35 HOH HOH . C 3 HOH A 36 536 36 HOH HOH . C 3 HOH A 37 537 37 HOH HOH . C 3 HOH A 38 538 38 HOH HOH . C 3 HOH A 39 539 39 HOH HOH . C 3 HOH A 40 540 40 HOH HOH . C 3 HOH A 41 541 41 HOH HOH . C 3 HOH A 42 542 42 HOH HOH . C 3 HOH A 43 543 43 HOH HOH . C 3 HOH A 44 544 44 HOH HOH . C 3 HOH A 45 545 45 HOH HOH . C 3 HOH A 46 546 46 HOH HOH . C 3 HOH A 47 547 47 HOH HOH . C 3 HOH A 48 548 48 HOH HOH . C 3 HOH A 49 549 49 HOH HOH . C 3 HOH A 50 550 50 HOH HOH . C 3 HOH A 51 551 51 HOH HOH . C 3 HOH A 52 552 52 HOH HOH . C 3 HOH A 53 553 53 HOH HOH . C 3 HOH A 54 554 54 HOH HOH . C 3 HOH A 55 555 55 HOH HOH . C 3 HOH A 56 556 56 HOH HOH . C 3 HOH A 57 557 57 HOH HOH . C 3 HOH A 58 558 58 HOH HOH . C 3 HOH A 59 559 59 HOH HOH . C 3 HOH A 60 560 60 HOH HOH . C 3 HOH A 61 561 61 HOH HOH . C 3 HOH A 62 562 62 HOH HOH . C 3 HOH A 63 563 63 HOH HOH . C 3 HOH A 64 564 64 HOH HOH . C 3 HOH A 65 565 65 HOH HOH . C 3 HOH A 66 566 66 HOH HOH . C 3 HOH A 67 567 67 HOH HOH . C 3 HOH A 68 568 68 HOH HOH . C 3 HOH A 69 569 69 HOH HOH . C 3 HOH A 70 570 70 HOH HOH . C 3 HOH A 71 571 71 HOH HOH . C 3 HOH A 72 572 72 HOH HOH . C 3 HOH A 73 573 73 HOH HOH . C 3 HOH A 74 574 74 HOH HOH . C 3 HOH A 75 575 75 HOH HOH . C 3 HOH A 76 576 76 HOH HOH . C 3 HOH A 77 577 77 HOH HOH . C 3 HOH A 78 578 78 HOH HOH . C 3 HOH A 79 579 79 HOH HOH . C 3 HOH A 80 580 80 HOH HOH . C 3 HOH A 81 581 81 HOH HOH . C 3 HOH A 82 582 82 HOH HOH . C 3 HOH A 83 583 83 HOH HOH . C 3 HOH A 84 584 84 HOH HOH . C 3 HOH A 85 585 85 HOH HOH . C 3 HOH A 86 586 86 HOH HOH . C 3 HOH A 87 587 87 HOH HOH . C 3 HOH A 88 588 88 HOH HOH . C 3 HOH A 89 589 89 HOH HOH . C 3 HOH A 90 590 90 HOH HOH . C 3 HOH A 91 591 91 HOH HOH . C 3 HOH A 92 592 92 HOH HOH . C 3 HOH A 93 593 93 HOH HOH . C 3 HOH A 94 594 94 HOH HOH . C 3 HOH A 95 595 95 HOH HOH . C 3 HOH A 96 596 96 HOH HOH . C 3 HOH A 97 597 97 HOH HOH . C 3 HOH A 98 598 98 HOH HOH . C 3 HOH A 99 599 99 HOH HOH . C 3 HOH A 100 600 100 HOH HOH . C 3 HOH A 101 601 101 HOH HOH . C 3 HOH A 102 602 102 HOH HOH . C 3 HOH A 103 603 103 HOH HOH . C 3 HOH A 104 604 104 HOH HOH . C 3 HOH A 105 605 105 HOH HOH . C 3 HOH A 106 606 106 HOH HOH . C 3 HOH A 107 607 107 HOH HOH . C 3 HOH A 108 608 108 HOH HOH . C 3 HOH A 109 609 109 HOH HOH . C 3 HOH A 110 610 110 HOH HOH . C 3 HOH A 111 611 111 HOH HOH . C 3 HOH A 112 612 112 HOH HOH . C 3 HOH A 113 613 113 HOH HOH . C 3 HOH A 114 614 114 HOH HOH . C 3 HOH A 115 615 115 HOH HOH . C 3 HOH A 116 616 116 HOH HOH . C 3 HOH A 117 617 117 HOH HOH . C 3 HOH A 118 618 118 HOH HOH . C 3 HOH A 119 619 119 HOH HOH . C 3 HOH A 120 620 120 HOH HOH . C 3 HOH A 121 621 121 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 C18 3FD . . . B 2 0.71 7.501 11.463 1 31.9 ? C18 3FD 401 A 1 HETATM 2 C C17 3FD . . . B 2 -0.158 7.268 10.394 1 35.99 ? C17 3FD 401 A 1 HETATM 3 C C16 3FD . . . B 2 -0.709 5.991 10.239 1 40.84 ? C16 3FD 401 A 1 HETATM 4 CL CL20 3FD . . . B 2 -1.775 5.623 8.916 1 44.64 ? CL20 3FD 401 A 1 HETATM 5 C C15 3FD . . . B 2 -0.418 4.99 11.16 1 39.94 ? C15 3FD 401 A 1 HETATM 6 C C14 3FD . . . B 2 0.431 5.226 12.212 1 34.31 ? C14 3FD 401 A 1 HETATM 7 C C13 3FD . . . B 2 0.996 6.479 12.363 1 31.04 ? C13 3FD 401 A 1 HETATM 8 C C12 3FD . . . B 2 1.901 6.699 13.536 1 30.31 ? C12 3FD 401 A 1 HETATM 9 N N11 3FD . . . B 2 1.744 5.612 14.516 1 29.48 ? N11 3FD 401 A 1 HETATM 10 C C6 3FD . . . B 2 0.963 5.778 15.644 1 27.15 ? C6 3FD 401 A 1 HETATM 11 N N7 3FD . . . B 2 0.172 6.804 15.816 1 26.76 ? N7 3FD 401 A 1 HETATM 12 C C8 3FD . . . B 2 -0.424 6.712 17.025 1 27.31 ? C8 3FD 401 A 1 HETATM 13 C C4 3FD . . . B 2 -1.362 7.509 17.709 1 27.85 ? C4 3FD 401 A 1 HETATM 14 N N10 3FD . . . B 2 -1.873 8.653 17.094 1 26.04 ? N10 3FD 401 A 1 HETATM 15 N N1 3FD . . . B 2 -1.761 7.108 18.927 1 25.91 ? N1 3FD 401 A 1 HETATM 16 C C2 3FD . . . B 2 -1.264 6.021 19.497 1 23.63 ? C2 3FD 401 A 1 HETATM 17 N N3 3FD . . . B 2 -0.4 5.237 18.868 1 23.13 ? N3 3FD 401 A 1 HETATM 18 C C9 3FD . . . B 2 0.043 5.538 17.648 1 24.59 ? C9 3FD 401 A 1 HETATM 19 N N5 3FD . . . B 2 0.91 4.95 16.754 1 25.74 ? N5 3FD 401 A 1 HETATM 20 C C21 3FD . . . B 2 1.594 3.66 16.986 1 27.59 ? C21 3FD 401 A 1 HETATM 21 O O22 3FD . . . B 2 3.02 3.682 16.706 1 28.13 ? O22 3FD 401 A 1 HETATM 22 C C24 3FD . . . B 2 1.081 2.55 16.025 1 27.49 ? C24 3FD 401 A 1 HETATM 23 O O26 3FD . . . B 2 -0.216 2.054 16.375 1 31.17 ? O26 3FD 401 A 1 HETATM 24 C C25 3FD . . . B 2 2.191 1.487 16.212 1 22.15 ? C25 3FD 401 A 1 HETATM 25 O O27 3FD . . . B 2 1.908 0.685 17.362 1 18.67 ? O27 3FD 401 A 1 HETATM 26 C C23 3FD . . . B 2 3.452 2.339 16.434 1 23.79 ? C23 3FD 401 A 1 HETATM 27 C C28 3FD . . . B 2 4.364 2.331 15.203 1 24.37 ? C28 3FD 401 A 1 HETATM 28 O O29 3FD . . . B 2 3.753 2.938 14.054 1 25.11 ? O29 3FD 401 A 1 HETATM 29 C C30 3FD . . . B 2 4.673 3.352 13.027 1 22.46 ? C30 3FD 401 A 1 HETATM 30 C C31 3FD . . . B 2 3.928 3.746 11.775 1 19.67 ? C31 3FD 401 A 1 HETATM 31 C C32 3FD . . . B 2 4.163 4.985 11.181 1 19.28 ? C32 3FD 401 A 1 HETATM 32 C C33 3FD . . . B 2 3.456 5.358 10.036 1 18.83 ? C33 3FD 401 A 1 HETATM 33 C C34 3FD . . . B 2 2.536 4.454 9.454 1 20.87 ? C34 3FD 401 A 1 HETATM 34 C C37 3FD . . . B 2 1.802 4.821 8.266 1 25.39 ? C37 3FD 401 A 1 HETATM 35 N N38 3FD . . . B 2 1.228 5.122 7.325 1 24.53 ? N38 3FD 401 A 1 HETATM 36 C C35 3FD . . . B 2 2.312 3.201 10.043 1 17.15 ? C35 3FD 401 A 1 HETATM 37 C C36 3FD . . . B 2 2.997 2.87 11.21 1 19.11 ? C36 3FD 401 A 1 HETATM 38 CL CL21 3FD . . . B 2 -1.062 3.401 11.008 1 49.6 ? CL21 3FD 401 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 38 #