data_5D11 # _model_server_result.job_id zSdCDEWFCZrFZBcHOQT-Dw _model_server_result.datetime_utc '2024-11-24 08:32:21' _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 5d11 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 5D11 # _exptl.entry_id 5D11 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 434.494 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[3-({4-(4-methylpiperazin-1-yl)-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}oxy)phenyl]prop-2-enamide _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 78.65 _cell.angle_beta 89.55 _cell.angle_gamma 90.29 _cell.entry_id 5D11 _cell.length_a 42.12 _cell.length_b 63.43 _cell.length_c 75.35 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D11 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 software_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F 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 SG CYS 98 A CYS 345 1_555 D CAA 56G . A 56G 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.633 ? covale ? covale2 B SG CYS 98 B CYS 345 1_555 F CAA 56G . B 56G 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.649 ? # _chem_comp.formula 'C22 H26 N8 O2' _chem_comp.formula_weight 434.494 _chem_comp.id 56G _chem_comp.mon_nstd_flag . _chem_comp.name N-[3-({4-(4-methylpiperazin-1-yl)-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}oxy)phenyl]prop-2-enamide _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 CAA CAK 56G doub 1 n n CAK CAW 56G sing 2 n n CAW NAS 56G sing 3 n n CAW OAD 56G doub 4 n n CAC NBE 56G sing 5 n n NAS CAY 56G sing 6 n n CAM NBE 56G sing 7 n n CAM CAO 56G sing 8 n n NBE CAL 56G sing 9 n n CAY CAF 56G doub 10 n y CAY CAH 56G sing 11 n y CAL CAN 56G sing 12 n n CAF CAE 56G sing 13 n y CAO NBF 56G sing 14 n n CAH CAZ 56G doub 15 n y NBF CAN 56G sing 16 n n NBF C4 56G sing 17 n n CAE CAG 56G doub 18 n y C4 N3 56G doub 19 n y C4 C5 56G sing 20 n y N3 C2 56G sing 21 n y CAZ CAG 56G sing 22 n y CAZ OAV 56G sing 23 n n C5 C6 56G doub 24 n y C2 OAV 56G sing 25 n n C2 N1 56G doub 26 n y C6 N1 56G sing 27 n y C6 NAT 56G sing 28 n n NAT CBA 56G sing 29 n n CBA CAI 56G sing 30 n y CBA NAP 56G doub 31 n y CAI CAX 56G doub 32 n y NAP NAU 56G sing 33 n y CAX NAU 56G sing 34 n y CAX CAB 56G sing 35 n n C5 H1 56G sing 36 n n CAN H2 56G sing 37 n n CAN H3 56G sing 38 n n CAL H4 56G sing 39 n n CAL H5 56G sing 40 n n CAC H7 56G sing 41 n n CAC H8 56G sing 42 n n CAC H9 56G sing 43 n n CAM H10 56G sing 44 n n CAM H11 56G sing 45 n n CAO H12 56G sing 46 n n CAO H13 56G sing 47 n n NAT H14 56G sing 48 n n CAI H15 56G sing 49 n n CAB H16 56G sing 50 n n CAB H17 56G sing 51 n n CAB H18 56G sing 52 n n NAU H19 56G sing 53 n n CAH H20 56G sing 54 n n CAG H21 56G sing 55 n n CAE H22 56G sing 56 n n CAF H23 56G sing 57 n n NAS H24 56G sing 58 n n CAK H25 56G sing 59 n n CAA H27 56G sing 60 n n CAA H28 56G sing 61 n n # _atom_sites.entry_id 5D11 _atom_sites.fract_transf_matrix[1][1] 0.023742 _atom_sites.fract_transf_matrix[1][2] 0.000118 _atom_sites.fract_transf_matrix[1][3] -0.000213 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015766 _atom_sites.fract_transf_matrix[2][3] -0.003164 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.013536 _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 C 2 GOL A 1 601 1 GOL GOL . D 3 56G A 1 602 2 56G DRG . E 2 GOL B 1 601 2 GOL GOL . F 3 56G B 1 602 3 56G DRG . G 4 HOH A 1 701 91 HOH HOH . G 4 HOH A 2 702 93 HOH HOH . G 4 HOH A 3 703 35 HOH HOH . G 4 HOH A 4 704 85 HOH HOH . G 4 HOH A 5 705 43 HOH HOH . G 4 HOH A 6 706 38 HOH HOH . G 4 HOH A 7 707 66 HOH HOH . G 4 HOH A 8 708 71 HOH HOH . G 4 HOH A 9 709 83 HOH HOH . G 4 HOH A 10 710 3 HOH HOH . G 4 HOH A 11 711 10 HOH HOH . G 4 HOH A 12 712 21 HOH HOH . G 4 HOH A 13 713 15 HOH HOH . G 4 HOH A 14 714 6 HOH HOH . G 4 HOH A 15 715 97 HOH HOH . G 4 HOH A 16 716 5 HOH HOH . G 4 HOH A 17 717 25 HOH HOH . G 4 HOH A 18 718 73 HOH HOH . G 4 HOH A 19 719 82 HOH HOH . G 4 HOH A 20 720 40 HOH HOH . G 4 HOH A 21 721 67 HOH HOH . G 4 HOH A 22 722 95 HOH HOH . G 4 HOH A 23 723 77 HOH HOH . G 4 HOH A 24 724 79 HOH HOH . G 4 HOH A 25 725 22 HOH HOH . G 4 HOH A 26 726 23 HOH HOH . G 4 HOH A 27 727 9 HOH HOH . G 4 HOH A 28 728 2 HOH HOH . G 4 HOH A 29 729 42 HOH HOH . G 4 HOH A 30 730 55 HOH HOH . G 4 HOH A 31 731 12 HOH HOH . G 4 HOH A 32 732 99 HOH HOH . G 4 HOH A 33 733 47 HOH HOH . G 4 HOH A 34 734 37 HOH HOH . G 4 HOH A 35 735 1 HOH HOH . G 4 HOH A 36 736 54 HOH HOH . G 4 HOH A 37 737 94 HOH HOH . G 4 HOH A 38 738 29 HOH HOH . G 4 HOH A 39 739 41 HOH HOH . G 4 HOH A 40 740 33 HOH HOH . G 4 HOH A 41 741 80 HOH HOH . G 4 HOH A 42 742 11 HOH HOH . G 4 HOH A 43 743 19 HOH HOH . G 4 HOH A 44 744 76 HOH HOH . G 4 HOH A 45 745 96 HOH HOH . G 4 HOH A 46 746 74 HOH HOH . G 4 HOH A 47 747 45 HOH HOH . G 4 HOH A 48 748 75 HOH HOH . G 4 HOH A 49 749 30 HOH HOH . G 4 HOH A 50 750 103 HOH HOH . G 4 HOH A 51 751 86 HOH HOH . G 4 HOH A 52 752 98 HOH HOH . H 4 HOH B 1 701 60 HOH HOH . H 4 HOH B 2 702 88 HOH HOH . H 4 HOH B 3 703 48 HOH HOH . H 4 HOH B 4 704 65 HOH HOH . H 4 HOH B 5 705 32 HOH HOH . H 4 HOH B 6 706 14 HOH HOH . H 4 HOH B 7 707 70 HOH HOH . H 4 HOH B 8 708 84 HOH HOH . H 4 HOH B 9 709 78 HOH HOH . H 4 HOH B 10 710 61 HOH HOH . H 4 HOH B 11 711 52 HOH HOH . H 4 HOH B 12 712 90 HOH HOH . H 4 HOH B 13 713 34 HOH HOH . H 4 HOH B 14 714 62 HOH HOH . H 4 HOH B 15 715 57 HOH HOH . H 4 HOH B 16 716 28 HOH HOH . H 4 HOH B 17 717 27 HOH HOH . H 4 HOH B 18 718 69 HOH HOH . H 4 HOH B 19 719 59 HOH HOH . H 4 HOH B 20 720 13 HOH HOH . H 4 HOH B 21 721 92 HOH HOH . H 4 HOH B 22 722 8 HOH HOH . H 4 HOH B 23 723 44 HOH HOH . H 4 HOH B 24 724 64 HOH HOH . H 4 HOH B 25 725 4 HOH HOH . H 4 HOH B 26 726 24 HOH HOH . H 4 HOH B 27 727 36 HOH HOH . H 4 HOH B 28 728 39 HOH HOH . H 4 HOH B 29 729 89 HOH HOH . H 4 HOH B 30 730 87 HOH HOH . H 4 HOH B 31 731 49 HOH HOH . H 4 HOH B 32 732 17 HOH HOH . H 4 HOH B 33 733 81 HOH HOH . H 4 HOH B 34 734 46 HOH HOH . H 4 HOH B 35 735 26 HOH HOH . H 4 HOH B 36 736 101 HOH HOH . H 4 HOH B 37 737 31 HOH HOH . H 4 HOH B 38 738 72 HOH HOH . H 4 HOH B 39 739 68 HOH HOH . H 4 HOH B 40 740 7 HOH HOH . H 4 HOH B 41 741 56 HOH HOH . H 4 HOH B 42 742 50 HOH HOH . H 4 HOH B 43 743 100 HOH HOH . H 4 HOH B 44 744 102 HOH HOH . H 4 HOH B 45 745 51 HOH HOH . H 4 HOH B 46 746 58 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 C4 56G . . . D 3 -12.773 -39.641 5.162 1 28.21 ? C4 56G 602 A 1 HETATM 2 C C5 56G . . . D 3 -13.012 -38.417 5.809 1 26.65 ? C5 56G 602 A 1 HETATM 3 C C6 56G . . . D 3 -12.016 -37.764 6.497 1 26.99 ? C6 56G 602 A 1 HETATM 4 N N1 56G . . . D 3 -10.851 -38.378 6.54 1 31.17 ? N1 56G 602 A 1 HETATM 5 N N3 56G . . . D 3 -11.531 -40.165 5.256 1 28.73 ? N3 56G 602 A 1 HETATM 6 C CAN 56G . . . D 3 -15.142 -39.945 4.54 1 30.41 ? CAN 56G 602 A 1 HETATM 7 C CAL 56G . . . D 3 -15.711 -40.101 3.309 1 32.73 ? CAL 56G 602 A 1 HETATM 8 N NBE 56G . . . D 3 -15.694 -41.528 2.883 1 37.07 ? NBE 56G 602 A 1 HETATM 9 C CAC 56G . . . D 3 -16.602 -41.708 1.697 1 37.11 ? CAC 56G 602 A 1 HETATM 10 C CAM 56G . . . D 3 -14.388 -42.123 2.679 1 31.66 ? CAM 56G 602 A 1 HETATM 11 C CAO 56G . . . D 3 -13.396 -41.646 3.791 1 33.89 ? CAO 56G 602 A 1 HETATM 12 N NBF 56G . . . D 3 -13.737 -40.317 4.461 1 29.09 ? NBF 56G 602 A 1 HETATM 13 N NAT 56G . . . D 3 -12.259 -36.564 7.16 1 30.67 ? NAT 56G 602 A 1 HETATM 14 C CBA 56G . . . D 3 -11.307 -35.877 7.9 1 27.61 ? CBA 56G 602 A 1 HETATM 15 C CAI 56G . . . D 3 -10.04 -36.184 8.264 1 27.03 ? CAI 56G 602 A 1 HETATM 16 C CAX 56G . . . D 3 -9.595 -35.139 8.973 1 26.36 ? CAX 56G 602 A 1 HETATM 17 C CAB 56G . . . D 3 -8.222 -34.963 9.618 1 28.53 ? CAB 56G 602 A 1 HETATM 18 N NAU 56G . . . D 3 -10.514 -34.212 9.026 1 25.28 ? NAU 56G 602 A 1 HETATM 19 N NAP 56G . . . D 3 -11.522 -34.646 8.402 1 27.13 ? NAP 56G 602 A 1 HETATM 20 C C2 56G . . . D 3 -10.569 -39.542 5.978 1 33.36 ? C2 56G 602 A 1 HETATM 21 O OAV 56G . . . D 3 -9.279 -39.977 6.172 1 38.09 ? OAV 56G 602 A 1 HETATM 22 C CAZ 56G . . . D 3 -8.986 -41.024 5.34 1 45.28 ? CAZ 56G 602 A 1 HETATM 23 C CAH 56G . . . D 3 -8.542 -40.786 4.029 1 46.59 ? CAH 56G 602 A 1 HETATM 24 C CAG 56G . . . D 3 -9.147 -42.339 5.791 1 45.62 ? CAG 56G 602 A 1 HETATM 25 C CAE 56G . . . D 3 -8.861 -43.396 4.917 1 52.45 ? CAE 56G 602 A 1 HETATM 26 C CAF 56G . . . D 3 -8.409 -43.171 3.606 1 45.64 ? CAF 56G 602 A 1 HETATM 27 C CAY 56G . . . D 3 -8.286 -41.862 3.13 1 48.89 ? CAY 56G 602 A 1 HETATM 28 N NAS 56G . . . D 3 -7.817 -41.82 1.86 1 46.73 ? NAS 56G 602 A 1 HETATM 29 C CAW 56G . . . D 3 -6.927 -40.934 1.442 1 35.53 ? CAW 56G 602 A 1 HETATM 30 O OAD 56G . . . D 3 -6.655 -39.893 2.021 1 41.6 ? OAD 56G 602 A 1 HETATM 31 C CAK 56G . . . D 3 -6.27 -41.276 0.131 1 34.83 ? CAK 56G 602 A 1 HETATM 32 C CAA 56G . . . D 3 -6.535 -40.221 -0.918 1 37.41 ? CAA 56G 602 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 218 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #