data_9D9K # _model_server_result.job_id h774Zb9sXdQVjgtUZM2I4w _model_server_result.datetime_utc '2024-12-26 13:08:27' _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 9d9k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":414}' # _entry.id 9D9K # _exptl.entry_id 9D9K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 346.427 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-{[(4-amino-5,6-dimethylthieno[2,3-d]pyrimidin-2-yl)methyl]sulfanyl}pyridine-3-carboxylic acid' _entity.pdbx_number_of_molecules 2 _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 9D9K _cell.length_a 108.711 _cell.length_b 108.711 _cell.length_c 265.044 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9D9K _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 10_465 -x-1,-y+1,z -1 0 0 0 -1 0 0 0 1 -108.711 108.711 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 N N N ? 4 O 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 covale ? covale1 A C SER 74 A SER 74 1_555 A N SEP 75 A SEP 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale2 A C SEP 75 A SEP 75 1_555 A N ALA 76 A ALA 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? # _chem_comp.formula 'C15 H14 N4 O2 S2' _chem_comp.formula_weight 346.427 _chem_comp.id A1A23 _chem_comp.mon_nstd_flag . _chem_comp.name '2-{[(4-amino-5,6-dimethylthieno[2,3-d]pyrimidin-2-yl)methyl]sulfanyl}pyridine-3-carboxylic acid' _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 S10 C9 A1A23 sing 1 n y S10 C2 A1A23 sing 2 n y C15 N14 A1A23 doub 3 n y C15 C16 A1A23 sing 4 n y C1 C2 A1A23 sing 5 n n N8 C9 A1A23 doub 6 n y N8 C7 A1A23 sing 7 n y N14 C13 A1A23 sing 8 n y C16 C17 A1A23 doub 9 n y C9 C4 A1A23 sing 10 n y C2 C3 A1A23 doub 11 n y C11 C7 A1A23 sing 12 n n C11 S12 A1A23 sing 13 n n C7 N6 A1A23 doub 14 n y C13 S12 A1A23 sing 15 n n C13 C18 A1A23 doub 16 n y C17 C18 A1A23 sing 17 n y C4 C3 A1A23 sing 18 n y C4 C5 A1A23 doub 19 n y C3 C23 A1A23 sing 20 n n C18 C19 A1A23 sing 21 n n N6 C5 A1A23 sing 22 n y C5 N22 A1A23 sing 23 n n C19 O20 A1A23 doub 24 n n C19 O21 A1A23 sing 25 n n C1 H1 A1A23 sing 26 n n C1 H2 A1A23 sing 27 n n C1 H3 A1A23 sing 28 n n C11 H4 A1A23 sing 29 n n C11 H5 A1A23 sing 30 n n C15 H6 A1A23 sing 31 n n C16 H7 A1A23 sing 32 n n C17 H8 A1A23 sing 33 n n C23 H9 A1A23 sing 34 n n C23 H10 A1A23 sing 35 n n C23 H11 A1A23 sing 36 n n N22 H12 A1A23 sing 37 n n N22 H13 A1A23 sing 38 n n O21 H14 A1A23 sing 39 n n # _atom_sites.entry_id 9D9K _atom_sites.fract_transf_matrix[1][1] 0.009199 _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] 0.009199 _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] 0.003773 _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 SO4 A 1 401 1 SO4 SO4 . C 2 SO4 A 1 402 2 SO4 SO4 . D 2 SO4 A 1 403 3 SO4 SO4 . E 2 SO4 A 1 404 4 SO4 SO4 . F 2 SO4 A 1 405 5 SO4 SO4 . G 2 SO4 A 1 406 6 SO4 SO4 . H 2 SO4 A 1 407 7 SO4 SO4 . I 2 SO4 A 1 408 8 SO4 SO4 . J 2 SO4 A 1 409 9 SO4 SO4 . K 2 SO4 A 1 410 10 SO4 SO4 . L 2 SO4 A 1 411 11 SO4 SO4 . M 3 CL A 1 412 12 CL CL . N 4 A1A23 A 1 413 401 A1A23 M17 . O 4 A1A23 A 1 414 402 A1A23 M17 . P 5 HOH A 1 501 24 HOH HOH . P 5 HOH A 2 502 23 HOH HOH . P 5 HOH A 3 503 10 HOH HOH . P 5 HOH A 4 504 19 HOH HOH . P 5 HOH A 5 505 30 HOH HOH . P 5 HOH A 6 506 26 HOH HOH . P 5 HOH A 7 507 32 HOH HOH . P 5 HOH A 8 508 8 HOH HOH . P 5 HOH A 9 509 7 HOH HOH . P 5 HOH A 10 510 5 HOH HOH . P 5 HOH A 11 511 25 HOH HOH . P 5 HOH A 12 512 1 HOH HOH . P 5 HOH A 13 513 13 HOH HOH . P 5 HOH A 14 514 17 HOH HOH . P 5 HOH A 15 515 2 HOH HOH . P 5 HOH A 16 516 4 HOH HOH . P 5 HOH A 17 517 21 HOH HOH . P 5 HOH A 18 518 14 HOH HOH . P 5 HOH A 19 519 12 HOH HOH . P 5 HOH A 20 520 6 HOH HOH . P 5 HOH A 21 521 29 HOH HOH . P 5 HOH A 22 522 31 HOH HOH . P 5 HOH A 23 523 28 HOH HOH . P 5 HOH A 24 524 3 HOH HOH . P 5 HOH A 25 525 22 HOH HOH . P 5 HOH A 26 526 15 HOH HOH . P 5 HOH A 27 527 20 HOH HOH . P 5 HOH A 28 528 11 HOH HOH . P 5 HOH A 29 529 18 HOH HOH . P 5 HOH A 30 530 27 HOH HOH . P 5 HOH A 31 531 9 HOH HOH . P 5 HOH A 32 532 16 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 A1A23 . . . O 4 -42.574 27.125 33.059 0.5 139.07 ? C1 A1A23 414 A 1 HETATM 2 C C11 A1A23 . . . O 4 -49.574 25.583 30.682 0.5 95.4 ? C11 A1A23 414 A 1 HETATM 3 C C13 A1A23 . . . O 4 -52.319 25.268 30.605 0.5 64.79 ? C13 A1A23 414 A 1 HETATM 4 C C15 A1A23 . . . O 4 -52.725 23.776 28.93 0.5 60.77 ? C15 A1A23 414 A 1 HETATM 5 C C16 A1A23 . . . O 4 -54.085 23.963 29.004 0.5 56.31 ? C16 A1A23 414 A 1 HETATM 6 C C17 A1A23 . . . O 4 -54.579 24.855 29.936 0.5 58.35 ? C17 A1A23 414 A 1 HETATM 7 C C18 A1A23 . . . O 4 -53.691 25.528 30.77 0.5 62.98 ? C18 A1A23 414 A 1 HETATM 8 C C19 A1A23 . . . O 4 -54.266 26.419 31.842 0.5 65.6 ? C19 A1A23 414 A 1 HETATM 9 C C2 A1A23 . . . O 4 -44.041 26.951 32.806 0.5 135.2 ? C2 A1A23 414 A 1 HETATM 10 C C23 A1A23 . . . O 4 -44.911 28.114 34.856 0.5 128.96 ? C23 A1A23 414 A 1 HETATM 11 C C3 A1A23 . . . O 4 -45.09 27.381 33.559 0.5 133.76 ? C3 A1A23 414 A 1 HETATM 12 C C4 A1A23 . . . O 4 -46.364 27.016 32.975 0.5 130.13 ? C4 A1A23 414 A 1 HETATM 13 C C5 A1A23 . . . O 4 -47.714 27.227 33.36 0.5 122.52 ? C5 A1A23 414 A 1 HETATM 14 C C7 A1A23 . . . O 4 -48.412 26.09 31.485 0.5 113.2 ? C7 A1A23 414 A 1 HETATM 15 C C9 A1A23 . . . O 4 -46.211 26.308 31.781 0.5 126.62 ? C9 A1A23 414 A 1 HETATM 16 N N14 A1A23 . . . O 4 -51.839 24.406 29.71 0.5 54.89 ? N14 A1A23 414 A 1 HETATM 17 N N22 A1A23 . . . O 4 -48.073 27.921 34.453 0.5 115.98 ? N22 A1A23 414 A 1 HETATM 18 N N6 A1A23 . . . O 4 -48.722 26.754 32.604 0.5 114.15 ? N6 A1A23 414 A 1 HETATM 19 N N8 A1A23 . . . O 4 -47.187 25.83 31.013 0.5 117.38 ? N8 A1A23 414 A 1 HETATM 20 O O20 A1A23 . . . O 4 -54.606 27.58 31.513 0.5 63.5 ? O20 A1A23 414 A 1 HETATM 21 O O21 A1A23 . . . O 4 -54.391 25.953 32.993 0.5 67.95 ? O21 A1A23 414 A 1 HETATM 22 S S10 A1A23 . . . O 4 -44.536 26.092 31.372 0.5 129.64 ? S10 A1A23 414 A 1 HETATM 23 S S12 A1A23 . . . O 4 -51.095 26.102 31.539 0.5 88.81 ? S12 A1A23 414 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #