data_4LI8
#
_model_server_result.job_id            Om77f3ilhu-JNFMAY90-Rg 
_model_server_result.datetime_utc      '2024-11-05 14:41:50' 
_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          4li8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1402}' 
#
_entry.id    4LI8 
#
_exptl.entry_id    4LI8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              524.607 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-[4-(4-fluorobenzoyl)piperidin-1-yl]-N-[(4-oxo-3,5,7,8-tetrahydro-4H-pyrano[4,3-d]pyrimidin-2-yl)methyl]-N-(thiophen-2-ylmethyl)acetamide 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          91.3 
_cell.angle_gamma         90 
_cell.entry_id            4LI8 
_cell.length_a            124.7 
_cell.length_b            43.1 
_cell.length_c            88.1 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4LI8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,K 1 1 
B,H,I,J,L 2 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
? 3 D N N 
? 3 I 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
metalc ? metalc1 A SG CYS 131 A CYS 1234 1_555 C ZN ZN . A ZN 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc2 A ND1 HIS 134 A HIS 1237 1_555 C ZN ZN . A ZN 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc3 A SG CYS 139 A CYS 1242 1_555 C ZN ZN . A ZN 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? 
metalc ? metalc4 A SG CYS 142 A CYS 1245 1_555 C ZN ZN . A ZN 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? 
metalc ? metalc5 B SG CYS 131 B CYS 1234 1_555 H ZN ZN . B ZN 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? 
metalc ? metalc6 B ND1 HIS 134 B HIS 1237 1_555 H ZN ZN . B ZN 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? 
metalc ? metalc7 B SG CYS 139 B CYS 1242 1_555 H ZN ZN . B ZN 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? 
metalc ? metalc8 B SG CYS 142 B CYS 1245 1_555 H ZN ZN . B ZN 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
#
_chem_comp.formula           'C27 H29 F N4 O4 S' 
_chem_comp.formula_weight    524.607 
_chem_comp.id                1XQ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-[4-(4-fluorobenzoyl)piperidin-1-yl]-N-[(4-oxo-3,5,7,8-tetrahydro-4H-pyrano[4,3-d]pyrimidin-2-yl)methyl]-N-(thiophen-2-ylmethyl)acetamide 
_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
C25 C26 1XQ sing 1 n y 
C25 C24 1XQ doub 2 n y 
C2 C1 1XQ sing 3 n n 
C2 C5 1XQ sing 4 n n 
C1 O1 1XQ sing 5 n n 
C23 C24 1XQ sing 6 n n 
C23 N3 1XQ sing 7 n n 
C26 C27 1XQ doub 8 n y 
C24 S1 1XQ sing 9 n y 
C10 C9 1XQ sing 10 n n 
C10 N4 1XQ sing 11 n n 
N1 C5 1XQ sing 12 n n 
N1 C6 1XQ doub 13 n n 
C11 N4 1XQ sing 14 n n 
C11 C12 1XQ sing 15 n n 
C5 C4 1XQ doub 16 n n 
O1 C3 1XQ sing 17 n n 
N3 C9 1XQ sing 18 n n 
N3 C8 1XQ sing 19 n n 
C27 S1 1XQ sing 20 n y 
C9 O3 1XQ doub 21 n n 
N4 C15 1XQ sing 22 n n 
C6 C8 1XQ sing 23 n n 
C6 N2 1XQ sing 24 n n 
C12 C13 1XQ sing 25 n n 
C4 C3 1XQ sing 26 n n 
C4 C7 1XQ sing 27 n n 
C15 C14 1XQ sing 28 n n 
C13 C14 1XQ sing 29 n n 
C13 C16 1XQ sing 30 n n 
N2 C7 1XQ sing 31 n n 
C7 O2 1XQ doub 32 n n 
C16 O4 1XQ doub 33 n n 
C16 C17 1XQ sing 34 n n 
C22 C17 1XQ doub 35 n y 
C22 C20 1XQ sing 36 n y 
C17 C18 1XQ sing 37 n y 
C20 C19 1XQ doub 38 n y 
C18 C21 1XQ doub 39 n y 
C19 C21 1XQ sing 40 n y 
C19 F1 1XQ sing 41 n n 
C1 H1 1XQ sing 42 n n 
C1 H2 1XQ sing 43 n n 
C2 H3 1XQ sing 44 n n 
C2 H4 1XQ sing 45 n n 
C3 H5 1XQ sing 46 n n 
C3 H6 1XQ sing 47 n n 
N2 H7 1XQ sing 48 n n 
C8 H8 1XQ sing 49 n n 
C8 H9 1XQ sing 50 n n 
C10 H10 1XQ sing 51 n n 
C10 H11 1XQ sing 52 n n 
C11 H13 1XQ sing 53 n n 
C11 H14 1XQ sing 54 n n 
C12 H15 1XQ sing 55 n n 
C12 H16 1XQ sing 56 n n 
C13 H17 1XQ sing 57 n n 
C14 H18 1XQ sing 58 n n 
C14 H19 1XQ sing 59 n n 
C15 H20 1XQ sing 60 n n 
C15 H21 1XQ sing 61 n n 
C18 H22 1XQ sing 62 n n 
C20 H23 1XQ sing 63 n n 
C21 H24 1XQ sing 64 n n 
C22 H25 1XQ sing 65 n n 
C23 H26 1XQ sing 66 n n 
C23 H27 1XQ sing 67 n n 
C25 H28 1XQ sing 68 n n 
C26 H29 1XQ sing 69 n n 
C27 H30 1XQ sing 70 n n 
#
_atom_sites.entry_id                     4LI8 
_atom_sites.fract_transf_matrix[1][1]    0.008019 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000182 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023202 
_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]    0.011354 
_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 2 ZN A 1 1401 1 ZN ZN . 
D 3 1XQ A 1 1402 1 1XQ LI1 . 
E 4 SO4 A 1 1403 1 SO4 SO4 . 
F 4 SO4 A 1 1404 3 SO4 SO4 . 
G 4 SO4 A 1 1405 4 SO4 SO4 . 
H 2 ZN B 1 1401 1 ZN ZN . 
I 3 1XQ B 1 1402 1 1XQ LI1 . 
J 4 SO4 B 1 1403 2 SO4 SO4 . 
K 5 HOH A 1 1501 2 HOH HOH . 
K 5 HOH A 2 1502 4 HOH HOH . 
K 5 HOH A 3 1503 7 HOH HOH . 
K 5 HOH A 4 1504 8 HOH HOH . 
K 5 HOH A 5 1505 9 HOH HOH . 
K 5 HOH A 6 1506 10 HOH HOH . 
K 5 HOH A 7 1507 11 HOH HOH . 
K 5 HOH A 8 1508 12 HOH HOH . 
K 5 HOH A 9 1509 15 HOH HOH . 
K 5 HOH A 10 1510 17 HOH HOH . 
K 5 HOH A 11 1511 21 HOH HOH . 
K 5 HOH A 12 1512 23 HOH HOH . 
K 5 HOH A 13 1513 25 HOH HOH . 
K 5 HOH A 14 1514 27 HOH HOH . 
K 5 HOH A 15 1515 29 HOH HOH . 
K 5 HOH A 16 1516 30 HOH HOH . 
K 5 HOH A 17 1517 32 HOH HOH . 
K 5 HOH A 18 1518 41 HOH HOH . 
K 5 HOH A 19 1519 46 HOH HOH . 
K 5 HOH A 20 1520 53 HOH HOH . 
K 5 HOH A 21 1521 65 HOH HOH . 
K 5 HOH A 22 1522 67 HOH HOH . 
K 5 HOH A 23 1523 69 HOH HOH . 
K 5 HOH A 24 1524 72 HOH HOH . 
K 5 HOH A 25 1525 79 HOH HOH . 
K 5 HOH A 26 1526 80 HOH HOH . 
K 5 HOH A 27 1527 82 HOH HOH . 
K 5 HOH A 28 1528 84 HOH HOH . 
K 5 HOH A 29 1529 85 HOH HOH . 
K 5 HOH A 30 1530 98 HOH HOH . 
K 5 HOH A 31 1531 101 HOH HOH . 
K 5 HOH A 32 1532 103 HOH HOH . 
K 5 HOH A 33 1533 127 HOH HOH . 
K 5 HOH A 34 1534 133 HOH HOH . 
K 5 HOH A 35 1535 138 HOH HOH . 
K 5 HOH A 36 1536 142 HOH HOH . 
K 5 HOH A 37 1537 143 HOH HOH . 
K 5 HOH A 38 1538 145 HOH HOH . 
K 5 HOH A 39 1539 148 HOH HOH . 
K 5 HOH A 40 1540 155 HOH HOH . 
K 5 HOH A 41 1541 156 HOH HOH . 
K 5 HOH A 42 1542 160 HOH HOH . 
K 5 HOH A 43 1543 168 HOH HOH . 
K 5 HOH A 44 1544 173 HOH HOH . 
K 5 HOH A 45 1545 179 HOH HOH . 
K 5 HOH A 46 1546 181 HOH HOH . 
L 5 HOH B 1 1501 1 HOH HOH . 
L 5 HOH B 2 1502 3 HOH HOH . 
L 5 HOH B 3 1503 6 HOH HOH . 
L 5 HOH B 4 1504 13 HOH HOH . 
L 5 HOH B 5 1505 14 HOH HOH . 
L 5 HOH B 6 1506 19 HOH HOH . 
L 5 HOH B 7 1507 22 HOH HOH . 
L 5 HOH B 8 1508 28 HOH HOH . 
L 5 HOH B 9 1509 31 HOH HOH . 
L 5 HOH B 10 1510 34 HOH HOH . 
L 5 HOH B 11 1511 37 HOH HOH . 
L 5 HOH B 12 1512 38 HOH HOH . 
L 5 HOH B 13 1513 42 HOH HOH . 
L 5 HOH B 14 1514 45 HOH HOH . 
L 5 HOH B 15 1515 47 HOH HOH . 
L 5 HOH B 16 1516 50 HOH HOH . 
L 5 HOH B 17 1517 55 HOH HOH . 
L 5 HOH B 18 1518 57 HOH HOH . 
L 5 HOH B 19 1519 58 HOH HOH . 
L 5 HOH B 20 1520 59 HOH HOH . 
L 5 HOH B 21 1521 63 HOH HOH . 
L 5 HOH B 22 1522 64 HOH HOH . 
L 5 HOH B 23 1523 70 HOH HOH . 
L 5 HOH B 24 1524 75 HOH HOH . 
L 5 HOH B 25 1525 87 HOH HOH . 
L 5 HOH B 26 1526 88 HOH HOH . 
L 5 HOH B 27 1527 89 HOH HOH . 
L 5 HOH B 28 1528 93 HOH HOH . 
L 5 HOH B 29 1529 94 HOH HOH . 
L 5 HOH B 30 1530 100 HOH HOH . 
L 5 HOH B 31 1531 107 HOH HOH . 
L 5 HOH B 32 1532 109 HOH HOH . 
L 5 HOH B 33 1533 122 HOH HOH . 
L 5 HOH B 34 1534 123 HOH HOH . 
L 5 HOH B 35 1535 124 HOH HOH . 
L 5 HOH B 36 1536 126 HOH HOH . 
L 5 HOH B 37 1537 128 HOH HOH . 
L 5 HOH B 38 1538 153 HOH HOH . 
L 5 HOH B 39 1539 154 HOH HOH . 
L 5 HOH B 40 1540 158 HOH HOH . 
L 5 HOH B 41 1541 159 HOH HOH . 
L 5 HOH B 42 1542 161 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 O O1 1XQ . . . D 3 -25.97 -13.114 7.942 1 40.8 ? O1 1XQ 1402 A 1 
HETATM 2 C C1 1XQ . . . D 3 -26.724 -12.623 6.838 1 34.99 ? C1 1XQ 1402 A 1 
HETATM 3 C C2 1XQ . . . D 3 -27.087 -11.161 7.136 1 28.46 ? C2 1XQ 1402 A 1 
HETATM 4 C C3 1XQ . . . D 3 -24.68 -12.513 8.088 1 34 ? C3 1XQ 1402 A 1 
HETATM 5 C C4 1XQ . . . D 3 -24.702 -11.006 7.875 1 28.26 ? C4 1XQ 1402 A 1 
HETATM 6 C C5 1XQ . . . D 3 -25.826 -10.382 7.436 1 28.58 ? C5 1XQ 1402 A 1 
HETATM 7 N N1 1XQ . . . D 3 -25.859 -9.004 7.231 1 31.38 ? N1 1XQ 1402 A 1 
HETATM 8 C C6 1XQ . . . D 3 -24.782 -8.336 7.483 1 29.05 ? C6 1XQ 1402 A 1 
HETATM 9 N N2 1XQ . . . D 3 -23.599 -8.91 7.937 1 22.18 ? N2 1XQ 1402 A 1 
HETATM 10 C C7 1XQ . . . D 3 -23.486 -10.226 8.149 1 24.98 ? C7 1XQ 1402 A 1 
HETATM 11 C C8 1XQ . . . D 3 -24.668 -6.845 7.295 1 27.79 ? C8 1XQ 1402 A 1 
HETATM 12 N N3 1XQ . . . D 3 -25.635 -5.984 7.986 1 31.37 ? N3 1XQ 1402 A 1 
HETATM 13 O O2 1XQ . . . D 3 -22.427 -10.691 8.548 1 27.41 ? O2 1XQ 1402 A 1 
HETATM 14 C C9 1XQ . . . D 3 -25.736 -6 9.341 1 29.48 ? C9 1XQ 1402 A 1 
HETATM 15 O O3 1XQ . . . D 3 -25.06 -6.766 10.042 1 27.68 ? O3 1XQ 1402 A 1 
HETATM 16 C C10 1XQ . . . D 3 -26.704 -5.044 10.054 1 26 ? C10 1XQ 1402 A 1 
HETATM 17 N N4 1XQ . . . D 3 -25.9 -4.246 11.024 1 30.82 ? N4 1XQ 1402 A 1 
HETATM 18 C C11 1XQ . . . D 3 -26.628 -3.112 11.597 1 29.86 ? C11 1XQ 1402 A 1 
HETATM 19 C C12 1XQ . . . D 3 -25.803 -2.571 12.775 1 30.83 ? C12 1XQ 1402 A 1 
HETATM 20 C C13 1XQ . . . D 3 -24.387 -2.117 12.352 1 35.4 ? C13 1XQ 1402 A 1 
HETATM 21 C C14 1XQ . . . D 3 -23.701 -3.224 11.517 1 33.88 ? C14 1XQ 1402 A 1 
HETATM 22 C C15 1XQ . . . D 3 -24.631 -3.794 10.437 1 30.64 ? C15 1XQ 1402 A 1 
HETATM 23 C C16 1XQ . . . D 3 -23.506 -1.743 13.56 1 32.53 ? C16 1XQ 1402 A 1 
HETATM 24 O O4 1XQ . . . D 3 -23.502 -2.492 14.536 1 32.87 ? O4 1XQ 1402 A 1 
HETATM 25 C C17 1XQ . . . D 3 -22.667 -0.502 13.484 1 28.02 ? C17 1XQ 1402 A 1 
HETATM 26 C C18 1XQ . . . D 3 -21.716 -0.232 14.504 1 29.76 ? C18 1XQ 1402 A 1 
HETATM 27 C C19 1XQ . . . D 3 -21.048 1.831 13.371 1 39.21 ? C19 1XQ 1402 A 1 
HETATM 28 C C20 1XQ . . . D 3 -21.982 1.568 12.357 1 26.6 ? C20 1XQ 1402 A 1 
HETATM 29 C C21 1XQ . . . D 3 -20.912 0.931 14.454 1 31.54 ? C21 1XQ 1402 A 1 
HETATM 30 C C22 1XQ . . . D 3 -22.784 0.416 12.418 1 27.3 ? C22 1XQ 1402 A 1 
HETATM 31 F F1 1XQ . . . D 3 -20.287 2.95 13.288 1 43.58 ? F1 1XQ 1402 A 1 
HETATM 32 C C23 1XQ . . . D 3 -26.358 -5.115 7.04 1 32.64 ? C23 1XQ 1402 A 1 
HETATM 33 C C24 1XQ . . . D 3 -25.656 -3.872 6.6 1 42.38 ? C24 1XQ 1402 A 1 
HETATM 34 C C25 1XQ . . . D 3 -26.112 -2.575 6.626 1 49.05 ? C25 1XQ 1402 A 1 
HETATM 35 C C26 1XQ . . . D 3 -25.168 -1.644 6.096 1 40.76 ? C26 1XQ 1402 A 1 
HETATM 36 C C27 1XQ . . . D 3 -24.016 -2.249 5.667 1 39.55 ? C27 1XQ 1402 A 1 
HETATM 37 S S1 1XQ . . . D 3 -24.057 -3.974 5.904 1 46.24 ? S1 1XQ 1402 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           37 
#