data_8VBY # _model_server_result.job_id v6kf89NfskKEFYuDd3aqaw _model_server_result.datetime_utc '2024-11-14 17:47:28' _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 8vby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":702}' # _entry.id 8VBY # _exptl.entry_id 8VBY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 459.906 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'methyl (1S,2R,3S,4R,5R)-4-{2-[(5-chlorothiophen-2-yl)ethynyl]-6-(methylamino)-9H-purin-9-yl}-2,3-dihydroxybicyclo[3.1.0]hexane-1-carboxylate' _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 8VBY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VBY _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _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,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA _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 # 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 130 A CYS 180 1_555 A SG CYS 139 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 138 A ASN 188 1_555 D C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? metalc ? metalc1 A O VAL 28 A VAL 78 1_555 O NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc2 A OD1 ASP 141 A ASP 191 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc3 A OD2 ASP 141 A ASP 191 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc4 A NE2 HIS 143 A HIS 193 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc5 A NE2 HIS 325 A HIS 375 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc6 A OE2 GLU 346 A GLU 396 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc7 A O LEU 368 A LEU 418 1_555 O NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc8 A OD1 ASP 371 A ASP 421 1_555 O NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc9 A OG SER 372 A SER 422 1_555 O NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? # _chem_comp.formula 'C20 H18 Cl N5 O4 S' _chem_comp.formula_weight 459.906 _chem_comp.id A1AAF _chem_comp.mon_nstd_flag . _chem_comp.name 'methyl (1S,2R,3S,4R,5R)-4-{2-[(5-chlorothiophen-2-yl)ethynyl]-6-(methylamino)-9H-purin-9-yl}-2,3-dihydroxybicyclo[3.1.0]hexane-1-carboxylate' _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 N1 C3 A1AAF sing 43 n y N1 C4 A1AAF doub 44 n y C1 N2 A1AAF sing 45 n n N2 C2 A1AAF sing 46 n n C2 C3 A1AAF doub 47 n y C2 N5 A1AAF sing 48 n y C3 C5 A1AAF sing 49 n y C4 N3 A1AAF sing 50 n y N3 C13 A1AAF sing 51 n n N3 C5 A1AAF sing 52 n y C5 N4 A1AAF doub 53 n y N4 C6 A1AAF sing 54 n y C6 C7 A1AAF sing 55 n n C6 N5 A1AAF doub 56 n y C7 C8 A1AAF trip 57 n n C8 C9 A1AAF sing 58 n n C9 C10 A1AAF doub 59 n y C9 S1 A1AAF sing 60 n y C10 C11 A1AAF sing 61 n y C11 C12 A1AAF doub 62 n y C12 CL1 A1AAF sing 63 n n C12 S1 A1AAF sing 64 n y C13 C14 A1AAF sing 65 n n C13 C18 A1AAF sing 66 n n C14 C16 A1AAF sing 67 n n C14 C15 A1AAF sing 68 n n C15 C16 A1AAF sing 69 n n C16 C19 A1AAF sing 70 n n C16 C17 A1AAF sing 71 n n C17 O2 A1AAF sing 72 n n C17 C18 A1AAF sing 73 n n C18 O1 A1AAF sing 74 n n C19 O3 A1AAF doub 75 n n C19 O4 A1AAF sing 76 n n O4 C20 A1AAF sing 77 n n C1 H1 A1AAF sing 78 n n C1 H3 A1AAF sing 79 n n C1 H2 A1AAF sing 80 n n O1 H14 A1AAF sing 81 n n C13 H8 A1AAF sing 82 n n C4 H5 A1AAF sing 83 n n C10 H6 A1AAF sing 84 n n C11 H7 A1AAF sing 85 n n C14 H9 A1AAF sing 86 n n C15 H10 A1AAF sing 87 n n C15 H11 A1AAF sing 88 n n C17 H12 A1AAF sing 89 n n C18 H13 A1AAF sing 90 n n C20 H18 A1AAF sing 91 n n C20 H16 A1AAF sing 92 n n C20 H17 A1AAF sing 93 n n N2 H4 A1AAF sing 94 n n O2 H15 A1AAF sing 95 n n # _atom_sites.entry_id 8VBY _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 42L A 1 701 701 42L 42L . C 3 A1AAF A 1 702 702 A1AAF MRS . D 4 NAG A 1 703 705 NAG NAG . E 5 Y01 A 1 704 709 Y01 Y01 . F 6 D10 A 1 705 713 D10 D10 . G 7 LNK A 1 706 714 LNK LNK . H 6 D10 A 1 707 715 D10 D10 . I 7 LNK A 1 708 717 LNK LNK . J 7 LNK A 1 709 718 LNK LNK . K 5 Y01 A 1 710 723 Y01 Y01 . L 5 Y01 A 1 711 727 Y01 Y01 . M 8 HP6 A 1 712 728 HP6 HP6 . N 9 ZN A 1 713 729 ZN ZN . O 10 NA A 1 714 730 NA NA . P 8 HP6 A 1 715 732 HP6 HP6 . Q 11 D12 A 1 716 734 D12 D12 . R 11 D12 A 1 717 736 D12 D12 . S 6 D10 A 1 718 738 D10 D10 . T 8 HP6 A 1 719 748 HP6 HP6 . U 8 HP6 A 1 720 749 HP6 HP6 . V 7 LNK A 1 721 750 LNK LNK . W 7 LNK A 1 722 751 LNK LNK . X 7 LNK A 1 723 752 LNK LNK . Y 6 D10 A 1 724 753 D10 D10 . Z 12 MYS A 1 725 754 MYS MYS . AA 11 D12 A 1 726 755 D12 D12 . BA 8 HP6 A 1 727 756 HP6 HP6 . CA 11 D12 A 1 728 758 D12 D12 . DA 13 OCT A 1 729 759 OCT OCT . EA 13 OCT A 1 730 762 OCT OCT . FA 8 HP6 A 1 731 763 HP6 HP6 . GA 7 LNK A 1 732 764 LNK LNK . HA 8 HP6 A 1 733 765 HP6 HP6 . IA 6 D10 A 1 734 766 D10 D10 . JA 6 D10 A 1 735 770 D10 D10 . KA 11 D12 A 1 736 772 D12 D12 . LA 8 HP6 A 1 737 774 HP6 HP6 . MA 5 Y01 A 1 738 776 Y01 Y01 . NA 11 D12 A 1 739 777 D12 D12 . OA 6 D10 A 1 740 778 D10 D10 . PA 6 D10 A 1 741 1 D10 D10 . QA 14 HOH A 1 801 12 HOH HOH . QA 14 HOH A 2 802 11 HOH HOH . QA 14 HOH A 3 803 7 HOH HOH . QA 14 HOH A 4 804 8 HOH HOH . QA 14 HOH A 5 805 3 HOH HOH . QA 14 HOH A 6 806 4 HOH HOH . QA 14 HOH A 7 807 10 HOH HOH . QA 14 HOH A 8 808 9 HOH HOH . QA 14 HOH A 9 809 6 HOH HOH . QA 14 HOH A 10 810 5 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 C1 A1AAF . . . C 3 161.398 148.838 144.975 1 42.17 ? C1 A1AAF 702 A 1 HETATM 2 O O1 A1AAF . . . C 3 154.318 144.031 141.737 1 59.41 ? O1 A1AAF 702 A 1 HETATM 3 C C2 A1AAF . . . C 3 159.436 147.369 144.964 1 47.45 ? C2 A1AAF 702 A 1 HETATM 4 C C13 A1AAF . . . C 3 155.686 144.563 143.719 1 44.2 ? C13 A1AAF 702 A 1 HETATM 5 C C3 A1AAF . . . C 3 158.788 146.273 144.366 1 40.9 ? C3 A1AAF 702 A 1 HETATM 6 C C4 A1AAF . . . C 3 158.196 144.497 143.333 1 44.31 ? C4 A1AAF 702 A 1 HETATM 7 C C5 A1AAF . . . C 3 157.414 146.193 144.507 1 48.45 ? C5 A1AAF 702 A 1 HETATM 8 C C6 A1AAF . . . C 3 157.338 148.059 145.687 1 46.42 ? C6 A1AAF 702 A 1 HETATM 9 C C7 A1AAF . . . C 3 156.603 149.042 146.406 1 39.05 ? C7 A1AAF 702 A 1 HETATM 10 C C8 A1AAF . . . C 3 155.994 149.877 147.017 1 43.68 ? C8 A1AAF 702 A 1 HETATM 11 C C9 A1AAF . . . C 3 155.282 150.871 147.747 1 47.03 ? C9 A1AAF 702 A 1 HETATM 12 C C10 A1AAF . . . C 3 153.911 150.958 147.838 1 39.94 ? C10 A1AAF 702 A 1 HETATM 13 C C11 A1AAF . . . C 3 153.49 152.062 148.639 1 41.21 ? C11 A1AAF 702 A 1 HETATM 14 C C12 A1AAF . . . C 3 154.566 152.757 149.121 1 55.19 ? C12 A1AAF 702 A 1 HETATM 15 C C14 A1AAF . . . C 3 155.194 143.68 144.842 1 42.37 ? C14 A1AAF 702 A 1 HETATM 16 C C15 A1AAF . . . C 3 153.836 143.028 144.787 1 39.08 ? C15 A1AAF 702 A 1 HETATM 17 C C16 A1AAF . . . C 3 155.072 142.257 144.357 1 43.96 ? C16 A1AAF 702 A 1 HETATM 18 C C17 A1AAF . . . C 3 155.49 142.241 142.905 1 49.5 ? C17 A1AAF 702 A 1 HETATM 19 C C18 A1AAF . . . C 3 155.54 143.717 142.433 1 51.46 ? C18 A1AAF 702 A 1 HETATM 20 C C19 A1AAF . . . C 3 155.547 141.147 145.221 1 54.41 ? C19 A1AAF 702 A 1 HETATM 21 C C20 A1AAF . . . C 3 155.713 140.355 147.412 1 47.33 ? C20 A1AAF 702 A 1 HETATM 22 N N1 A1AAF . . . C 3 159.26 145.208 143.632 1 41.89 ? N1 A1AAF 702 A 1 HETATM 23 N N2 A1AAF . . . C 3 160.8 147.536 144.879 1 48.02 ? N2 A1AAF 702 A 1 HETATM 24 N N3 A1AAF . . . C 3 157.054 145.048 143.841 1 45.35 ? N3 A1AAF 702 A 1 HETATM 25 N N4 A1AAF . . . C 3 156.612 147.052 145.157 1 53.08 ? N4 A1AAF 702 A 1 HETATM 26 N N5 A1AAF . . . C 3 158.668 148.264 145.632 1 50.71 ? N5 A1AAF 702 A 1 HETATM 27 O O2 A1AAF . . . C 3 154.559 141.505 142.127 1 56.61 ? O2 A1AAF 702 A 1 HETATM 28 O O3 A1AAF . . . C 3 155.926 140.09 144.74 1 55.36 ? O3 A1AAF 702 A 1 HETATM 29 O O4 A1AAF . . . C 3 155.492 141.461 146.539 1 58.91 ? O4 A1AAF 702 A 1 HETATM 30 S S1 A1AAF . . . C 3 156.049 152.116 148.632 1 61.55 ? S1 A1AAF 702 A 1 HETATM 31 CL CL1 A1AAF . . . C 3 154.53 154.149 150.125 1 75.93 ? CL1 A1AAF 702 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #