data_9D0X
#
_model_server_result.job_id            mp4WttlxaRoneWQzlkEviA 
_model_server_result.datetime_utc      '2025-09-06 23:24:07' 
_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          9d0x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":502}' 
#
_entry.id    9D0X 
#
_exptl.entry_id    9D0X 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              880.041 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (3R)-3-(5-{4-[(2-{4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]-3-methylbenzene-1-sulfonyl}-7-azaspiro[3.5]nonan-7-yl)methyl]piperidin-1-yl}-4-fluoro-3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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    ? 
_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                      5 
_struct_asym.id                             E 
_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
covale ? covale1 B C TYR 159 C TYR 159 1_555 B N TPO 160 C TPO 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale2 B C TPO 160 C TPO 160 1_555 B N HIS 161 C HIS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
metalc ? metalc1 A SG CYS 286 B CYS 323 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc2 A SG CYS 289 B CYS 326 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc3 A SG CYS 354 B CYS 391 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc4 A SG CYS 357 B CYS 394 1_555 D ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
#
_chem_comp.formula           'C46 H54 F N9 O6 S' 
_chem_comp.formula_weight    880.041 
_chem_comp.id                A1A1I 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (3R)-3-(5-{4-[(2-{4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]-3-methylbenzene-1-sulfonyl}-7-azaspiro[3.5]nonan-7-yl)methyl]piperidin-1-yl}-4-fluoro-3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione 
_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
C38 N8 A1A1I doub 1 n y 
C38 C37 A1A1I sing 2 n y 
N8 C35 A1A1I sing 3 n y 
C39 C37 A1A1I sing 4 n n 
C39 C40 A1A1I doub 5 n n 
C37 C36 A1A1I doub 6 n y 
C40 C41 A1A1I sing 7 n n 
C35 N6 A1A1I sing 8 n n 
C35 N7 A1A1I doub 9 n y 
N6 C34 A1A1I sing 10 n n 
C36 N7 A1A1I sing 11 n y 
C36 N9 A1A1I sing 12 n n 
C41 N9 A1A1I sing 13 n n 
C41 O6 A1A1I doub 14 n n 
C34 C33 A1A1I doub 15 n y 
C34 C2 A1A1I sing 16 n y 
N9 C42 A1A1I sing 17 n n 
C1 C2 A1A1I sing 18 n n 
C33 C32 A1A1I sing 19 n y 
C2 C3 A1A1I doub 20 n y 
C46 C42 A1A1I sing 21 n n 
C46 C45 A1A1I sing 22 n n 
C42 C43 A1A1I sing 23 n n 
C32 C4 A1A1I doub 24 n y 
C3 C4 A1A1I sing 25 n y 
C4 S1 A1A1I sing 26 n n 
O5 S1 A1A1I doub 27 n n 
C45 C44 A1A1I sing 28 n n 
C43 C44 A1A1I sing 29 n n 
S1 O1 A1A1I doub 30 n n 
S1 C5 A1A1I sing 31 n n 
C5 C8 A1A1I sing 32 n n 
C5 C6 A1A1I sing 33 n n 
C8 C7 A1A1I sing 34 n n 
C6 C7 A1A1I sing 35 n n 
C7 C9 A1A1I sing 36 n n 
C7 C12 A1A1I sing 37 n n 
C9 C10 A1A1I sing 38 n n 
C12 C11 A1A1I sing 39 n n 
C10 N1 A1A1I sing 40 n n 
C11 N1 A1A1I sing 41 n n 
N1 C13 A1A1I sing 42 n n 
C13 C14 A1A1I sing 43 n n 
C14 C18 A1A1I sing 44 n n 
C14 C15 A1A1I sing 45 n n 
C18 C17 A1A1I sing 46 n n 
C15 C16 A1A1I sing 47 n n 
C17 N2 A1A1I sing 48 n n 
C16 N2 A1A1I sing 49 n n 
N2 C19 A1A1I sing 50 n n 
C19 C20 A1A1I doub 51 n y 
C19 C31 A1A1I sing 52 n y 
C20 C21 A1A1I sing 53 n y 
F1 C31 A1A1I sing 54 n n 
C31 C23 A1A1I doub 55 n y 
C21 C22 A1A1I doub 56 n y 
C23 C22 A1A1I sing 57 n y 
C23 N3 A1A1I sing 58 n n 
C22 N4 A1A1I sing 59 n n 
N3 C30 A1A1I sing 60 n n 
N3 C24 A1A1I sing 61 n n 
N4 C24 A1A1I sing 62 n n 
N4 C25 A1A1I sing 63 n n 
C26 C25 A1A1I sing 64 n n 
C26 C27 A1A1I sing 65 n n 
O2 C29 A1A1I doub 66 n n 
O3 C28 A1A1I doub 67 n n 
C29 N5 A1A1I sing 68 n n 
C29 C25 A1A1I sing 69 n n 
C24 O4 A1A1I doub 70 n n 
C28 N5 A1A1I sing 71 n n 
C28 C27 A1A1I sing 72 n n 
C1 H1 A1A1I sing 73 n n 
C1 H2 A1A1I sing 74 n n 
C1 H3 A1A1I sing 75 n n 
C10 H4 A1A1I sing 76 n n 
C10 H5 A1A1I sing 77 n n 
C11 H6 A1A1I sing 78 n n 
C11 H7 A1A1I sing 79 n n 
C12 H8 A1A1I sing 80 n n 
C12 H9 A1A1I sing 81 n n 
C13 H10 A1A1I sing 82 n n 
C13 H11 A1A1I sing 83 n n 
C14 H12 A1A1I sing 84 n n 
C15 H13 A1A1I sing 85 n n 
C15 H14 A1A1I sing 86 n n 
C16 H15 A1A1I sing 87 n n 
C16 H16 A1A1I sing 88 n n 
C17 H17 A1A1I sing 89 n n 
C17 H18 A1A1I sing 90 n n 
C18 H19 A1A1I sing 91 n n 
C18 H20 A1A1I sing 92 n n 
C20 H21 A1A1I sing 93 n n 
C21 H22 A1A1I sing 94 n n 
C25 H23 A1A1I sing 95 n n 
C26 H24 A1A1I sing 96 n n 
C26 H25 A1A1I sing 97 n n 
C27 H26 A1A1I sing 98 n n 
C27 H27 A1A1I sing 99 n n 
C3 H28 A1A1I sing 100 n n 
C30 H29 A1A1I sing 101 n n 
C30 H30 A1A1I sing 102 n n 
C30 H31 A1A1I sing 103 n n 
C32 H32 A1A1I sing 104 n n 
C33 H33 A1A1I sing 105 n n 
C38 H34 A1A1I sing 106 n n 
C39 H35 A1A1I sing 107 n n 
C40 H36 A1A1I sing 108 n n 
C42 H37 A1A1I sing 109 n n 
C43 H38 A1A1I sing 110 n n 
C43 H39 A1A1I sing 111 n n 
C44 H40 A1A1I sing 112 n n 
C44 H41 A1A1I sing 113 n n 
C45 H42 A1A1I sing 114 n n 
C45 H43 A1A1I sing 115 n n 
C46 H44 A1A1I sing 116 n n 
C46 H45 A1A1I sing 117 n n 
C5 H46 A1A1I sing 118 n n 
C6 H47 A1A1I sing 119 n n 
C6 H48 A1A1I sing 120 n n 
C8 H49 A1A1I sing 121 n n 
C8 H50 A1A1I sing 122 n n 
C9 H51 A1A1I sing 123 n n 
C9 H52 A1A1I sing 124 n n 
N5 H54 A1A1I sing 125 n n 
N6 H55 A1A1I sing 126 n n 
#
_atom_sites.entry_id                     9D0X 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 4 ZN B 1 501 501 ZN ZN . 
E 5 A1A1I B 1 502 502 A1A1I 640 . 
#
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 C1 A1A1I . . . E 5 166.978 170.648 134.468 1 20.46 ? C1 A1A1I 502 B 1 
HETATM 2 C C10 A1A1I . . . E 5 172.102 169.113 142.889 1 32.52 ? C10 A1A1I 502 B 1 
HETATM 3 C C11 A1A1I . . . E 5 169.892 168.198 142.76 1 25.45 ? C11 A1A1I 502 B 1 
HETATM 4 C C12 A1A1I . . . E 5 170.457 167.555 141.514 1 25.66 ? C12 A1A1I 502 B 1 
HETATM 5 C C13 A1A1I . . . E 5 171.38 167.492 144.524 1 28.83 ? C13 A1A1I 502 B 1 
HETATM 6 C C14 A1A1I . . . E 5 170.985 167.652 145.971 1 25.96 ? C14 A1A1I 502 B 1 
HETATM 7 C C15 A1A1I . . . E 5 172.001 166.967 146.862 1 18.46 ? C15 A1A1I 502 B 1 
HETATM 8 C C16 A1A1I . . . E 5 171.754 167.323 148.312 1 24.11 ? C16 A1A1I 502 B 1 
HETATM 9 C C17 A1A1I . . . E 5 171.859 169.606 147.349 1 30.02 ? C17 A1A1I 502 B 1 
HETATM 10 C C18 A1A1I . . . E 5 170.765 169.084 146.431 1 21.95 ? C18 A1A1I 502 B 1 
HETATM 11 C C19 A1A1I . . . E 5 172.567 169.101 149.731 1 18.59 ? C19 A1A1I 502 B 1 
HETATM 12 C C2 A1A1I . . . E 5 168.432 170.548 134.846 1 18.99 ? C2 A1A1I 502 B 1 
HETATM 13 C C20 A1A1I . . . E 5 173.19 170.331 149.947 1 21.17 ? C20 A1A1I 502 B 1 
HETATM 14 C C21 A1A1I . . . E 5 173.732 170.661 151.167 1 34.23 ? C21 A1A1I 502 B 1 
HETATM 15 C C22 A1A1I . . . E 5 173.668 169.729 152.198 1 28.84 ? C22 A1A1I 502 B 1 
HETATM 16 C C23 A1A1I . . . E 5 173.057 168.48 151.989 1 18.67 ? C23 A1A1I 502 B 1 
HETATM 17 C C24 A1A1I . . . E 5 173.791 168.536 154.107 1 28.27 ? C24 A1A1I 502 B 1 
HETATM 18 C C25 A1A1I . . . E 5 174.809 170.819 154.215 1 18.42 ? C25 A1A1I 502 B 1 
HETATM 19 C C26 A1A1I . . . E 5 174.424 172.196 153.691 1 22.88 ? C26 A1A1I 502 B 1 
HETATM 20 C C27 A1A1I . . . E 5 175.315 173.3 154.231 1 35.38 ? C27 A1A1I 502 B 1 
HETATM 21 C C28 A1A1I . . . E 5 176.773 172.983 154.177 1 37.2 ? C28 A1A1I 502 B 1 
HETATM 22 C C29 A1A1I . . . E 5 176.289 170.577 154.112 1 24.31 ? C29 A1A1I 502 B 1 
HETATM 23 C C3 A1A1I . . . E 5 168.874 169.547 135.704 1 24.94 ? C3 A1A1I 502 B 1 
HETATM 24 C C30 A1A1I . . . E 5 172.644 166.434 153.404 1 19.08 ? C30 A1A1I 502 B 1 
HETATM 25 C C31 A1A1I . . . E 5 172.513 168.168 150.756 1 27.7 ? C31 A1A1I 502 B 1 
HETATM 26 C C32 A1A1I . . . E 5 171.122 170.356 135.539 1 28.74 ? C32 A1A1I 502 B 1 
HETATM 27 C C33 A1A1I . . . E 5 170.703 171.346 134.691 1 28.75 ? C33 A1A1I 502 B 1 
HETATM 28 C C34 A1A1I . . . E 5 169.362 171.452 134.337 1 20.06 ? C34 A1A1I 502 B 1 
HETATM 29 C C35 A1A1I . . . E 5 169.404 173.682 133.183 1 28.08 ? C35 A1A1I 502 B 1 
HETATM 30 C C36 A1A1I . . . E 5 170.877 175.334 133.628 1 28.27 ? C36 A1A1I 502 B 1 
HETATM 31 C C37 A1A1I . . . E 5 170.34 176.118 132.592 1 23.86 ? C37 A1A1I 502 B 1 
HETATM 32 C C38 A1A1I . . . E 5 169.284 175.546 131.891 1 27.69 ? C38 A1A1I 502 B 1 
HETATM 33 C C39 A1A1I . . . E 5 170.892 177.395 132.342 1 24.7 ? C39 A1A1I 502 B 1 
HETATM 34 C C4 A1A1I . . . E 5 170.202 169.45 136.044 1 24.75 ? C4 A1A1I 502 B 1 
HETATM 35 C C40 A1A1I . . . E 5 171.917 177.856 133.081 1 25.31 ? C40 A1A1I 502 B 1 
HETATM 36 C C41 A1A1I . . . E 5 172.466 177.063 134.134 1 27.64 ? C41 A1A1I 502 B 1 
HETATM 37 C C42 A1A1I . . . E 5 172.474 174.958 135.459 1 25.66 ? C42 A1A1I 502 B 1 
HETATM 38 C C43 A1A1I . . . E 5 172.521 175.584 136.852 1 26.52 ? C43 A1A1I 502 B 1 
HETATM 39 C C44 A1A1I . . . E 5 173.513 174.733 137.618 1 21.58 ? C44 A1A1I 502 B 1 
HETATM 40 C C45 A1A1I . . . E 5 174.386 174.065 136.616 1 23.4 ? C45 A1A1I 502 B 1 
HETATM 41 C C46 A1A1I . . . E 5 173.927 174.529 135.249 1 34.19 ? C46 A1A1I 502 B 1 
HETATM 42 C C5 A1A1I . . . E 5 171.277 169.059 138.565 1 25.48 ? C5 A1A1I 502 B 1 
HETATM 43 C C6 A1A1I . . . E 5 170.139 169.208 139.578 1 25.95 ? C6 A1A1I 502 B 1 
HETATM 44 C C7 A1A1I . . . E 5 171.08 168.677 140.682 1 29.38 ? C7 A1A1I 502 B 1 
HETATM 45 C C8 A1A1I . . . E 5 172.054 168.21 139.575 1 25.31 ? C8 A1A1I 502 B 1 
HETATM 46 C C9 A1A1I . . . E 5 171.642 169.763 141.602 1 28.23 ? C9 A1A1I 502 B 1 
HETATM 47 F F1 A1A1I . . . E 5 171.924 166.977 150.531 1 48.82 ? F1 A1A1I 502 B 1 
HETATM 48 N N1 A1A1I . . . E 5 170.972 168.596 143.659 1 28.68 ? N1 A1A1I 502 B 1 
HETATM 49 N N2 A1A1I . . . E 5 172.048 168.736 148.51 1 20.37 ? N2 A1A1I 502 B 1 
HETATM 50 N N3 A1A1I . . . E 5 173.141 167.772 153.172 1 9.9 ? N3 A1A1I 502 B 1 
HETATM 51 N N4 A1A1I . . . E 5 174.107 169.741 153.514 1 26.56 ? N4 A1A1I 502 B 1 
HETATM 52 N N5 A1A1I . . . E 5 177.133 171.655 154.198 1 25.01 ? N5 A1A1I 502 B 1 
HETATM 53 N N6 A1A1I . . . E 5 168.903 172.456 133.461 1 24.68 ? N6 A1A1I 502 B 1 
HETATM 54 N N7 A1A1I . . . E 5 170.417 174.129 133.927 1 30.43 ? N7 A1A1I 502 B 1 
HETATM 55 N N8 A1A1I . . . E 5 168.822 174.353 132.176 1 32.55 ? N8 A1A1I 502 B 1 
HETATM 56 N N9 A1A1I . . . E 5 171.927 175.808 134.389 1 26.31 ? N9 A1A1I 502 B 1 
HETATM 57 O O1 A1A1I . . . E 5 169.61 167.363 137.494 1 34.27 ? O1 A1A1I 502 B 1 
HETATM 58 O O2 A1A1I . . . E 5 176.742 169.461 153.965 1 46.05 ? O2 A1A1I 502 B 1 
HETATM 59 O O3 A1A1I . . . E 5 177.637 173.838 154.117 1 45.37 ? O3 A1A1I 502 B 1 
HETATM 60 O O4 A1A1I . . . E 5 174.034 168.219 155.258 1 39.57 ? O4 A1A1I 502 B 1 
HETATM 61 O O5 A1A1I . . . E 5 171.888 167.517 136.551 1 35.75 ? O5 A1A1I 502 B 1 
HETATM 62 O O6 A1A1I . . . E 5 173.405 177.47 134.822 1 40.67 ? O6 A1A1I 502 B 1 
HETATM 63 S S1 A1A1I . . . E 5 170.747 168.168 137.136 1 30.04 ? S1 A1A1I 502 B 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    36 
_model_server_stats.query_time_ms           374 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           63 
#