data_8SI8 # _model_server_result.job_id 4cLxf16cP8agMoNybhp5EA _model_server_result.datetime_utc '2025-04-22 16:46:16' _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 8si8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"IB","auth_seq_id":1306}' # _entry.id 8SI8 # _exptl.entry_id 8SI8 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 556.401 _entity.id 3 _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 4 _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 8SI8 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SI8 _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB _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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 G N N ? 3 AA N N ? 3 QA N N ? 3 IB N 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 15 A CYS 16 1_555 A SG CYS 43 A CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf2 A SG CYS 41 A CYS 42 1_555 A SG CYS 43 A CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf3 A SG CYS 1055 A CYS 1056 1_555 A SG CYS 1065 A CYS 1066 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 B SG CYS 15 B CYS 16 1_555 B SG CYS 43 B CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf5 B SG CYS 41 B CYS 42 1_555 B SG CYS 43 B CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf6 B SG CYS 1055 B CYS 1056 1_555 B SG CYS 1065 B CYS 1066 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf7 C SG CYS 15 C CYS 16 1_555 C SG CYS 43 C CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf8 C SG CYS 41 C CYS 42 1_555 C SG CYS 43 C CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf9 C SG CYS 1055 C CYS 1056 1_555 C SG CYS 1065 C CYS 1066 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 D SG CYS 15 D CYS 16 1_555 D SG CYS 43 D CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf11 D SG CYS 41 D CYS 42 1_555 D SG CYS 43 D CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf12 D SG CYS 1055 D CYS 1056 1_555 D SG CYS 1065 D CYS 1066 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? # _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 8SI8 _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 E 2 POV A 1 1301 1302 POV POV . F 2 POV A 1 1302 1305 POV POV . G 3 3FD A 1 1303 1306 3FD VER . H 4 CLR A 1 1304 1307 CLR CLR . I 2 POV A 1 1305 1309 POV POV . J 2 POV A 1 1306 1311 POV POV . K 2 POV A 1 1307 1312 POV POV . L 2 POV A 1 1308 1313 POV POV . M 2 POV A 1 1309 1314 POV POV . N 2 POV A 1 1310 1315 POV POV . O 2 POV A 1 1311 1316 POV POV . P 2 POV A 1 1312 1317 POV POV . Q 5 DU0 A 1 1313 1318 DU0 DU0 . R 2 POV A 1 1314 1301 POV POV . S 2 POV A 1 1315 1304 POV POV . T 2 POV A 1 1316 1310 POV POV . U 6 CA A 1 1317 1 CA CA . V 2 POV B 1 1301 1304 POV POV . W 2 POV B 1 1302 1310 POV POV . X 2 POV B 1 1303 1302 POV POV . Y 2 POV B 1 1304 1304 POV POV . Z 2 POV B 1 1305 1305 POV POV . AA 3 3FD B 1 1306 1306 3FD VER . BA 4 CLR B 1 1307 1307 CLR CLR . CA 2 POV B 1 1308 1309 POV POV . DA 2 POV B 1 1309 1311 POV POV . EA 2 POV B 1 1310 1312 POV POV . FA 2 POV B 1 1311 1313 POV POV . GA 2 POV B 1 1312 1314 POV POV . HA 2 POV B 1 1313 1315 POV POV . IA 2 POV B 1 1314 1316 POV POV . JA 2 POV B 1 1315 1317 POV POV . KA 5 DU0 B 1 1316 1318 DU0 DU0 . LA 2 POV B 1 1317 1301 POV POV . MA 2 POV B 1 1318 1317 POV POV . NA 2 POV C 1 1301 1310 POV POV . OA 2 POV C 1 1302 1302 POV POV . PA 2 POV C 1 1303 1305 POV POV . QA 3 3FD C 1 1304 1306 3FD VER . RA 4 CLR C 1 1305 1307 CLR CLR . SA 2 POV C 1 1306 1309 POV POV . TA 2 POV C 1 1307 1311 POV POV . UA 2 POV C 1 1308 1312 POV POV . VA 2 POV C 1 1309 1313 POV POV . WA 2 POV C 1 1310 1314 POV POV . XA 2 POV C 1 1311 1315 POV POV . YA 2 POV C 1 1312 1316 POV POV . ZA 5 DU0 C 1 1313 1318 DU0 DU0 . AB 2 POV C 1 1314 1301 POV POV . BB 2 POV C 1 1315 1317 POV POV . CB 5 DU0 C 1 1316 1318 DU0 DU0 . DB 2 POV D 1 1301 1301 POV POV . EB 2 POV D 1 1302 1304 POV POV . FB 2 POV D 1 1303 1310 POV POV . GB 2 POV D 1 1304 1302 POV POV . HB 2 POV D 1 1305 1305 POV POV . IB 3 3FD D 1 1306 1306 3FD VER . JB 4 CLR D 1 1307 1307 CLR CLR . KB 2 POV D 1 1308 1309 POV POV . LB 2 POV D 1 1309 1311 POV POV . MB 2 POV D 1 1310 1312 POV POV . NB 2 POV D 1 1311 1313 POV POV . OB 2 POV D 1 1312 1314 POV POV . PB 2 POV D 1 1313 1315 POV POV . QB 2 POV D 1 1314 1316 POV POV . # 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 . . . IB 3 149.622 122.308 146.933 1 0 ? C18 3FD 1306 D 1 HETATM 2 C C17 3FD . . . IB 3 149.513 122.256 148.308 1 0 ? C17 3FD 1306 D 1 HETATM 3 C C16 3FD . . . IB 3 148.284 122.286 148.905 1 0 ? C16 3FD 1306 D 1 HETATM 4 CL CL20 3FD . . . IB 3 148.137 122.202 150.666 1 0 ? CL20 3FD 1306 D 1 HETATM 5 C C15 3FD . . . IB 3 147.155 122.378 148.148 1 0 ? C15 3FD 1306 D 1 HETATM 6 C C14 3FD . . . IB 3 147.261 122.437 146.78 1 0 ? C14 3FD 1306 D 1 HETATM 7 C C13 3FD . . . IB 3 148.489 122.408 146.164 1 0 ? C13 3FD 1306 D 1 HETATM 8 C C12 3FD . . . IB 3 148.53 122.469 144.645 1 0 ? C12 3FD 1306 D 1 HETATM 9 N N11 3FD . . . IB 3 149.826 122.766 144.059 1 0 ? N11 3FD 1306 D 1 HETATM 10 C C6 3FD . . . IB 3 149.925 123.587 142.866 1 0 ? C6 3FD 1306 D 1 HETATM 11 N N7 3FD . . . IB 3 148.945 124.313 142.372 1 0 ? N7 3FD 1306 D 1 HETATM 12 C C8 3FD . . . IB 3 149.404 124.939 141.27 1 0 ? C8 3FD 1306 D 1 HETATM 13 C C4 3FD . . . IB 3 148.844 125.822 140.335 1 0 ? C4 3FD 1306 D 1 HETATM 14 N N10 3FD . . . IB 3 147.46 126.175 140.527 1 0 ? N10 3FD 1306 D 1 HETATM 15 N N1 3FD . . . IB 3 149.57 126.284 139.331 1 0 ? N1 3FD 1306 D 1 HETATM 16 C C2 3FD . . . IB 3 150.837 125.908 139.212 1 0 ? C2 3FD 1306 D 1 HETATM 17 N N3 3FD . . . IB 3 151.395 125.086 140.075 1 0 ? N3 3FD 1306 D 1 HETATM 18 C C9 3FD . . . IB 3 150.698 124.579 141.117 1 0 ? C9 3FD 1306 D 1 HETATM 19 N N5 3FD . . . IB 3 151.015 123.743 142.129 1 0 ? N5 3FD 1306 D 1 HETATM 20 C C21 3FD . . . IB 3 152.195 123.204 142.292 1 0 ? C21 3FD 1306 D 1 HETATM 21 O O22 3FD . . . IB 3 152.072 121.675 142.355 1 0 ? O22 3FD 1306 D 1 HETATM 22 C C24 3FD . . . IB 3 152.871 123.618 143.649 1 0 ? C24 3FD 1306 D 1 HETATM 23 O O26 3FD . . . IB 3 153.914 124.66 143.41 1 0 ? O26 3FD 1306 D 1 HETATM 24 C C25 3FD . . . IB 3 153.423 122.573 144.074 1 0 ? C25 3FD 1306 D 1 HETATM 25 O O27 3FD . . . IB 3 154.838 122.788 144.119 1 0 ? O27 3FD 1306 D 1 HETATM 26 C C23 3FD . . . IB 3 153.111 121.355 143.005 1 0 ? C23 3FD 1306 D 1 HETATM 27 C C28 3FD . . . IB 3 152.777 120.172 143.809 1 0 ? C28 3FD 1306 D 1 HETATM 28 O O29 3FD . . . IB 3 152.469 119.139 142.943 1 0 ? O29 3FD 1306 D 1 HETATM 29 C C30 3FD . . . IB 3 151.697 118.185 143.593 1 0 ? C30 3FD 1306 D 1 HETATM 30 C C31 3FD . . . IB 3 151.806 116.948 142.734 1 0 ? C31 3FD 1306 D 1 HETATM 31 C C32 3FD . . . IB 3 152.511 115.868 143.184 1 0 ? C32 3FD 1306 D 1 HETATM 32 C C33 3FD . . . IB 3 152.607 114.759 142.39 1 0 ? C33 3FD 1306 D 1 HETATM 33 C C34 3FD . . . IB 3 152.009 114.739 141.153 1 0 ? C34 3FD 1306 D 1 HETATM 34 C C37 3FD . . . IB 3 152.129 113.5 140.29 1 0 ? C37 3FD 1306 D 1 HETATM 35 N N38 3FD . . . IB 3 152.229 112.57 139.667 1 0 ? N38 3FD 1306 D 1 HETATM 36 C C35 3FD . . . IB 3 151.307 115.83 140.706 1 0 ? C35 3FD 1306 D 1 HETATM 37 C C36 3FD . . . IB 3 151.209 116.94 141.502 1 0 ? C36 3FD 1306 D 1 HETATM 38 CL CL21 3FD . . . IB 3 145.577 122.411 148.96 1 0 ? CL21 3FD 1306 D 1 HETATM 39 H H18 3FD . . . IB 3 150.591 122.28 146.463 1 0 ? H18 3FD 1306 D 1 HETATM 40 H H17 3FD . . . IB 3 150.396 122.174 148.922 1 0 ? H17 3FD 1306 D 1 HETATM 41 H H14 3FD . . . IB 3 146.373 122.518 146.186 1 0 ? H14 3FD 1306 D 1 HETATM 42 H H12 3FD . . . IB 3 147.792 123.186 144.328 1 0 ? H12 3FD 1306 D 1 HETATM 43 H H12A 3FD . . . IB 3 148.237 121.501 144.29 1 0 ? H12A 3FD 1306 D 1 HETATM 44 H HN11 3FD . . . IB 3 150.654 122.369 144.449 1 0 ? HN11 3FD 1306 D 1 HETATM 45 H HN10 3FD . . . IB 3 146.939 125.72 141.251 1 0 ? HN10 3FD 1306 D 1 HETATM 46 H HN1A 3FD . . . IB 3 147.036 126.881 139.964 1 0 ? HN1A 3FD 1306 D 1 HETATM 47 H H2 3FD . . . IB 3 151.439 126.285 138.397 1 0 ? H2 3FD 1306 D 1 HETATM 48 H H21 3FD . . . IB 3 152.866 123.457 141.484 1 0 ? H21 3FD 1306 D 1 HETATM 49 H H24 3FD . . . IB 3 152.174 123.976 144.386 1 0 ? H24 3FD 1306 D 1 HETATM 50 H HO26 3FD . . . IB 3 153.681 125.433 143.898 1 0 ? HO26 3FD 1306 D 1 HETATM 51 H H25 3FD . . . IB 3 153.052 122.302 145.044 1 0 ? H25 3FD 1306 D 1 HETATM 52 H HO27 3FD . . . IB 3 155.097 123.198 143.313 1 0 ? HO27 3FD 1306 D 1 HETATM 53 H H23 3FD . . . IB 3 153.956 121.188 142.362 1 0 ? H23 3FD 1306 D 1 HETATM 54 H H28 3FD . . . IB 3 151.892 120.399 144.376 1 0 ? H28 3FD 1306 D 1 HETATM 55 H H28A 3FD . . . IB 3 153.605 119.916 144.45 1 0 ? H28A 3FD 1306 D 1 HETATM 56 H H30 3FD . . . IB 3 150.669 118.511 143.657 1 0 ? H30 3FD 1306 D 1 HETATM 57 H H30A 3FD . . . IB 3 152.104 118.001 144.576 1 0 ? H30A 3FD 1306 D 1 HETATM 58 H H32 3FD . . . IB 3 152.984 115.889 144.154 1 0 ? H32 3FD 1306 D 1 HETATM 59 H H33 3FD . . . IB 3 153.162 113.905 142.742 1 0 ? H33 3FD 1306 D 1 HETATM 60 H H35 3FD . . . IB 3 150.834 115.812 139.738 1 0 ? H35 3FD 1306 D 1 HETATM 61 H H36 3FD . . . IB 3 150.661 117.807 141.172 1 0 ? H36 3FD 1306 D 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 160 _model_server_stats.query_time_ms 364 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 61 #