data_4AGD # _model_server_result.job_id M25XgyUFyJ_LXJLZidjwBQ _model_server_result.datetime_utc '2024-11-30 05:55:10' _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 4agd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2000}' # _entry.id 4AGD # _exptl.entry_id 4AGD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.474 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide' _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 94.34 _cell.angle_gamma 90 _cell.entry_id 4AGD _cell.length_a 134.694 _cell.length_b 56.98 _cell.length_c 52.72 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AGD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _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 # _chem_comp.formula 'C22 H27 F N4 O2' _chem_comp.formula_weight 398.474 _chem_comp.id B49 _chem_comp.mon_nstd_flag . _chem_comp.name 'N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SUNITINIB # 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 C4 C14 B49 sing 70 n n C4 H4 B49 sing 71 n n C4 H4A B49 sing 72 n n C4 H4B B49 sing 73 n n C5 C6 B49 doub 74 n y C5 C15 B49 sing 75 n y C5 H5 B49 sing 76 n n C6 C16 B49 sing 77 n y C6 H6 B49 sing 78 n n C7 C15 B49 doub 79 n y C7 C17 B49 sing 80 n y C7 H7 B49 sing 81 n n C13 C3 B49 sing 82 n n C13 C18 B49 doub 83 n y C13 C19 B49 sing 84 n y C15 F29 B49 sing 85 n n C17 C20 B49 sing 86 n n C17 C16 B49 doub 87 n y C20 C21 B49 sing 88 n n C20 C12 B49 doub 89 z n C21 N24 B49 sing 90 n n C21 O27 B49 doub 91 n n C22 C19 B49 sing 92 n n C22 N25 B49 sing 93 n n C22 O28 B49 doub 94 n n C3 H3 B49 sing 95 n n C3 H3A B49 sing 96 n n C3 H3B B49 sing 97 n n C12 C18 B49 sing 98 n n C12 H12 B49 sing 99 n n C14 C19 B49 doub 100 n y C14 N23 B49 sing 101 n y C16 N24 B49 sing 102 n n C18 N23 B49 sing 103 n y N23 HN23 B49 sing 104 n n N24 HN24 B49 sing 105 n n N25 HN25 B49 sing 106 n n N25 C37 B49 sing 107 n n C37 C38 B49 sing 108 n n C38 N4 B49 sing 109 n n N4 C39 B49 sing 110 n n N4 C40 B49 sing 111 n n C40 C41 B49 sing 112 n n C39 C42 B49 sing 113 n n C37 H14 B49 sing 114 n n C37 H15 B49 sing 115 n n C38 H16 B49 sing 116 n n C38 H17 B49 sing 117 n n C39 H18 B49 sing 118 n n C39 H19 B49 sing 119 n n C40 H20 B49 sing 120 n n C40 H21 B49 sing 121 n n C41 H22 B49 sing 122 n n C41 H23 B49 sing 123 n n C41 H24 B49 sing 124 n n C42 H25 B49 sing 125 n n C42 H26 B49 sing 126 n n C42 H27 B49 sing 127 n n # _atom_sites.entry_id 4AGD _atom_sites.fract_transf_matrix[1][1] 0.007424 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000563 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01755 _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] 0.019023 _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 B49 A 1 2000 2000 B49 B49 . C 3 HOH A 1 2001 2001 HOH HOH . C 3 HOH A 2 2002 2002 HOH HOH . C 3 HOH A 3 2003 2003 HOH HOH . C 3 HOH A 4 2004 2004 HOH HOH . C 3 HOH A 5 2005 2005 HOH HOH . C 3 HOH A 6 2006 2006 HOH HOH . C 3 HOH A 7 2007 2007 HOH HOH . C 3 HOH A 8 2008 2008 HOH HOH . C 3 HOH A 9 2009 2009 HOH HOH . C 3 HOH A 10 2010 2010 HOH HOH . C 3 HOH A 11 2011 2011 HOH HOH . C 3 HOH A 12 2012 2012 HOH HOH . C 3 HOH A 13 2013 2013 HOH HOH . C 3 HOH A 14 2014 2014 HOH HOH . C 3 HOH A 15 2015 2015 HOH HOH . C 3 HOH A 16 2016 2016 HOH HOH . C 3 HOH A 17 2017 2017 HOH HOH . C 3 HOH A 18 2018 2018 HOH HOH . C 3 HOH A 19 2019 2019 HOH HOH . C 3 HOH A 20 2020 2020 HOH HOH . C 3 HOH A 21 2021 2021 HOH HOH . C 3 HOH A 22 2022 2022 HOH HOH . C 3 HOH A 23 2023 2023 HOH HOH . C 3 HOH A 24 2024 2024 HOH HOH . C 3 HOH A 25 2025 2025 HOH HOH . C 3 HOH A 26 2026 2026 HOH HOH . C 3 HOH A 27 2027 2027 HOH HOH . C 3 HOH A 28 2028 2028 HOH HOH . C 3 HOH A 29 2029 2029 HOH HOH . C 3 HOH A 30 2030 2030 HOH HOH . C 3 HOH A 31 2031 2031 HOH HOH . C 3 HOH A 32 2032 2032 HOH HOH . C 3 HOH A 33 2033 2033 HOH HOH . C 3 HOH A 34 2034 2034 HOH HOH . C 3 HOH A 35 2035 2035 HOH HOH . C 3 HOH A 36 2036 2036 HOH HOH . C 3 HOH A 37 2037 2037 HOH HOH . C 3 HOH A 38 2038 2038 HOH HOH . C 3 HOH A 39 2039 2039 HOH HOH . C 3 HOH A 40 2040 2040 HOH HOH . C 3 HOH A 41 2041 2041 HOH HOH . C 3 HOH A 42 2042 2042 HOH HOH . C 3 HOH A 43 2043 2043 HOH HOH . C 3 HOH A 44 2044 2044 HOH HOH . C 3 HOH A 45 2045 2045 HOH HOH . C 3 HOH A 46 2046 2046 HOH HOH . C 3 HOH A 47 2047 2047 HOH HOH . C 3 HOH A 48 2048 2048 HOH HOH . C 3 HOH A 49 2049 2049 HOH HOH . C 3 HOH A 50 2050 2050 HOH HOH . C 3 HOH A 51 2051 2051 HOH HOH . C 3 HOH A 52 2052 2052 HOH HOH . C 3 HOH A 53 2053 2053 HOH HOH . C 3 HOH A 54 2054 2054 HOH HOH . C 3 HOH A 55 2055 2055 HOH HOH . C 3 HOH A 56 2056 2056 HOH HOH . C 3 HOH A 57 2057 2057 HOH HOH . C 3 HOH A 58 2058 2058 HOH HOH . C 3 HOH A 59 2059 2059 HOH HOH . C 3 HOH A 60 2060 2060 HOH HOH . C 3 HOH A 61 2061 2061 HOH HOH . C 3 HOH A 62 2062 2062 HOH HOH . C 3 HOH A 63 2063 2063 HOH HOH . C 3 HOH A 64 2064 2064 HOH HOH . C 3 HOH A 65 2066 2066 HOH HOH . C 3 HOH A 66 2067 2067 HOH HOH . C 3 HOH A 67 2068 2068 HOH HOH . C 3 HOH A 68 2069 2069 HOH HOH . C 3 HOH A 69 2070 2070 HOH HOH . C 3 HOH A 70 2071 2071 HOH HOH . C 3 HOH A 71 2072 2072 HOH HOH . C 3 HOH A 72 2073 2073 HOH HOH . C 3 HOH A 73 2074 2074 HOH HOH . C 3 HOH A 74 2075 2075 HOH HOH . C 3 HOH A 75 2076 2076 HOH HOH . C 3 HOH A 76 2077 2077 HOH HOH . C 3 HOH A 77 2078 2078 HOH HOH . C 3 HOH A 78 2079 2079 HOH HOH . C 3 HOH A 79 2080 2080 HOH HOH . C 3 HOH A 80 2081 2081 HOH HOH . C 3 HOH A 81 2082 2082 HOH HOH . C 3 HOH A 82 2083 2083 HOH HOH . C 3 HOH A 83 2084 2084 HOH HOH . C 3 HOH A 84 2085 2085 HOH HOH . C 3 HOH A 85 2086 2086 HOH HOH . C 3 HOH A 86 2087 2087 HOH HOH . C 3 HOH A 87 2088 2088 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 B49 . . . B 2 50.682 0.367 -16.161 1 48.44 ? C4 B49 2000 A 1 HETATM 2 C C5 B49 . . . B 2 42.976 -4.097 -12.093 1 46.93 ? C5 B49 2000 A 1 HETATM 3 C C6 B49 . . . B 2 43.108 -2.817 -12.696 1 43.16 ? C6 B49 2000 A 1 HETATM 4 C C7 B49 . . . B 2 45.297 -4.67 -12.56 1 45.29 ? C7 B49 2000 A 1 HETATM 5 C C13 B49 . . . B 2 50.404 -3.166 -14.744 1 48.75 ? C13 B49 2000 A 1 HETATM 6 C C15 B49 . . . B 2 44.056 -5.026 -12.021 1 46.91 ? C15 B49 2000 A 1 HETATM 7 C C17 B49 . . . B 2 45.434 -3.366 -13.177 1 43.9 ? C17 B49 2000 A 1 HETATM 8 C C20 B49 . . . B 2 46.622 -2.683 -13.838 1 43.86 ? C20 B49 2000 A 1 HETATM 9 C C21 B49 . . . B 2 46 -1.391 -14.221 1 40.96 ? C21 B49 2000 A 1 HETATM 10 C C22 B49 . . . B 2 52.749 -2.204 -15.773 1 57.19 ? C22 B49 2000 A 1 HETATM 11 C C3 B49 . . . B 2 50.672 -4.641 -14.265 1 43.4 ? C3 B49 2000 A 1 HETATM 12 C C12 B49 . . . B 2 47.945 -3.172 -14.021 1 43.39 ? C12 B49 2000 A 1 HETATM 13 C C14 B49 . . . B 2 50.436 -1.027 -15.562 1 49.83 ? C14 B49 2000 A 1 HETATM 14 C C16 B49 . . . B 2 44.352 -2.479 -13.233 1 41.24 ? C16 B49 2000 A 1 HETATM 15 C C18 B49 . . . B 2 49.144 -2.546 -14.615 1 45.93 ? C18 B49 2000 A 1 HETATM 16 C C19 B49 . . . B 2 51.278 -2.153 -15.375 1 51.55 ? C19 B49 2000 A 1 HETATM 17 N N23 B49 . . . B 2 49.221 -1.305 -15.109 1 47.9 ? N23 B49 2000 A 1 HETATM 18 N N24 B49 . . . B 2 44.698 -1.328 -13.849 1 38.68 ? N24 B49 2000 A 1 HETATM 19 N N25 B49 . . . B 2 53.348 -1.134 -16.341 1 64.68 ? N25 B49 2000 A 1 HETATM 20 O O27 B49 . . . B 2 46.569 -0.5 -14.792 1 39.38 ? O27 B49 2000 A 1 HETATM 21 O O28 B49 . . . B 2 53.489 -3.181 -15.613 1 55.46 ? O28 B49 2000 A 1 HETATM 22 F F29 B49 . . . B 2 43.84 -6.21 -11.441 1 48.65 ? F29 B49 2000 A 1 HETATM 23 C C37 B49 . . . B 2 54.767 -1.151 -16.725 1 72.35 ? C37 B49 2000 A 1 HETATM 24 C C38 B49 . . . B 2 55.744 -0.029 -16.262 1 75.73 ? C38 B49 2000 A 1 HETATM 25 N N4 B49 . . . B 2 57.062 -0.256 -16.965 1 81.36 ? N4 B49 2000 A 1 HETATM 26 C C39 B49 . . . B 2 58.179 -0.113 -15.931 1 83.55 ? C39 B49 2000 A 1 HETATM 27 C C40 B49 . . . B 2 57.2 0.651 -18.232 1 83.04 ? C40 B49 2000 A 1 HETATM 28 C C41 B49 . . . B 2 57.147 0.083 -19.684 1 82.57 ? C41 B49 2000 A 1 HETATM 29 C C42 B49 . . . B 2 59.693 -0.492 -16.2 1 84.17 ? C42 B49 2000 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 29 #