data_4YTI # _model_server_result.job_id x9SmezUJcOitxa8ALp5Y-w _model_server_result.datetime_utc '2025-01-02 18:04:51' _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 4yti # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":4000}' # _entry.id 4YTI # _exptl.entry_id 4YTI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 392.378 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R)-2-methyl-2-[[2-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]-N-[2,2,2-tris(fluoranyl)ethyl]butanamide _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 4YTI _cell.length_a 94.932 _cell.length_b 100.981 _cell.length_c 68.407 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YTI _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 # 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 GLU 170 A GLU 1006 1_555 A N PTR 171 A PTR 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale2 A C PTR 171 A PTR 1007 1_555 A N PTR 172 A PTR 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale3 A C PTR 172 A PTR 1008 1_555 A N LYS 173 A LYS 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? # _chem_comp.formula 'C18 H19 F3 N6 O' _chem_comp.formula_weight 392.378 _chem_comp.id VJK _chem_comp.mon_nstd_flag . _chem_comp.name (2R)-2-methyl-2-[[2-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]-N-[2,2,2-tris(fluoranyl)ethyl]butanamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Decernotinib;Adelatinib;VX-509 # 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 F2 C6 VJK sing 405 n n F C6 VJK sing 406 n n C6 F1 VJK sing 407 n n C6 C5 VJK sing 408 n n C17 N5 VJK doub 409 n y C17 C16 VJK sing 410 n y N5 C13 VJK sing 411 n y C16 C15 VJK doub 412 n y C13 N4 VJK sing 413 n y C13 C14 VJK doub 414 n y N4 C12 VJK sing 415 n y C5 N VJK sing 416 n n C15 C14 VJK sing 417 n y C14 C11 VJK sing 418 n y C12 C11 VJK doub 419 n y C11 C10 VJK sing 420 n n N C4 VJK sing 421 n n C10 N2 VJK doub 422 n y C10 N3 VJK sing 423 n y O C4 VJK doub 424 n n N2 C9 VJK sing 425 n y C C1 VJK sing 426 n n N3 C7 VJK doub 427 n y C4 C2 VJK sing 428 n n C9 C8 VJK doub 429 n y C7 C8 VJK sing 430 n y C7 N1 VJK sing 431 n n C1 C2 VJK sing 432 n n C2 N1 VJK sing 433 n n C2 C3 VJK sing 434 n n C1 H1 VJK sing 435 n n C1 H2 VJK sing 436 n n C3 H3 VJK sing 437 n n C3 H4 VJK sing 438 n n C3 H5 VJK sing 439 n n C5 H6 VJK sing 440 n n C5 H7 VJK sing 441 n n C8 H8 VJK sing 442 n n C9 H9 VJK sing 443 n n C12 H10 VJK sing 444 n n N H11 VJK sing 445 n n C H12 VJK sing 446 n n C H13 VJK sing 447 n n C H14 VJK sing 448 n n N1 H15 VJK sing 449 n n C15 H16 VJK sing 450 n n C16 H17 VJK sing 451 n n C17 H18 VJK sing 452 n n N4 H19 VJK sing 453 n n # _atom_sites.entry_id 4YTI _atom_sites.fract_transf_matrix[1][1] 0.010534 _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] 0.009903 _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] 0.014618 _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 VJK A 1 4000 4000 VJK 509 . C 3 HOH A 1 4101 13 HOH HOH . C 3 HOH A 2 4102 38 HOH HOH . C 3 HOH A 3 4103 14 HOH HOH . C 3 HOH A 4 4104 10 HOH HOH . C 3 HOH A 5 4105 11 HOH HOH . C 3 HOH A 6 4106 7 HOH HOH . C 3 HOH A 7 4107 2 HOH HOH . C 3 HOH A 8 4108 6 HOH HOH . C 3 HOH A 9 4109 30 HOH HOH . C 3 HOH A 10 4110 26 HOH HOH . C 3 HOH A 11 4111 4 HOH HOH . C 3 HOH A 12 4112 28 HOH HOH . C 3 HOH A 13 4113 20 HOH HOH . C 3 HOH A 14 4114 36 HOH HOH . C 3 HOH A 15 4115 34 HOH HOH . C 3 HOH A 16 4116 8 HOH HOH . C 3 HOH A 17 4117 15 HOH HOH . C 3 HOH A 18 4118 9 HOH HOH . C 3 HOH A 19 4119 27 HOH HOH . C 3 HOH A 20 4120 17 HOH HOH . C 3 HOH A 21 4121 21 HOH HOH . C 3 HOH A 22 4122 3 HOH HOH . C 3 HOH A 23 4123 16 HOH HOH . C 3 HOH A 24 4124 29 HOH HOH . C 3 HOH A 25 4125 19 HOH HOH . C 3 HOH A 26 4126 31 HOH HOH . C 3 HOH A 27 4127 22 HOH HOH . C 3 HOH A 28 4128 33 HOH HOH . C 3 HOH A 29 4129 35 HOH HOH . C 3 HOH A 30 4130 5 HOH HOH . C 3 HOH A 31 4131 32 HOH HOH . C 3 HOH A 32 4132 23 HOH HOH . C 3 HOH A 33 4133 24 HOH HOH . C 3 HOH A 34 4134 40 HOH HOH . C 3 HOH A 35 4135 18 HOH HOH . C 3 HOH A 36 4136 25 HOH HOH . C 3 HOH A 37 4137 39 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 VJK . . . B 2 13.989 14.299 5.17 1 52.26 ? C1 VJK 4000 A 1 HETATM 2 C C2 VJK . . . B 2 15.383 14.891 5.437 1 53.92 ? C2 VJK 4000 A 1 HETATM 3 C C3 VJK . . . B 2 15.412 15.639 6.757 1 54.5 ? C3 VJK 4000 A 1 HETATM 4 C C4 VJK . . . B 2 15.781 15.888 4.329 1 58.25 ? C4 VJK 4000 A 1 HETATM 5 C C5 VJK . . . B 2 16.813 14.917 2.273 1 58.6 ? C5 VJK 4000 A 1 HETATM 6 C C6 VJK . . . B 2 15.796 14.909 1.174 1 58.17 ? C6 VJK 4000 A 1 HETATM 7 C C7 VJK . . . B 2 16.574 12.518 4.919 1 45.68 ? C7 VJK 4000 A 1 HETATM 8 C C8 VJK . . . B 2 17.831 11.908 5.151 1 43.83 ? C8 VJK 4000 A 1 HETATM 9 C C9 VJK . . . B 2 18.002 10.595 4.741 1 42.86 ? C9 VJK 4000 A 1 HETATM 10 C C10 VJK . . . B 2 15.768 10.611 3.977 1 40 ? C10 VJK 4000 A 1 HETATM 11 C C11 VJK . . . B 2 14.658 9.923 3.307 1 33.71 ? C11 VJK 4000 A 1 HETATM 12 C C12 VJK . . . B 2 14.738 8.607 2.925 1 32.42 ? C12 VJK 4000 A 1 HETATM 13 C C13 VJK . . . B 2 12.768 9.329 2.12 1 32.7 ? C13 VJK 4000 A 1 HETATM 14 F F2 VJK . . . B 2 16.271 14.43 0.112 1 59.43 ? F2 VJK 4000 A 1 HETATM 15 F F VJK . . . B 2 15.36 16.057 0.878 1 59.24 ? F VJK 4000 A 1 HETATM 16 F F1 VJK . . . B 2 14.779 14.239 1.452 1 57.96 ? F1 VJK 4000 A 1 HETATM 17 N N VJK . . . B 2 16.835 15.488 3.621 1 59.31 ? N VJK 4000 A 1 HETATM 18 O O VJK . . . B 2 15.125 16.911 4.101 1 57.75 ? O VJK 4000 A 1 HETATM 19 C C VJK . . . B 2 13.096 15.056 4.189 1 51.7 ? C VJK 4000 A 1 HETATM 20 N N1 VJK . . . B 2 16.359 13.791 5.475 1 49.91 ? N1 VJK 4000 A 1 HETATM 21 N N3 VJK . . . B 2 15.551 11.889 4.317 1 43.91 ? N3 VJK 4000 A 1 HETATM 22 N N2 VJK . . . B 2 17.05 9.86 4.168 1 42 ? N2 VJK 4000 A 1 HETATM 23 C C14 VJK . . . B 2 13.335 10.399 2.828 1 32.58 ? C14 VJK 4000 A 1 HETATM 24 C C15 VJK . . . B 2 12.667 11.62 2.745 1 32.57 ? C15 VJK 4000 A 1 HETATM 25 C C16 VJK . . . B 2 11.519 11.73 1.96 1 30.65 ? C16 VJK 4000 A 1 HETATM 26 C C17 VJK . . . B 2 11.06 10.624 1.285 1 29.74 ? C17 VJK 4000 A 1 HETATM 27 N N5 VJK . . . B 2 11.647 9.406 1.35 1 31.78 ? N5 VJK 4000 A 1 HETATM 28 N N4 VJK . . . B 2 13.6 8.244 2.217 1 33.04 ? N4 VJK 4000 A 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 444 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #