data_2VF0 # _model_server_result.job_id t0w0mWlMN-W7UymNGjyRCw _model_server_result.datetime_utc '2024-12-22 11:43:29' _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 2vf0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1266}' # _entry.id 2VF0 # _exptl.entry_id 2VF0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 500.503 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC 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 120 _cell.entry_id 2VF0 _cell.length_a 127.16 _cell.length_b 127.16 _cell.length_c 67.95 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VF0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PQS _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 _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 # 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 C CXM 1 A CXM 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale2 A SG CYS 146 A CYS 146 1_555 C C6 NDU . A NDU 1265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.929 ? covale ? covale3 B C CXM 1 B CXM 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale4 B SG CYS 146 B CYS 146 1_555 E C6 NDU . B NDU 1265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.874 ? # _chem_comp.formula 'C27 H24 N4 O6' _chem_comp.formula_weight 500.503 _chem_comp.id F89 _chem_comp.mon_nstd_flag . _chem_comp.name 'S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'FOLATE ANALOG 1843U89' # 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 C1 O1A F89 doub 105 n n C1 N2 F89 sing 106 n y C1 C1A F89 sing 107 n y N2 C3 F89 sing 108 n y N2 HN2 F89 sing 109 n n C3 C3M F89 sing 110 n n C3 N4 F89 doub 111 n y C3M H3M1 F89 sing 112 n n C3M H3M2 F89 sing 113 n n C3M H3M3 F89 sing 114 n n N4 C4A F89 sing 115 n y C4A C5 F89 doub 116 n y C4A C1A F89 sing 117 n y C5 C6 F89 sing 118 n y C5 H5 F89 sing 119 n n C6 C6A F89 doub 120 n y C6 H6 F89 sing 121 n n C6A C7 F89 sing 122 n y C6A C1B F89 sing 123 n y C7 C8 F89 doub 124 n y C7 H7 F89 sing 125 n n C8 C9 F89 sing 126 n y C8 H8 F89 sing 127 n n C9 C10 F89 doub 128 n y C9 C11 F89 sing 129 n n C10 C1B F89 sing 130 n y C10 H10 F89 sing 131 n n C1B C1A F89 doub 132 n y C11 N12 F89 sing 133 n n C11 H111 F89 sing 134 n n C11 H112 F89 sing 135 n n N12 C13 F89 sing 136 n n N12 HN12 F89 sing 137 n n C13 C14 F89 doub 138 n y C13 C18 F89 sing 139 n y C14 C15 F89 sing 140 n y C14 H14 F89 sing 141 n n C15 C16 F89 doub 142 n y C15 C19 F89 sing 143 n n C16 C17 F89 sing 144 n y C16 C F89 sing 145 n n C17 C18 F89 doub 146 n y C17 H17 F89 sing 147 n n C18 H18 F89 sing 148 n n C19 N F89 sing 149 n n C19 H191 F89 sing 150 n n C19 H192 F89 sing 151 n n C O F89 doub 152 n n C N F89 sing 153 n n N CA F89 sing 154 n n CA CT F89 sing 155 n n CA CB F89 sing 156 n n CA HA F89 sing 157 n n CT O1 F89 doub 158 n n CT O2 F89 sing 159 n n O2 HO2 F89 sing 160 n n CB CG F89 sing 161 n n CB HB1 F89 sing 162 n n CB HB2 F89 sing 163 n n CG CD F89 sing 164 n n CG HG1 F89 sing 165 n n CG HG2 F89 sing 166 n n CD OE1 F89 doub 167 n n CD OE2 F89 sing 168 n n OE2 HOE2 F89 sing 169 n n # _atom_sites.entry_id 2VF0 _atom_sites.fract_transf_matrix[1][1] 0.007864 _atom_sites.fract_transf_matrix[1][2] 0.00454 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009081 _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] 0.014717 _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 NDU A 1 1265 1265 NDU NDU . D 3 F89 A 1 1266 1266 F89 F89 . E 2 NDU B 1 1265 1265 NDU NDU . F 3 F89 B 1 1266 1266 F89 F89 . G 4 SO4 B 1 1268 1268 SO4 SO4 . H 5 HOH A 1 2001 2001 HOH HOH . H 5 HOH A 2 2002 2002 HOH HOH . H 5 HOH A 3 2003 2003 HOH HOH . H 5 HOH A 4 2004 2004 HOH HOH . H 5 HOH A 5 2005 2005 HOH HOH . H 5 HOH A 6 2006 2006 HOH HOH . H 5 HOH A 7 2007 2007 HOH HOH . H 5 HOH A 8 2008 2008 HOH HOH . H 5 HOH A 9 2009 2009 HOH HOH . H 5 HOH A 10 2010 2010 HOH HOH . H 5 HOH A 11 2011 2011 HOH HOH . H 5 HOH A 12 2012 2012 HOH HOH . H 5 HOH A 13 2013 2013 HOH HOH . I 5 HOH B 1 2001 2001 HOH HOH . I 5 HOH B 2 2002 2002 HOH HOH . I 5 HOH B 3 2003 2003 HOH HOH . I 5 HOH B 4 2004 2004 HOH HOH . I 5 HOH B 5 2005 2005 HOH HOH . I 5 HOH B 6 2006 2006 HOH HOH . I 5 HOH B 7 2007 2007 HOH HOH . I 5 HOH B 8 2008 2008 HOH HOH . I 5 HOH B 9 2009 2009 HOH HOH . I 5 HOH B 10 2010 2010 HOH HOH . I 5 HOH B 11 2011 2011 HOH HOH . I 5 HOH B 12 2012 2012 HOH HOH . I 5 HOH B 13 2013 2013 HOH HOH . I 5 HOH B 14 2014 2014 HOH HOH . I 5 HOH B 15 2015 2015 HOH HOH . I 5 HOH B 16 2016 2016 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 F89 . . . D 3 14.578 18.308 32.899 1 39.72 ? C1 F89 1266 A 1 HETATM 2 O O1A F89 . . . D 3 15.148 18.294 33.974 1 39.62 ? O1A F89 1266 A 1 HETATM 3 N N2 F89 . . . D 3 13.614 19.243 32.715 1 39.79 ? N2 F89 1266 A 1 HETATM 4 C C3 F89 . . . D 3 12.87 19.36 31.466 1 40.38 ? C3 F89 1266 A 1 HETATM 5 C C3M F89 . . . D 3 11.831 20.41 31.291 1 38.71 ? C3M F89 1266 A 1 HETATM 6 N N4 F89 . . . D 3 13.112 18.549 30.478 1 40.69 ? N4 F89 1266 A 1 HETATM 7 C C4A F89 . . . D 3 14.11 17.483 30.504 1 40.38 ? C4A F89 1266 A 1 HETATM 8 C C5 F89 . . . D 3 14.299 16.654 29.389 1 39.81 ? C5 F89 1266 A 1 HETATM 9 C C6 F89 . . . D 3 15.254 15.622 29.375 1 41.03 ? C6 F89 1266 A 1 HETATM 10 C C6A F89 . . . D 3 16.088 15.377 30.495 1 41.68 ? C6A F89 1266 A 1 HETATM 11 C C7 F89 . . . D 3 17.073 14.337 30.465 1 42.15 ? C7 F89 1266 A 1 HETATM 12 C C8 F89 . . . D 3 17.916 14.104 31.563 1 42.83 ? C8 F89 1266 A 1 HETATM 13 C C9 F89 . . . D 3 17.788 14.917 32.737 1 43.88 ? C9 F89 1266 A 1 HETATM 14 C C10 F89 . . . D 3 16.811 15.95 32.81 1 42.76 ? C10 F89 1266 A 1 HETATM 15 C C1B F89 . . . D 3 15.944 16.21 31.699 1 41.63 ? C1B F89 1266 A 1 HETATM 16 C C1A F89 . . . D 3 14.931 17.281 31.711 1 40.66 ? C1A F89 1266 A 1 HETATM 17 C C11 F89 . . . D 3 18.664 14.762 33.994 1 45.47 ? C11 F89 1266 A 1 HETATM 18 N N12 F89 . . . D 3 19.24 13.434 34.266 1 47.48 ? N12 F89 1266 A 1 HETATM 19 C C13 F89 . . . D 3 18.406 12.38 34.829 1 49.11 ? C13 F89 1266 A 1 HETATM 20 C C14 F89 . . . D 3 17.022 12.726 35.082 1 50.68 ? C14 F89 1266 A 1 HETATM 21 C C15 F89 . . . D 3 16.19 11.773 35.619 1 52.77 ? C15 F89 1266 A 1 HETATM 22 C C16 F89 . . . D 3 16.629 10.489 35.921 1 53.57 ? C16 F89 1266 A 1 HETATM 23 C C17 F89 . . . D 3 17.993 10.104 35.68 1 52.05 ? C17 F89 1266 A 1 HETATM 24 C C18 F89 . . . D 3 18.868 11.072 35.125 1 49.84 ? C18 F89 1266 A 1 HETATM 25 C C19 F89 . . . D 3 15.141 12.11 36.685 1 53.56 ? C19 F89 1266 A 1 HETATM 26 C C F89 . . . D 3 15.454 9.749 36.502 1 54.61 ? C F89 1266 A 1 HETATM 27 O O F89 . . . D 3 15.486 8.527 36.469 1 55.16 ? O F89 1266 A 1 HETATM 28 N N F89 . . . D 3 14.661 10.712 37.023 1 54.65 ? N F89 1266 A 1 HETATM 29 C CA F89 . . . D 3 13.374 10.553 37.875 1 55.14 ? CA F89 1266 A 1 HETATM 30 C CT F89 . . . D 3 13.791 10.04 39.35 1 56.7 ? CT F89 1266 A 1 HETATM 31 O O1 F89 . . . D 3 14.277 8.737 39.325 1 57.58 ? O1 F89 1266 A 1 HETATM 32 O O2 F89 . . . D 3 13.601 10.783 40.338 1 57.61 ? O2 F89 1266 A 1 HETATM 33 C CB F89 . . . D 3 12.398 9.525 37.076 1 54.06 ? CB F89 1266 A 1 HETATM 34 C CG F89 . . . D 3 11.984 10.132 35.62 1 55.17 ? CG F89 1266 A 1 HETATM 35 C CD F89 . . . D 3 11.363 9.028 34.728 1 56.54 ? CD F89 1266 A 1 HETATM 36 O OE1 F89 . . . D 3 10.265 9.123 34.146 1 55.9 ? OE1 F89 1266 A 1 HETATM 37 O OE2 F89 . . . D 3 12.232 7.955 34.687 1 56.11 ? OE2 F89 1266 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 37 #