data_4L2X # _model_server_result.job_id eKtgpIOVeGnAxWbup1kYSA _model_server_result.datetime_utc '2024-11-25 03:49:57' _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 4l2x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4L2X # _exptl.entry_id 4L2X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 441.335 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '({[6-(4-cyclopropylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic acid)' _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 4L2X _cell.length_a 111.34 _cell.length_b 111.34 _cell.length_c 68.77 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L2X _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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 _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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 # 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 OD1 ASP 125 F ASP 103 1_555 D MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc2 A OD2 ASP 125 F ASP 103 1_555 E MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc3 A OD2 ASP 129 F ASP 107 1_555 D MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc4 A OD2 ASP 129 F ASP 107 1_555 E MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc5 A OD2 ASP 265 F ASP 243 1_555 F MG MG . F MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc6 B OAV YL2 . F YL2 401 1_555 D MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc7 B OAZ YL2 . F YL2 401 1_555 D MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc8 B OAV YL2 . F YL2 401 1_555 E MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc9 B OAY YL2 . F YL2 401 1_555 F MG MG . F MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.726 ? metalc ? metalc10 B OAW YL2 . F YL2 401 1_555 F MG MG . F MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc11 D MG MG . F MG 403 1_555 G O HOH . F HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc12 D MG MG . F MG 403 1_555 G O HOH . F HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc13 E MG MG . F MG 404 1_555 G O HOH . F HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc14 E MG MG . F MG 404 1_555 G O HOH . F HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc15 E MG MG . F MG 404 1_555 G O HOH . F HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc16 F MG MG . F MG 405 1_555 G O HOH . F HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc17 F MG MG . F MG 405 1_555 G O HOH . F HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc18 F MG MG . F MG 405 1_555 G O HOH . F HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? # _chem_comp.formula 'C16 H17 N3 O6 P2 S' _chem_comp.formula_weight 441.335 _chem_comp.id YL2 _chem_comp.mon_nstd_flag . _chem_comp.name '({[6-(4-cyclopropylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic 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 OAW PAS YL2 doub 386 n n OAU PAS YL2 sing 387 n n C2 N1 YL2 doub 388 n y C2 N3 YL2 sing 389 n y PAS OAV YL2 sing 390 n n PAS CAR YL2 sing 391 n n N1 C6 YL2 sing 392 n y N3 C4 YL2 doub 393 n y C6 SAE YL2 sing 394 n y C6 C5 YL2 doub 395 n y SAE CAD YL2 sing 396 n y CAR NAJ YL2 sing 397 n n CAR PAT YL2 sing 398 n n C4 C5 YL2 sing 399 n y C4 NAJ YL2 sing 400 n n C5 CAC YL2 sing 401 n y OAY PAT YL2 doub 402 n n CAD CAC YL2 doub 403 n y CAD CAK YL2 sing 404 n n CAP CAO YL2 doub 405 n y CAP CAK YL2 sing 406 n y PAT OAX YL2 sing 407 n n PAT OAZ YL2 sing 408 n n CAO CAN YL2 sing 409 n y CAK CAL YL2 doub 410 n y CAN CAQ YL2 sing 411 n n CAN CAM YL2 doub 412 n y CAL CAM YL2 sing 413 n y CAQ CBB YL2 sing 414 n n CAQ CBA YL2 sing 415 n n CBB CBA YL2 sing 416 n n OAU H1 YL2 sing 417 n n OAV H2 YL2 sing 418 n n CAR H3 YL2 sing 419 n n OAX H4 YL2 sing 420 n n OAZ H5 YL2 sing 421 n n NAJ H6 YL2 sing 422 n n C2 H7 YL2 sing 423 n n CAC H8 YL2 sing 424 n n CAP H9 YL2 sing 425 n n CAO H10 YL2 sing 426 n n CAL H11 YL2 sing 427 n n CAM H12 YL2 sing 428 n n CAQ H13 YL2 sing 429 n n CBA H14 YL2 sing 430 n n CBA H15 YL2 sing 431 n n CBB H16 YL2 sing 432 n n CBB H17 YL2 sing 433 n n # _atom_sites.entry_id 4L2X _atom_sites.fract_transf_matrix[1][1] 0.008981 _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] 0.008981 _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] 0.014541 _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 YL2 F 1 401 1 YL2 YL2 . C 3 POP F 1 402 1 POP POP . D 4 MG F 1 403 1 MG MG . E 4 MG F 1 404 1 MG MG . F 4 MG F 1 405 1 MG MG . G 5 HOH F 1 501 1 HOH HOH . G 5 HOH F 2 502 2 HOH HOH . G 5 HOH F 3 503 3 HOH HOH . G 5 HOH F 4 504 4 HOH HOH . G 5 HOH F 5 505 5 HOH HOH . G 5 HOH F 6 506 6 HOH HOH . G 5 HOH F 7 507 7 HOH HOH . G 5 HOH F 8 508 8 HOH HOH . G 5 HOH F 9 509 9 HOH HOH . G 5 HOH F 10 510 10 HOH HOH . G 5 HOH F 11 511 11 HOH HOH . G 5 HOH F 12 512 12 HOH HOH . G 5 HOH F 13 513 13 HOH HOH . G 5 HOH F 14 514 14 HOH HOH . G 5 HOH F 15 515 15 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 O OAU YL2 . . . B 2 16.297 32.823 -10.531 1 48.18 ? OAU YL2 401 F 1 HETATM 2 P PAS YL2 . . . B 2 16.597 33.944 -9.6 1 55.03 ? PAS YL2 401 F 1 HETATM 3 O OAV YL2 . . . B 2 17.839 33.958 -8.757 1 50.21 ? OAV YL2 401 F 1 HETATM 4 O OAW YL2 . . . B 2 16.578 35.125 -10.678 1 53.23 ? OAW YL2 401 F 1 HETATM 5 C CAR YL2 . . . B 2 15.227 34.086 -8.349 1 51.61 ? CAR YL2 401 F 1 HETATM 6 P PAT YL2 . . . B 2 15.588 35.604 -7.355 1 51.22 ? PAT YL2 401 F 1 HETATM 7 O OAX YL2 . . . B 2 14.583 35.607 -6.141 1 35.1 ? OAX YL2 401 F 1 HETATM 8 O OAZ YL2 . . . B 2 16.857 35.503 -6.598 1 57.61 ? OAZ YL2 401 F 1 HETATM 9 O OAY YL2 . . . B 2 15.456 36.555 -8.455 1 46.13 ? OAY YL2 401 F 1 HETATM 10 N NAJ YL2 . . . B 2 15.046 32.831 -7.513 1 56.65 ? NAJ YL2 401 F 1 HETATM 11 C C4 YL2 . . . B 2 14.48 31.781 -8.118 1 59.45 ? C4 YL2 401 F 1 HETATM 12 N N3 YL2 . . . B 2 13.486 32.09 -8.923 1 53.94 ? N3 YL2 401 F 1 HETATM 13 C C2 YL2 . . . B 2 12.825 31.121 -9.623 1 65.15 ? C2 YL2 401 F 1 HETATM 14 N N1 YL2 . . . B 2 13.266 29.831 -9.5 1 67.04 ? N1 YL2 401 F 1 HETATM 15 C C6 YL2 . . . B 2 14.292 29.545 -8.682 1 68.23 ? C6 YL2 401 F 1 HETATM 16 S SAE YL2 . . . B 2 15.04 28.072 -8.388 1 62.64 ? SAE YL2 401 F 1 HETATM 17 C C5 YL2 . . . B 2 14.937 30.494 -7.965 1 67.56 ? C5 YL2 401 F 1 HETATM 18 C CAC YL2 . . . B 2 15.952 29.931 -7.213 1 62.6 ? CAC YL2 401 F 1 HETATM 19 C CAD YL2 . . . B 2 16.1 28.579 -7.348 1 67.86 ? CAD YL2 401 F 1 HETATM 20 C CAK YL2 . . . B 2 17.004 27.708 -6.798 1 73.89 ? CAK YL2 401 F 1 HETATM 21 C CAP YL2 . . . B 2 17.68 27.915 -5.608 1 66.63 ? CAP YL2 401 F 1 HETATM 22 C CAO YL2 . . . B 2 18.575 26.974 -5.117 1 62.33 ? CAO YL2 401 F 1 HETATM 23 C CAL YL2 . . . B 2 17.306 26.516 -7.469 1 79.71 ? CAL YL2 401 F 1 HETATM 24 C CAM YL2 . . . B 2 18.205 25.577 -6.984 1 69.38 ? CAM YL2 401 F 1 HETATM 25 C CAN YL2 . . . B 2 18.845 25.799 -5.799 1 62.34 ? CAN YL2 401 F 1 HETATM 26 C CAQ YL2 . . . B 2 19.776 24.816 -5.38 1 58.19 ? CAQ YL2 401 F 1 HETATM 27 C CBA YL2 . . . B 2 20.075 24.577 -3.974 1 53.75 ? CBA YL2 401 F 1 HETATM 28 C CBB YL2 . . . B 2 19.245 23.73 -4.71 1 58.13 ? CBB YL2 401 F 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #