data_1PD8 # _model_server_result.job_id DgALvaK0tdmDH9zGLKah7g _model_server_result.datetime_utc '2024-10-18 16:22:14' _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 1pd8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 1PD8 # _exptl.entry_id 1PD8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.432 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,4-DIAMINO-5-METHYL-6-[(3,4,5-TRIMETHOXY-N-METHYLANILINO)METHYL]PYRIDO[2,3-D]PYRIMIDINE _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 120 _cell.entry_id 1PD8 _cell.length_a 85.873 _cell.length_b 85.873 _cell.length_c 77.637 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PD8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C19 H24 N6 O3' _chem_comp.formula_weight 384.432 _chem_comp.id CO4 _chem_comp.mon_nstd_flag . _chem_comp.name 2,4-DIAMINO-5-METHYL-6-[(3,4,5-TRIMETHOXY-N-METHYLANILINO)METHYL]PYRIDO[2,3-D]PYRIMIDINE _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 N2' C2D CO4 sing 70 n n N2' "H2'1" CO4 sing 71 n n N2' "H2'2" CO4 sing 72 n n C2D N3' CO4 doub 73 n y C2D N1' CO4 sing 74 n y N3' C4D CO4 sing 75 n y C4D N4' CO4 sing 76 n n C4D C4A CO4 doub 77 n y N4' "H4'1" CO4 sing 78 n n N4' "H4'2" CO4 sing 79 n n C4A C5D CO4 sing 80 n y C4A C8A CO4 sing 81 n y C5D C6D CO4 doub 82 n y C5D C51 CO4 sing 83 n n C6D C7' CO4 sing 84 n y C6D C8' CO4 sing 85 n n C7' N8' CO4 doub 86 n y C7' H7' CO4 sing 87 n n N8' C8A CO4 sing 88 n y C8A N1' CO4 doub 89 n y C8' N9' CO4 sing 90 n n C8' "H8'1" CO4 sing 91 n n C8' "H8'2" CO4 sing 92 n n N9' C1' CO4 sing 93 n n N9' C9' CO4 sing 94 n n C1' C6' CO4 doub 95 n y C1' C2' CO4 sing 96 n y C6' C5' CO4 sing 97 n y C6' H6' CO4 sing 98 n n C5' O5' CO4 sing 99 n n C5' C4' CO4 doub 100 n y O5' C5B CO4 sing 101 n n C5B H5B1 CO4 sing 102 n n C5B H5B2 CO4 sing 103 n n C5B H5B3 CO4 sing 104 n n C4' O4' CO4 sing 105 n n C4' C3' CO4 sing 106 n y O4' C4B CO4 sing 107 n n C4B H4B1 CO4 sing 108 n n C4B H4B2 CO4 sing 109 n n C4B H4B3 CO4 sing 110 n n C3' O3' CO4 sing 111 n n C3' C2' CO4 doub 112 n y O3' C3B CO4 sing 113 n n C3B H3B1 CO4 sing 114 n n C3B H3B2 CO4 sing 115 n n C3B H3B3 CO4 sing 116 n n C2' H2' CO4 sing 117 n n C9' "H9'1" CO4 sing 118 n n C9' "H9'2" CO4 sing 119 n n C9' "H9'3" CO4 sing 120 n n C51 H511 CO4 sing 121 n n C51 H512 CO4 sing 122 n n C51 H513 CO4 sing 123 n n # _atom_sites.entry_id 1PD8 _atom_sites.fract_transf_matrix[1][1] 0.011645 _atom_sites.fract_transf_matrix[1][2] 0.006723 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013447 _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] 0.01288 _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 NDP A 1 300 187 NDP COE . C 3 CO4 A 1 301 187 CO4 COE . D 4 HOH A 1 188 188 HOH WAT . D 4 HOH A 2 189 189 HOH WAT . D 4 HOH A 3 190 190 HOH WAT . D 4 HOH A 4 191 191 HOH WAT . D 4 HOH A 5 192 192 HOH WAT . D 4 HOH A 6 193 193 HOH WAT . D 4 HOH A 7 194 194 HOH WAT . D 4 HOH A 8 195 195 HOH WAT . D 4 HOH A 9 196 196 HOH WAT . D 4 HOH A 10 197 197 HOH WAT . D 4 HOH A 11 198 198 HOH WAT . D 4 HOH A 12 199 199 HOH WAT . D 4 HOH A 13 200 200 HOH WAT . D 4 HOH A 14 201 201 HOH WAT . D 4 HOH A 15 202 202 HOH WAT . D 4 HOH A 16 203 203 HOH WAT . D 4 HOH A 17 204 204 HOH WAT . D 4 HOH A 18 205 205 HOH WAT . D 4 HOH A 19 206 206 HOH WAT . D 4 HOH A 20 207 207 HOH WAT . D 4 HOH A 21 208 208 HOH WAT . D 4 HOH A 22 209 209 HOH WAT . D 4 HOH A 23 210 210 HOH WAT . D 4 HOH A 24 211 211 HOH WAT . D 4 HOH A 25 212 212 HOH WAT . D 4 HOH A 26 213 213 HOH WAT . D 4 HOH A 27 214 214 HOH WAT . D 4 HOH A 28 215 215 HOH WAT . D 4 HOH A 29 216 216 HOH WAT . D 4 HOH A 30 217 217 HOH WAT . D 4 HOH A 31 218 218 HOH WAT . D 4 HOH A 32 219 219 HOH WAT . D 4 HOH A 33 220 220 HOH WAT . D 4 HOH A 34 221 221 HOH WAT . D 4 HOH A 35 222 222 HOH WAT . D 4 HOH A 36 223 223 HOH WAT . D 4 HOH A 37 224 224 HOH WAT . D 4 HOH A 38 225 225 HOH WAT . D 4 HOH A 39 226 226 HOH WAT . D 4 HOH A 40 227 227 HOH WAT . D 4 HOH A 41 228 228 HOH WAT . D 4 HOH A 42 229 229 HOH WAT . D 4 HOH A 43 230 230 HOH WAT . D 4 HOH A 44 231 231 HOH WAT . D 4 HOH A 45 232 232 HOH WAT . D 4 HOH A 46 233 233 HOH WAT . D 4 HOH A 47 234 234 HOH WAT . D 4 HOH A 48 235 235 HOH WAT . D 4 HOH A 49 236 236 HOH WAT . D 4 HOH A 50 237 237 HOH WAT . D 4 HOH A 51 238 238 HOH WAT . D 4 HOH A 52 239 239 HOH WAT . D 4 HOH A 53 240 240 HOH WAT . D 4 HOH A 54 241 241 HOH WAT . D 4 HOH A 55 242 242 HOH WAT . D 4 HOH A 56 243 243 HOH WAT . D 4 HOH A 57 244 244 HOH WAT . D 4 HOH A 58 245 245 HOH WAT . D 4 HOH A 59 246 246 HOH WAT . D 4 HOH A 60 247 247 HOH WAT . D 4 HOH A 61 248 248 HOH WAT . D 4 HOH A 62 249 249 HOH WAT . D 4 HOH A 63 250 250 HOH WAT . D 4 HOH A 64 251 251 HOH WAT . D 4 HOH A 65 252 252 HOH WAT . D 4 HOH A 66 253 253 HOH WAT . D 4 HOH A 67 254 254 HOH WAT . # 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 N N2' CO4 . . . C 3 27.121 12.447 -5.588 1 23.39 ? N2' CO4 301 A 1 HETATM 2 C C2D CO4 . . . C 3 27.376 12.679 -4.33 1 23.8 ? C2D CO4 301 A 1 HETATM 3 N N3' CO4 . . . C 3 26.532 12.6 -3.284 1 24.62 ? N3' CO4 301 A 1 HETATM 4 C C4D CO4 . . . C 3 26.959 12.856 -2.06 1 24.69 ? C4D CO4 301 A 1 HETATM 5 N N4' CO4 . . . C 3 25.962 12.765 -1.139 1 24.2 ? N4' CO4 301 A 1 HETATM 6 C C4A CO4 . . . C 3 28.291 13.275 -1.759 1 25.68 ? C4A CO4 301 A 1 HETATM 7 C C5D CO4 . . . C 3 28.849 13.615 -0.47 1 28.38 ? C5D CO4 301 A 1 HETATM 8 C C6D CO4 . . . C 3 30.189 13.891 -0.349 1 30.46 ? C6D CO4 301 A 1 HETATM 9 C C7' CO4 . . . C 3 30.951 13.939 -1.55 1 30.07 ? C7' CO4 301 A 1 HETATM 10 N N8' CO4 . . . C 3 30.49 13.635 -2.776 1 28.76 ? N8' CO4 301 A 1 HETATM 11 C C8A CO4 . . . C 3 29.126 13.293 -2.881 1 26.24 ? C8A CO4 301 A 1 HETATM 12 N N1' CO4 . . . C 3 28.689 12.988 -4.175 1 24.56 ? N1' CO4 301 A 1 HETATM 13 C C8' CO4 . . . C 3 30.932 14.233 0.97 1 32.81 ? C8' CO4 301 A 1 HETATM 14 N N9' CO4 . . . C 3 32.361 14.387 1.121 1 32.88 ? N9' CO4 301 A 1 HETATM 15 C C1' CO4 . . . C 3 33.007 15.515 0.648 1 34.16 ? C1' CO4 301 A 1 HETATM 16 C C6' CO4 . . . C 3 32.26 16.698 0.37 1 33.06 ? C6' CO4 301 A 1 HETATM 17 C C5' CO4 . . . C 3 33.042 17.736 -0.111 1 34.95 ? C5' CO4 301 A 1 HETATM 18 O O5' CO4 . . . C 3 32.365 18.914 -0.322 1 37.17 ? O5' CO4 301 A 1 HETATM 19 C C5B CO4 . . . C 3 30.95 18.727 -0.166 1 35.96 ? C5B CO4 301 A 1 HETATM 20 C C4' CO4 . . . C 3 34.411 17.706 -0.31 1 35.32 ? C4' CO4 301 A 1 HETATM 21 O O4' CO4 . . . C 3 35.085 18.869 -0.783 1 36.29 ? O4' CO4 301 A 1 HETATM 22 C C4B CO4 . . . C 3 36.466 18.587 -1.009 1 36.43 ? C4B CO4 301 A 1 HETATM 23 C C3' CO4 . . . C 3 35.076 16.53 0.014 1 34.7 ? C3' CO4 301 A 1 HETATM 24 O O3' CO4 . . . C 3 36.444 16.619 -0.154 1 34.63 ? O3' CO4 301 A 1 HETATM 25 C C3B CO4 . . . C 3 37.141 15.379 0.108 1 34.61 ? C3B CO4 301 A 1 HETATM 26 C C2' CO4 . . . C 3 34.417 15.422 0.524 1 34.31 ? C2' CO4 301 A 1 HETATM 27 C C9' CO4 . . . C 3 33.31 13.299 1.385 1 33.98 ? C9' CO4 301 A 1 HETATM 28 C C51 CO4 . . . C 3 27.956 13.615 0.752 1 28.05 ? C51 CO4 301 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #