data_5VQR
#
_model_server_result.job_id            -NjqLvYcc3hfWAZSf9XU4A 
_model_server_result.datetime_utc      '2025-01-10 08:28:29' 
_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          5vqr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":601}' 
#
_entry.id    5VQR 
#
_exptl.entry_id    5VQR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              496.514 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-(6-cyano-3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-4-methylnaphthalen-1-yl)-N-methylprop-2-enamide 
_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          99.69 
_cell.angle_gamma         90 
_cell.entry_id            5VQR 
_cell.length_a            162.43 
_cell.length_b            73.73 
_cell.length_c            108.35 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VQR 
_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    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 
_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           'C28 H24 N4 O5' 
_chem_comp.formula_weight    496.514 
_chem_comp.id                9KG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-(6-cyano-3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-4-methylnaphthalen-1-yl)-N-methylprop-2-enamide 
_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
O3 C9 9KG doub 1 n n 
C8 C7 9KG sing 2 n n 
C8 N1 9KG sing 3 n n 
C9 N1 9KG sing 4 n n 
C9 N2 9KG sing 5 n n 
C7 O2 9KG sing 6 n n 
N1 C12 9KG sing 7 n n 
N2 C10 9KG sing 8 n n 
C12 C11 9KG doub 9 n n 
O2 C2 9KG sing 10 n n 
C10 C11 9KG sing 11 n n 
C10 O4 9KG doub 12 n n 
C1 C2 9KG doub 13 n y 
C1 C6 9KG sing 14 n y 
C2 C3 9KG sing 15 n y 
C6 C5 9KG doub 16 n y 
C3 O1 9KG sing 17 n n 
C3 C4 9KG doub 18 n y 
O1 C13 9KG sing 19 n n 
C5 C4 9KG sing 20 n y 
C13 C18 9KG doub 21 n y 
C13 C14 9KG sing 22 n y 
C27 N3 9KG sing 23 n n 
C18 C17 9KG sing 24 n y 
C24 C14 9KG sing 25 n n 
C14 C15 9KG doub 26 n y 
C17 N3 9KG sing 27 n n 
C17 C16 9KG doub 28 n y 
N3 C25 9KG sing 29 n n 
O5 C25 9KG doub 30 n n 
C15 C16 9KG sing 31 n y 
C15 C19 9KG sing 32 n y 
C25 C26 9KG sing 33 n n 
C16 C22 9KG sing 34 n y 
C19 C20 9KG doub 35 n y 
C26 C28 9KG doub 36 n n 
C22 C21 9KG doub 37 n y 
C20 C21 9KG sing 38 n y 
C20 C23 9KG sing 39 n n 
C23 N4 9KG trip 40 n n 
N2 H1 9KG sing 41 n n 
C4 H2 9KG sing 42 n n 
C6 H3 9KG sing 43 n n 
C7 H4 9KG sing 44 n n 
C7 H5 9KG sing 45 n n 
C1 H6 9KG sing 46 n n 
C11 H7 9KG sing 47 n n 
C12 H8 9KG sing 48 n n 
C18 H9 9KG sing 49 n n 
C19 H10 9KG sing 50 n n 
C21 H11 9KG sing 51 n n 
C22 H12 9KG sing 52 n n 
C24 H13 9KG sing 53 n n 
C24 H14 9KG sing 54 n n 
C24 H15 9KG sing 55 n n 
C26 H16 9KG sing 56 n n 
C27 H17 9KG sing 57 n n 
C27 H18 9KG sing 58 n n 
C27 H19 9KG sing 59 n n 
C28 H20 9KG sing 60 n n 
C28 H21 9KG sing 61 n n 
C5 H22 9KG sing 62 n n 
C8 H23 9KG sing 63 n n 
C8 H24 9KG sing 64 n n 
#
_atom_sites.entry_id                     5VQR 
_atom_sites.fract_transf_matrix[1][1]    0.006156 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001051 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013563 
_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]    0.009363 
_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 3 9KG A 1 601 1 9KG 684 . 
D 4 SO4 A 1 602 1 SO4 SO4 . 
E 5 HOH A 1 701 24 HOH HOH . 
E 5 HOH A 2 702 9 HOH HOH . 
E 5 HOH A 3 703 5 HOH HOH . 
E 5 HOH A 4 704 27 HOH HOH . 
E 5 HOH A 5 705 6 HOH HOH . 
E 5 HOH A 6 706 7 HOH HOH . 
E 5 HOH A 7 707 15 HOH HOH . 
E 5 HOH A 8 708 35 HOH HOH . 
E 5 HOH A 9 709 4 HOH HOH . 
E 5 HOH A 10 710 17 HOH HOH . 
E 5 HOH A 11 711 21 HOH HOH . 
E 5 HOH A 12 712 8 HOH HOH . 
E 5 HOH A 13 713 26 HOH HOH . 
E 5 HOH A 14 714 20 HOH HOH . 
E 5 HOH A 15 715 22 HOH HOH . 
E 5 HOH A 16 716 23 HOH HOH . 
E 5 HOH A 17 717 30 HOH HOH . 
E 5 HOH A 18 718 14 HOH HOH . 
E 5 HOH A 19 719 12 HOH HOH . 
E 5 HOH A 20 720 28 HOH HOH . 
E 5 HOH A 21 721 38 HOH HOH . 
E 5 HOH A 22 722 36 HOH HOH . 
E 5 HOH A 23 723 19 HOH HOH . 
E 5 HOH A 24 724 16 HOH HOH . 
F 5 HOH B 1 501 11 HOH HOH . 
F 5 HOH B 2 502 3 HOH HOH . 
F 5 HOH B 3 503 40 HOH HOH . 
F 5 HOH B 4 504 29 HOH HOH . 
F 5 HOH B 5 505 37 HOH HOH . 
F 5 HOH B 6 506 18 HOH HOH . 
F 5 HOH B 7 507 2 HOH HOH . 
F 5 HOH B 8 508 31 HOH HOH . 
F 5 HOH B 9 509 10 HOH HOH . 
F 5 HOH B 10 510 34 HOH HOH . 
F 5 HOH B 11 511 1 HOH HOH . 
F 5 HOH B 12 512 13 HOH HOH . 
F 5 HOH B 13 513 32 HOH HOH . 
F 5 HOH B 14 514 25 HOH HOH . 
F 5 HOH B 15 515 39 HOH HOH . 
F 5 HOH B 16 516 33 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 N N1 9KG . . . C 3 844.167 -36.982 140.194 1 59.04 ? N1 9KG 601 A 1 
HETATM 2 C C2 9KG . . . C 3 846.28 -34.28 142.279 1 63.89 ? C2 9KG 601 A 1 
HETATM 3 N N2 9KG . . . C 3 844.607 -39.216 140.611 1 60.12 ? N2 9KG 601 A 1 
HETATM 4 N N3 9KG . . . C 3 842.154 -30.916 145.699 1 80 ? N3 9KG 601 A 1 
HETATM 5 C C4 9KG . . . C 3 846.816 -34.286 144.64 1 67.89 ? C4 9KG 601 A 1 
HETATM 6 N N4 9KG . . . C 3 839.365 -36.717 150.028 1 71.44 ? N4 9KG 601 A 1 
HETATM 7 C C6 9KG . . . C 3 848.561 -33.909 143.006 1 63.98 ? C6 9KG 601 A 1 
HETATM 8 C C7 9KG . . . C 3 845.747 -35.092 140.019 1 62.94 ? C7 9KG 601 A 1 
HETATM 9 C C9 9KG . . . C 3 844.929 -38.094 139.889 1 60.11 ? C9 9KG 601 A 1 
HETATM 10 C C1 9KG . . . C 3 847.623 -34.03 141.987 1 60.57 ? C1 9KG 601 A 1 
HETATM 11 C C10 9KG . . . C 3 843.657 -39.384 141.576 1 63.2 ? C10 9KG 601 A 1 
HETATM 12 C C11 9KG . . . C 3 842.899 -38.177 141.847 1 64.23 ? C11 9KG 601 A 1 
HETATM 13 C C12 9KG . . . C 3 843.19 -37.057 141.156 1 64.34 ? C12 9KG 601 A 1 
HETATM 14 C C13 9KG . . . C 3 843.633 -34.166 144.705 1 68.07 ? C13 9KG 601 A 1 
HETATM 15 C C14 9KG . . . C 3 843.013 -35.065 145.569 1 72.14 ? C14 9KG 601 A 1 
HETATM 16 C C15 9KG . . . C 3 842.075 -34.603 146.539 1 70.38 ? C15 9KG 601 A 1 
HETATM 17 C C16 9KG . . . C 3 841.774 -33.204 146.602 1 75.64 ? C16 9KG 601 A 1 
HETATM 18 C C17 9KG . . . C 3 842.43 -32.305 145.696 1 75.23 ? C17 9KG 601 A 1 
HETATM 19 C C18 9KG . . . C 3 843.335 -32.808 144.755 1 71.45 ? C18 9KG 601 A 1 
HETATM 20 C C19 9KG . . . C 3 841.43 -35.495 147.443 1 71.71 ? C19 9KG 601 A 1 
HETATM 21 C C20 9KG . . . C 3 840.518 -35.033 148.387 1 75.09 ? C20 9KG 601 A 1 
HETATM 22 C C21 9KG . . . C 3 840.233 -33.675 148.449 1 76.15 ? C21 9KG 601 A 1 
HETATM 23 C C22 9KG . . . C 3 840.834 -32.77 147.58 1 81.93 ? C22 9KG 601 A 1 
HETATM 24 C C23 9KG . . . C 3 839.874 -35.97 149.302 1 73.45 ? C23 9KG 601 A 1 
HETATM 25 C C24 9KG . . . C 3 843.342 -36.554 145.49 1 72.83 ? C24 9KG 601 A 1 
HETATM 26 C C25 9KG . . . C 3 842.75 -30.017 146.548 1 87.52 ? C25 9KG 601 A 1 
HETATM 27 C C26 9KG . . . C 3 843.735 -30.495 147.504 1 82.64 ? C26 9KG 601 A 1 
HETATM 28 C C27 9KG . . . C 3 841.149 -30.514 144.705 1 75.62 ? C27 9KG 601 A 1 
HETATM 29 C C28 9KG . . . C 3 844.399 -29.655 148.321 1 80.65 ? C28 9KG 601 A 1 
HETATM 30 C C3 9KG . . . C 3 845.86 -34.401 143.613 1 65.28 ? C3 9KG 601 A 1 
HETATM 31 C C5 9KG . . . C 3 848.155 -34.037 144.331 1 66.42 ? C5 9KG 601 A 1 
HETATM 32 C C8 9KG . . . C 3 844.47 -35.745 139.465 1 60.08 ? C8 9KG 601 A 1 
HETATM 33 O O1 9KG . . . C 3 844.511 -34.659 143.773 1 64.37 ? O1 9KG 601 A 1 
HETATM 34 O O2 9KG . . . C 3 845.423 -34.378 141.198 1 65.05 ? O2 9KG 601 A 1 
HETATM 35 O O3 9KG . . . C 3 845.831 -38.134 139.048 1 54.37 ? O3 9KG 601 A 1 
HETATM 36 O O4 9KG . . . C 3 843.475 -40.456 142.144 1 69.37 ? O4 9KG 601 A 1 
HETATM 37 O O5 9KG . . . C 3 842.468 -28.812 146.51 1 92.75 ? O5 9KG 601 A 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           32 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           37 
#