data_6MCK # _model_server_result.job_id 85xDxKZbOEUh_BBCTbOumw _model_server_result.datetime_utc '2025-07-01 15:58:37' _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 6mck # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":900}' # _entry.id 6MCK # _exptl.entry_id 6MCK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 413.472 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide _entity.pdbx_number_of_molecules 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.67 _cell.angle_gamma 90 _cell.entry_id 6MCK _cell.length_a 127.41 _cell.length_b 263.83 _cell.length_c 164.13 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6MCK _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA _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 ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 Q N N ? 2 R N N ? 2 S N N ? 2 T N N ? 2 U N N ? 2 V N N ? 2 W N N ? 2 X N N # _chem_comp.formula 'C24 H23 N5 O2' _chem_comp.formula_weight 413.472 _chem_comp.id JDP _chem_comp.mon_nstd_flag . _chem_comp.name 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CB-5083 # 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 O01 C02 JDP doub 173 n n N31 C02 JDP sing 174 n n C02 C03 JDP sing 175 n n C09 C08 JDP sing 176 n y C09 C10 JDP doub 177 n y C03 C08 JDP doub 178 n y C03 C04 JDP sing 179 n y C08 C07 JDP sing 180 n y C11 C10 JDP sing 181 n n C04 C05 JDP doub 182 n y C10 N12 JDP sing 183 n y C07 N12 JDP sing 184 n y C07 C06 JDP doub 185 n y N12 C13 JDP sing 186 n n C05 C06 JDP sing 187 n y C13 N30 JDP doub 188 n y C13 N14 JDP sing 189 n y N30 C29 JDP sing 190 n y N14 C15 JDP doub 191 n y C29 C28 JDP sing 192 n n C29 C24 JDP doub 193 n y C28 C27 JDP sing 194 n n C15 C24 JDP sing 195 n y C15 N16 JDP sing 196 n n C22 C21 JDP doub 197 n y C22 C23 JDP sing 198 n y C24 C25 JDP sing 199 n n C21 C20 JDP sing 200 n y C23 C18 JDP doub 201 n y N16 C17 JDP sing 202 n n C27 O26 JDP sing 203 n n C20 C19 JDP doub 204 n y C18 C19 JDP sing 205 n y C18 C17 JDP sing 206 n n C25 O26 JDP sing 207 n n C22 H1 JDP sing 208 n n C21 H2 JDP sing 209 n n C04 H3 JDP sing 210 n n C05 H4 JDP sing 211 n n C06 H5 JDP sing 212 n n C09 H6 JDP sing 213 n n C11 H7 JDP sing 214 n n C11 H8 JDP sing 215 n n C11 H9 JDP sing 216 n n N16 H10 JDP sing 217 n n C17 H11 JDP sing 218 n n C17 H12 JDP sing 219 n n C19 H13 JDP sing 220 n n C20 H14 JDP sing 221 n n C23 H15 JDP sing 222 n n C25 H16 JDP sing 223 n n C25 H17 JDP sing 224 n n C27 H18 JDP sing 225 n n C27 H19 JDP sing 226 n n C28 H20 JDP sing 227 n n C28 H21 JDP sing 228 n n N31 H22 JDP sing 229 n n N31 H23 JDP sing 230 n n # _atom_sites.entry_id 6MCK _atom_sites.fract_transf_matrix[1][1] 0.007849 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001909 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00379 _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] 0.00627 _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 M 2 JDP A 1 900 900 JDP CB5 . N 2 JDP B 1 900 900 JDP CB5 . O 2 JDP C 1 900 900 JDP CB5 . P 2 JDP D 1 900 900 JDP CB5 . Q 2 JDP E 1 900 900 JDP CB5 . R 2 JDP F 1 900 900 JDP CB5 . S 2 JDP G 1 900 900 JDP CB5 . T 2 JDP H 1 900 900 JDP CB5 . U 2 JDP I 1 900 900 JDP CB5 . V 2 JDP J 1 900 900 JDP CB5 . W 2 JDP K 1 900 900 JDP CB5 . X 2 JDP L 1 900 900 JDP CB5 . Y 3 HOH A 1 1001 26 HOH HOH . Y 3 HOH A 2 1002 13 HOH HOH . Y 3 HOH A 3 1003 1 HOH HOH . Z 3 HOH B 1 1001 14 HOH HOH . Z 3 HOH B 2 1002 2 HOH HOH . Z 3 HOH B 3 1003 27 HOH HOH . AA 3 HOH C 1 1001 28 HOH HOH . AA 3 HOH C 2 1002 15 HOH HOH . AA 3 HOH C 3 1003 3 HOH HOH . BA 3 HOH D 1 1001 4 HOH HOH . BA 3 HOH D 2 1002 29 HOH HOH . BA 3 HOH D 3 1003 16 HOH HOH . CA 3 HOH E 1 1001 5 HOH HOH . CA 3 HOH E 2 1002 17 HOH HOH . DA 3 HOH F 1 1001 18 HOH HOH . DA 3 HOH F 2 1002 6 HOH HOH . DA 3 HOH F 3 1003 31 HOH HOH . EA 3 HOH G 1 1001 7 HOH HOH . EA 3 HOH G 2 1002 19 HOH HOH . EA 3 HOH G 3 1003 25 HOH HOH . FA 3 HOH H 1 1001 8 HOH HOH . FA 3 HOH H 2 1002 20 HOH HOH . GA 3 HOH I 1 1001 21 HOH HOH . GA 3 HOH I 2 1002 9 HOH HOH . HA 3 HOH J 1 1001 32 HOH HOH . HA 3 HOH J 2 1002 22 HOH HOH . HA 3 HOH J 3 1003 10 HOH HOH . IA 3 HOH K 1 1001 33 HOH HOH . IA 3 HOH K 2 1002 23 HOH HOH . IA 3 HOH K 3 1003 11 HOH HOH . JA 3 HOH L 1 1001 24 HOH HOH . JA 3 HOH L 2 1002 12 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 C22 JDP . . . T 2 21.057 49.201 -8.986 1 145.33 ? C22 JDP 900 H 1 HETATM 2 C C21 JDP . . . T 2 21.13 47.841 -8.703 1 141.53 ? C21 JDP 900 H 1 HETATM 3 O O01 JDP . . . T 2 29.398 50.339 -6.695 1 158.39 ? O01 JDP 900 H 1 HETATM 4 C C02 JDP . . . T 2 28.383 49.707 -6.45 1 151.19 ? C02 JDP 900 H 1 HETATM 5 C C03 JDP . . . T 2 27.145 49.868 -7.241 1 147.78 ? C03 JDP 900 H 1 HETATM 6 C C04 JDP . . . T 2 25.965 49.368 -6.731 1 147.46 ? C04 JDP 900 H 1 HETATM 7 C C05 JDP . . . T 2 24.793 49.508 -7.433 1 150.98 ? C05 JDP 900 H 1 HETATM 8 C C06 JDP . . . T 2 24.752 50.148 -8.641 1 151.61 ? C06 JDP 900 H 1 HETATM 9 C C07 JDP . . . T 2 25.919 50.658 -9.151 1 148.14 ? C07 JDP 900 H 1 HETATM 10 C C08 JDP . . . T 2 27.126 50.541 -8.477 1 147.22 ? C08 JDP 900 H 1 HETATM 11 C C09 JDP . . . T 2 28.099 51.191 -9.339 1 148.62 ? C09 JDP 900 H 1 HETATM 12 C C10 JDP . . . T 2 27.501 51.667 -10.452 1 145.16 ? C10 JDP 900 H 1 HETATM 13 C C11 JDP . . . T 2 28.117 52.406 -11.617 1 139.91 ? C11 JDP 900 H 1 HETATM 14 N N12 JDP . . . T 2 26.147 51.336 -10.335 1 147.68 ? N12 JDP 900 H 1 HETATM 15 C C13 JDP . . . T 2 25.172 51.622 -11.209 1 151.3 ? C13 JDP 900 H 1 HETATM 16 N N14 JDP . . . T 2 24.491 50.597 -11.687 1 154.04 ? N14 JDP 900 H 1 HETATM 17 C C15 JDP . . . T 2 23.507 50.856 -12.527 1 160.26 ? C15 JDP 900 H 1 HETATM 18 N N16 JDP . . . T 2 22.887 49.769 -13.029 1 162.31 ? N16 JDP 900 H 1 HETATM 19 C C17 JDP . . . T 2 21.528 49.348 -12.763 1 159.25 ? C17 JDP 900 H 1 HETATM 20 C C18 JDP . . . T 2 21.396 48.823 -11.345 1 153.5 ? C18 JDP 900 H 1 HETATM 21 C C19 JDP . . . T 2 21.462 47.458 -11.073 1 149.54 ? C19 JDP 900 H 1 HETATM 22 C C20 JDP . . . T 2 21.331 46.974 -9.765 1 145.23 ? C20 JDP 900 H 1 HETATM 23 C C23 JDP . . . T 2 21.188 49.7 -10.283 1 147.29 ? C23 JDP 900 H 1 HETATM 24 C C24 JDP . . . T 2 23.222 52.192 -12.882 1 160.63 ? C24 JDP 900 H 1 HETATM 25 C C25 JDP . . . T 2 22.146 52.57 -13.848 1 165.39 ? C25 JDP 900 H 1 HETATM 26 O O26 JDP . . . T 2 22.499 53.821 -14.457 1 173.24 ? O26 JDP 900 H 1 HETATM 27 C C27 JDP . . . T 2 22.632 54.911 -13.516 1 170.54 ? C27 JDP 900 H 1 HETATM 28 C C28 JDP . . . T 2 23.814 54.637 -12.593 1 167.11 ? C28 JDP 900 H 1 HETATM 29 C C29 JDP . . . T 2 24.002 53.167 -12.313 1 159.7 ? C29 JDP 900 H 1 HETATM 30 N N30 JDP . . . T 2 24.979 52.889 -11.46 1 152.44 ? N30 JDP 900 H 1 HETATM 31 N N31 JDP . . . T 2 28.328 48.849 -5.395 1 149.09 ? N31 JDP 900 H 1 # _model_server_stats.io_time_ms 320 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #