data_7MY5 # _model_server_result.job_id bvA16WwJG9Ld2BrhTT5tcQ _model_server_result.datetime_utc '2024-11-26 09:28:07' _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 7my5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 7MY5 # _exptl.entry_id 7MY5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 395.409 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-2-(2-methylphenyl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide _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 90 _cell.entry_id 7MY5 _cell.length_a 89.591 _cell.length_b 89.591 _cell.length_c 133.076 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7MY5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall 'I 4 2' _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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 1,2,3,4,5,6,7,8 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_445 -x-1,-y-1,z -1 0 0 0 -1 0 0 0 1 -89.591 -89.591 0 3 'crystal symmetry operation' 3_455 -y-1,x,z 0 -1 0 1 0 0 0 0 1 -89.591 0 0 4 'crystal symmetry operation' 4_545 y,-x-1,z 0 1 0 -1 0 0 0 0 1 0 -89.591 0 5 'crystal symmetry operation' 5_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -89.591 0 0 6 'crystal symmetry operation' 6_545 x,-y-1,-z 1 0 0 0 -1 0 0 0 -1 0 -89.591 0 7 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 8_445 -y-1,-x-1,-z 0 -1 0 -1 0 0 0 0 -1 -89.591 -89.591 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A NE2 HIS 61 A HIS 41 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc2 A OE1 GLU 81 A GLU 80 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc3 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc4 A OD1 ASP 109 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc5 A OE2 GLU 120 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc6 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc7 B MN MN . A MN 201 1_555 D O13 Y5V . A Y5V 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc8 B MN MN . A MN 201 1_555 D O15 Y5V . A Y5V 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc9 C MN MN . A MN 202 1_555 D O13 Y5V . A Y5V 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc10 C MN MN . A MN 202 1_555 D O10 Y5V . A Y5V 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc11 C MN MN . A MN 202 1_555 I O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc12 C MN MN . A MN 202 1_555 I O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? # _chem_comp.formula 'C21 H21 N3 O5' _chem_comp.formula_weight 395.409 _chem_comp.id Y5V _chem_comp.mon_nstd_flag . _chem_comp.name 5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-2-(2-methylphenyl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide _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 O15 C14 Y5V doub 489 n n O13 C12 Y5V sing 490 n n C14 C12 Y5V sing 491 n n C14 N16 Y5V sing 492 n n C12 C11 Y5V doub 493 n n N16 C17 Y5V sing 494 n n O10 C09 Y5V doub 495 n n C11 C09 Y5V sing 496 n n C11 N18 Y5V sing 497 n n C17 N18 Y5V doub 498 n n C17 C19 Y5V sing 499 n n C09 N08 Y5V sing 500 n n C20 C19 Y5V doub 501 n y C20 C21 Y5V sing 502 n y C19 C24 Y5V sing 503 n y C21 C22 Y5V doub 504 n y C24 C25 Y5V sing 505 n n C24 C23 Y5V doub 506 n y N08 C07 Y5V sing 507 n n C22 C23 Y5V sing 508 n y C07 C06 Y5V sing 509 n n C06 C05 Y5V sing 510 n n C04 C05 Y5V doub 511 n y C04 C03 Y5V sing 512 n y C05 C26 Y5V sing 513 n y C01 O02 Y5V sing 514 n n O02 C03 Y5V sing 515 n n C03 C28 Y5V doub 516 n y C26 C27 Y5V doub 517 n y C28 C27 Y5V sing 518 n y C28 O29 Y5V sing 519 n n C21 H1 Y5V sing 520 n n C20 H2 Y5V sing 521 n n C22 H3 Y5V sing 522 n n C23 H4 Y5V sing 523 n n C01 H5 Y5V sing 524 n n C01 H6 Y5V sing 525 n n C01 H7 Y5V sing 526 n n C04 H8 Y5V sing 527 n n C06 H9 Y5V sing 528 n n C06 H10 Y5V sing 529 n n C07 H11 Y5V sing 530 n n C07 H12 Y5V sing 531 n n C25 H13 Y5V sing 532 n n C25 H14 Y5V sing 533 n n C25 H15 Y5V sing 534 n n C26 H16 Y5V sing 535 n n C27 H17 Y5V sing 536 n n N08 H18 Y5V sing 537 n n N16 H19 Y5V sing 538 n n O13 H20 Y5V sing 539 n n O29 H21 Y5V sing 540 n n # _atom_sites.entry_id 7MY5 _atom_sites.fract_transf_matrix[1][1] 0.011162 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011162 _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] 0.007515 _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 MN A 1 201 201 MN MN . C 2 MN A 1 202 202 MN MN . D 3 Y5V A 1 203 301 Y5V 503 . E 4 QQ4 A 1 204 401 QQ4 PVP . F 5 SO4 A 1 205 1 SO4 SO4 . G 5 SO4 A 1 206 2 SO4 SO4 . H 5 SO4 A 1 207 3 SO4 SO4 . I 6 HOH A 1 301 2 HOH HOH . I 6 HOH A 2 302 5 HOH HOH . I 6 HOH A 3 303 3 HOH HOH . I 6 HOH A 4 304 1 HOH HOH . I 6 HOH A 5 305 8 HOH HOH . I 6 HOH A 6 306 10 HOH HOH . I 6 HOH A 7 307 6 HOH HOH . I 6 HOH A 8 308 9 HOH HOH . I 6 HOH A 9 309 7 HOH HOH . I 6 HOH A 10 310 4 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 C21 Y5V . . . D 3 -13.449 -35.32 -13.516 1 109.54 ? C21 Y5V 203 A 1 HETATM 2 C C20 Y5V . . . D 3 -14.096 -36.274 -14.278 1 107.58 ? C20 Y5V 203 A 1 HETATM 3 C C19 Y5V . . . D 3 -13.378 -37.059 -15.161 1 110.25 ? C19 Y5V 203 A 1 HETATM 4 C C17 Y5V . . . D 3 -14.125 -38.104 -15.97 1 90.12 ? C17 Y5V 203 A 1 HETATM 5 C C14 Y5V . . . D 3 -15.533 -38.844 -17.951 1 67.64 ? C14 Y5V 203 A 1 HETATM 6 C C12 Y5V . . . D 3 -15.581 -40.224 -17.396 1 56.76 ? C12 Y5V 203 A 1 HETATM 7 C C22 Y5V . . . D 3 -12.079 -35.161 -13.637 1 120.27 ? C22 Y5V 203 A 1 HETATM 8 C C23 Y5V . . . D 3 -11.359 -35.956 -14.516 1 123.53 ? C23 Y5V 203 A 1 HETATM 9 C C11 Y5V . . . D 3 -14.884 -40.543 -16.145 1 84.21 ? C11 Y5V 203 A 1 HETATM 10 C C01 Y5V . . . D 3 -10.511 -40.074 -12.079 1 93.86 ? C01 Y5V 203 A 1 HETATM 11 C C03 Y5V . . . D 3 -12.463 -40.738 -10.983 1 119.65 ? C03 Y5V 203 A 1 HETATM 12 C C04 Y5V . . . D 3 -12.849 -41.866 -11.679 1 116.47 ? C04 Y5V 203 A 1 HETATM 13 C C05 Y5V . . . D 3 -14.193 -42.185 -11.821 1 115.8 ? C05 Y5V 203 A 1 HETATM 14 C C06 Y5V . . . D 3 -14.634 -43.43 -12.599 1 113.33 ? C06 Y5V 203 A 1 HETATM 15 C C07 Y5V . . . D 3 -13.941 -43.576 -13.954 1 102.1 ? C07 Y5V 203 A 1 HETATM 16 C C09 Y5V . . . D 3 -14.934 -41.96 -15.618 1 79.18 ? C09 Y5V 203 A 1 HETATM 17 C C24 Y5V . . . D 3 -12.006 -36.913 -15.279 1 114.44 ? C24 Y5V 203 A 1 HETATM 18 C C25 Y5V . . . D 3 -11.21 -37.785 -16.246 1 84.78 ? C25 Y5V 203 A 1 HETATM 19 C C26 Y5V . . . D 3 -15.151 -41.365 -11.261 1 102.56 ? C26 Y5V 203 A 1 HETATM 20 C C27 Y5V . . . D 3 -14.766 -40.241 -10.559 1 104.08 ? C27 Y5V 203 A 1 HETATM 21 C C28 Y5V . . . D 3 -13.431 -39.92 -10.418 1 115.6 ? C28 Y5V 203 A 1 HETATM 22 N N08 Y5V . . . D 3 -14.001 -42.282 -14.583 1 92.51 ? N08 Y5V 203 A 1 HETATM 23 N N16 Y5V . . . D 3 -14.827 -37.797 -17.237 1 67.36 ? N16 Y5V 203 A 1 HETATM 24 N N18 Y5V . . . D 3 -14.179 -39.492 -15.433 1 90.74 ? N18 Y5V 203 A 1 HETATM 25 O O02 Y5V . . . D 3 -11.099 -40.452 -10.867 1 116.9 ? O02 Y5V 203 A 1 HETATM 26 O O10 Y5V . . . D 3 -15.678 -42.769 -16.054 1 83.69 ? O10 Y5V 203 A 1 HETATM 27 O O13 Y5V . . . D 3 -16.272 -41.197 -18.126 1 73.8 ? O13 Y5V 203 A 1 HETATM 28 O O15 Y5V . . . D 3 -16.093 -38.599 -18.971 1 57.13 ? O15 Y5V 203 A 1 HETATM 29 O O29 Y5V . . . D 3 -13.09 -38.771 -9.703 1 107.24 ? O29 Y5V 203 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #