data_8PT9
#
_model_server_result.job_id            H3-KMwfrLvnvWZr272CcHw 
_model_server_result.datetime_utc      '2024-10-11 02:18:20' 
_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          8pt9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":401}' 
#
_entry.id    8PT9 
#
_exptl.entry_id    8PT9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              592.644 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'methyl (1S,3S)-1-methyl-3-[[3-[[3-methyl-4-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]carbamoyl]phenyl]carbamoyl]-4-oxidanylidene-cyclohexane-1-carboxylate' 
_entity.pdbx_number_of_molecules    3 
_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            8PT9 
_cell.length_a            106.552 
_cell.length_b            106.552 
_cell.length_c            99.795 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8PT9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        144 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D 1 1 
B,E,G 2 1 
C,F 3 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 D N N 
? 2 E N N 
? 2 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 SG CYS 118 A CYS 116 1_555 D C3 DVI . A DVI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.724 ? 
covale ? covale2 B SG CYS 118 B CYS 116 1_555 E C3 DVI . B DVI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.723 ? 
covale ? covale3 C SG CYS 118 C CYS 116 1_555 F C3 DVI . C DVI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? 
#
_chem_comp.formula           'C33 H32 N6 O5' 
_chem_comp.formula_weight    592.644 
_chem_comp.id                DVI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'methyl (1S,3S)-1-methyl-3-[[3-[[3-methyl-4-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]carbamoyl]phenyl]carbamoyl]-4-oxidanylidene-cyclohexane-1-carboxylate' 
_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
O C15 DVI sing 83 n n 
O C14 DVI sing 84 n n 
C5 C6 DVI sing 85 n n 
C5 C4 DVI sing 86 n n 
C7 C4 DVI sing 87 n n 
C6 C1 DVI sing 88 n n 
C4 C14 DVI sing 89 n n 
C4 C3 DVI sing 90 n n 
C14 O1 DVI doub 91 n n 
C1 O4 DVI doub 92 n n 
C1 C2 DVI sing 93 n n 
C3 C2 DVI sing 94 n n 
O2 C16 DVI doub 95 n n 
C2 C16 DVI sing 96 n n 
C16 N2 DVI sing 97 n n 
N2 C17 DVI sing 98 n n 
C43 N44 DVI doub 99 n y 
C43 C42 DVI sing 100 n y 
C17 C18 DVI doub 101 n y 
C17 C22 DVI sing 102 n y 
C18 C19 DVI sing 103 n y 
N44 C45 DVI sing 104 n y 
C42 C41 DVI doub 105 n y 
C22 C21 DVI doub 106 n y 
C19 C20 DVI doub 107 n y 
C21 C20 DVI sing 108 n y 
C21 C23 DVI sing 109 n n 
C45 C40 DVI doub 110 n y 
C41 C40 DVI sing 111 n y 
C40 C37 DVI sing 112 n n 
C23 O24 DVI doub 113 n n 
C23 N25 DVI sing 114 n n 
N25 C26 DVI sing 115 n n 
C27 C26 DVI doub 116 n y 
C27 C28 DVI sing 117 n y 
C39 C28 DVI sing 118 n n 
C37 N38 DVI doub 119 n y 
C37 C36 DVI sing 120 n y 
C26 C31 DVI sing 121 n y 
C28 C29 DVI doub 122 n y 
N38 C33 DVI sing 123 n y 
C36 C35 DVI doub 124 n y 
C31 C30 DVI doub 125 n y 
C29 C30 DVI sing 126 n y 
C29 N32 DVI sing 127 n n 
C33 N32 DVI sing 128 n n 
C33 N34 DVI doub 129 n y 
C35 N34 DVI sing 130 n y 
C7 H1 DVI sing 131 n n 
C7 H2 DVI sing 132 n n 
C7 H3 DVI sing 133 n n 
C15 H4 DVI sing 134 n n 
C15 H5 DVI sing 135 n n 
C15 H6 DVI sing 136 n n 
C18 H7 DVI sing 137 n n 
C19 H8 DVI sing 138 n n 
C20 H9 DVI sing 139 n n 
C22 H10 DVI sing 140 n n 
C27 H11 DVI sing 141 n n 
C2 H12 DVI sing 142 n n 
C30 H13 DVI sing 143 n n 
C31 H14 DVI sing 144 n n 
C35 H15 DVI sing 145 n n 
C36 H16 DVI sing 146 n n 
C39 H17 DVI sing 147 n n 
C39 H18 DVI sing 148 n n 
C39 H19 DVI sing 149 n n 
C41 H20 DVI sing 150 n n 
C42 H21 DVI sing 151 n n 
C43 H22 DVI sing 152 n n 
C45 H23 DVI sing 153 n n 
C6 H24 DVI sing 154 n n 
C6 H25 DVI sing 155 n n 
C5 H26 DVI sing 156 n n 
C5 H27 DVI sing 157 n n 
C3 H28 DVI sing 158 n n 
C3 H29 DVI sing 159 n n 
N2 H30 DVI sing 160 n n 
N25 H31 DVI sing 161 n n 
N32 H32 DVI sing 162 n n 
#
_atom_sites.entry_id                     8PT9 
_atom_sites.fract_transf_matrix[1][1]    0.009385 
_atom_sites.fract_transf_matrix[1][2]    0.005418 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010837 
_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]    0.010021 
_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
D 2 DVI A 1 401 401 DVI 38B . 
E 2 DVI B 1 401 401 DVI 38B . 
F 2 DVI C 1 401 401 DVI 38B . 
G 3 HOH B 1 501 2 HOH HOH . 
G 3 HOH B 2 502 1 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 C16 DVI . . . F 2 -3.53 -3.943 -7.231 1 107.62 ? C16 DVI 401 C 1 
HETATM 2 C C7 DVI . . . F 2 -0.358 -2.516 -3.746 1 105.8 ? C7 DVI 401 C 1 
HETATM 3 C C14 DVI . . . F 2 -2.398 -1.462 -4.546 1 110.97 ? C14 DVI 401 C 1 
HETATM 4 C C15 DVI . . . F 2 -3.161 0.224 -6.161 1 108.27 ? C15 DVI 401 C 1 
HETATM 5 C C17 DVI . . . F 2 -4.479 -2.293 -8.577 1 105.44 ? C17 DVI 401 C 1 
HETATM 6 C C18 DVI . . . F 2 -5.446 -3.123 -9.117 1 104.17 ? C18 DVI 401 C 1 
HETATM 7 C C19 DVI . . . F 2 -6.146 -2.729 -10.244 1 105.15 ? C19 DVI 401 C 1 
HETATM 8 C C20 DVI . . . F 2 -5.883 -1.505 -10.832 1 104 ? C20 DVI 401 C 1 
HETATM 9 C C21 DVI . . . F 2 -4.924 -0.681 -10.282 1 102.8 ? C21 DVI 401 C 1 
HETATM 10 C C22 DVI . . . F 2 -4.221 -1.068 -9.159 1 104.48 ? C22 DVI 401 C 1 
HETATM 11 C C23 DVI . . . F 2 -4.626 0.631 -10.907 1 101.27 ? C23 DVI 401 C 1 
HETATM 12 C C26 DVI . . . F 2 -2.943 1.982 -11.814 1 97.42 ? C26 DVI 401 C 1 
HETATM 13 C C27 DVI . . . F 2 -1.724 2.56 -11.538 1 96.39 ? C27 DVI 401 C 1 
HETATM 14 C C28 DVI . . . F 2 -1.257 3.619 -12.294 1 95.9 ? C28 DVI 401 C 1 
HETATM 15 C C29 DVI . . . F 2 -2.008 4.113 -13.339 1 94.76 ? C29 DVI 401 C 1 
HETATM 16 C C2 DVI . . . F 2 -3.146 -4.3 -5.826 1 109.08 ? C2 DVI 401 C 1 
HETATM 17 C C30 DVI . . . F 2 -3.225 3.525 -13.625 1 96.42 ? C30 DVI 401 C 1 
HETATM 18 C C31 DVI . . . F 2 -3.692 2.464 -12.87 1 98.75 ? C31 DVI 401 C 1 
HETATM 19 C C33 DVI . . . F 2 -0.898 6.203 -13.701 1 94.17 ? C33 DVI 401 C 1 
HETATM 20 C C35 DVI . . . F 2 0.624 7.87 -14.239 1 92.29 ? C35 DVI 401 C 1 
HETATM 21 C C36 DVI . . . F 2 0.559 8.348 -12.948 1 94.27 ? C36 DVI 401 C 1 
HETATM 22 C C37 DVI . . . F 2 -0.265 7.716 -12.043 1 96.09 ? C37 DVI 401 C 1 
HETATM 23 C C39 DVI . . . F 2 0.076 4.196 -11.931 1 97.09 ? C39 DVI 401 C 1 
HETATM 24 C C1 DVI . . . F 2 -4.258 -3.809 -4.941 1 112.25 ? C1 DVI 401 C 1 
HETATM 25 C C40 DVI . . . F 2 -0.328 8.229 -10.656 1 99.71 ? C40 DVI 401 C 1 
HETATM 26 C C41 DVI . . . F 2 0.529 9.24 -10.259 1 101.76 ? C41 DVI 401 C 1 
HETATM 27 C C42 DVI . . . F 2 0.466 9.707 -8.958 1 99.34 ? C42 DVI 401 C 1 
HETATM 28 C C43 DVI . . . F 2 -0.452 9.147 -8.092 1 101.56 ? C43 DVI 401 C 1 
HETATM 29 C C45 DVI . . . F 2 -1.224 7.704 -9.745 1 100.1 ? C45 DVI 401 C 1 
HETATM 30 C C6 DVI . . . F 2 -4.047 -3.368 -3.513 1 111.25 ? C6 DVI 401 C 1 
HETATM 31 C C5 DVI . . . F 2 -2.579 -3.418 -3.137 1 108.96 ? C5 DVI 401 C 1 
HETATM 32 C C4 DVI . . . F 2 -1.767 -2.785 -4.242 1 107.31 ? C4 DVI 401 C 1 
HETATM 33 C C3 DVI . . . F 2 -1.777 -3.739 -5.423 1 106.09 ? C3 DVI 401 C 1 
HETATM 34 N N2 DVI . . . F 2 -3.789 -2.667 -7.48 1 107.05 ? N2 DVI 401 C 1 
HETATM 35 N N25 DVI . . . F 2 -3.353 0.946 -11.062 1 100.02 ? N25 DVI 401 C 1 
HETATM 36 N N32 DVI . . . F 2 -1.612 5.14 -14.118 1 94.6 ? N32 DVI 401 C 1 
HETATM 37 N N34 DVI . . . F 2 -0.103 6.815 -14.59 1 92.53 ? N34 DVI 401 C 1 
HETATM 38 N N38 DVI . . . F 2 -0.988 6.654 -12.435 1 96.25 ? N38 DVI 401 C 1 
HETATM 39 N N44 DVI . . . F 2 -1.266 8.174 -8.499 1 101.66 ? N44 DVI 401 C 1 
HETATM 40 O O2 DVI . . . F 2 -3.628 -4.82 -8.065 1 105.88 ? O2 DVI 401 C 1 
HETATM 41 O O1 DVI . . . F 2 -2.506 -0.625 -3.674 1 115.86 ? O1 DVI 401 C 1 
HETATM 42 O O DVI . . . F 2 -2.9 -1.141 -5.855 1 112.38 ? O DVI 401 C 1 
HETATM 43 O O4 DVI . . . F 2 -5.384 -3.774 -5.402 1 112.5 ? O4 DVI 401 C 1 
HETATM 44 O O24 DVI . . . F 2 -5.543 1.336 -11.26 1 101.44 ? O24 DVI 401 C 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           44 
#