data_4GSY
#
_model_server_result.job_id            a_JzWI2se7R129uY8VvzIQ 
_model_server_result.datetime_utc      '2025-03-09 02:33:47' 
_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          4gsy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    4GSY 
#
_exptl.entry_id    4GSY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              503.47 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]methyl}-2-[3-(trifluoromethyl)phenoxy]benzoic acid' 
_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          102.99 
_cell.angle_gamma         90 
_cell.entry_id            4GSY 
_cell.length_a            45.984 
_cell.length_b            90.635 
_cell.length_c            48.409 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4GSY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 2 1 
A,B,C,D,E,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 C N N 
? 2 D N N 
#
_chem_comp.formula           'C25 H24 F3 N3 O5' 
_chem_comp.formula_weight    503.47 
_chem_comp.id                0Y5 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]methyl}-2-[3-(trifluoromethyl)phenoxy]benzoic acid' 
_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
O9 C8 0Y5 doub 1 n n 
N7 C8 0Y5 sing 2 n n 
N7 C5 0Y5 sing 3 n n 
C8 C2 0Y5 sing 4 n n 
F31 C30 0Y5 sing 5 n n 
O6 C5 0Y5 doub 6 n n 
C5 N4 0Y5 sing 7 n n 
C2 C1 0Y5 sing 8 n n 
C2 C3 0Y5 doub 9 n n 
F32 C30 0Y5 sing 10 n n 
C30 F33 0Y5 sing 11 n n 
C30 C28 0Y5 sing 12 n n 
N4 C3 0Y5 sing 13 n n 
N4 C10 0Y5 sing 14 n n 
C28 C27 0Y5 doub 15 n y 
C28 C29 0Y5 sing 16 n y 
C27 C26 0Y5 sing 17 n y 
C10 C15 0Y5 sing 18 n n 
C10 C11 0Y5 sing 19 n n 
C26 C25 0Y5 doub 20 n y 
C29 C24 0Y5 doub 21 n y 
C15 N14 0Y5 sing 22 n n 
C11 C12 0Y5 sing 23 n n 
C24 C25 0Y5 sing 24 n y 
C24 O23 0Y5 sing 25 n n 
N14 C16 0Y5 sing 26 n n 
N14 C13 0Y5 sing 27 n n 
C12 C13 0Y5 sing 28 n n 
O23 C21 0Y5 sing 29 n n 
C22 C21 0Y5 doub 30 n y 
C22 C17 0Y5 sing 31 n y 
C16 C17 0Y5 sing 32 n n 
C21 C20 0Y5 sing 33 n y 
C17 C18 0Y5 doub 34 n y 
C20 C19 0Y5 doub 35 n y 
C20 C34 0Y5 sing 36 n n 
C18 C19 0Y5 sing 37 n y 
O36 C34 0Y5 doub 38 n n 
C34 O35 0Y5 sing 39 n n 
C26 H1 0Y5 sing 40 n n 
C19 H2 0Y5 sing 41 n n 
C27 H3 0Y5 sing 42 n n 
C18 H4 0Y5 sing 43 n n 
C25 H5 0Y5 sing 44 n n 
C22 H6 0Y5 sing 45 n n 
C29 H7 0Y5 sing 46 n n 
C3 H8 0Y5 sing 47 n n 
C12 H9 0Y5 sing 48 n n 
C12 H10 0Y5 sing 49 n n 
C11 H11 0Y5 sing 50 n n 
C11 H12 0Y5 sing 51 n n 
C13 H13 0Y5 sing 52 n n 
C13 H14 0Y5 sing 53 n n 
C15 H15 0Y5 sing 54 n n 
C15 H16 0Y5 sing 55 n n 
C10 H17 0Y5 sing 56 n n 
C1 H18 0Y5 sing 57 n n 
C1 H19 0Y5 sing 58 n n 
C1 H20 0Y5 sing 59 n n 
C16 H21 0Y5 sing 60 n n 
C16 H22 0Y5 sing 61 n n 
N7 H23 0Y5 sing 62 n n 
O35 H25 0Y5 sing 63 n n 
#
_atom_sites.entry_id                     4GSY 
_atom_sites.fract_transf_matrix[1][1]    0.021747 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005017 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011033 
_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]    0.0212 
_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 0Y5 A 1 301 1 0Y5 0Y5 . 
D 2 0Y5 B 1 301 2 0Y5 0Y5 . 
E 3 HOH A 1 401 1 HOH HOH . 
E 3 HOH A 2 402 2 HOH HOH . 
E 3 HOH A 3 403 6 HOH HOH . 
E 3 HOH A 4 404 9 HOH HOH . 
E 3 HOH A 5 405 10 HOH HOH . 
E 3 HOH A 6 406 12 HOH HOH . 
E 3 HOH A 7 407 13 HOH HOH . 
E 3 HOH A 8 408 17 HOH HOH . 
E 3 HOH A 9 409 18 HOH HOH . 
E 3 HOH A 10 410 21 HOH HOH . 
E 3 HOH A 11 411 22 HOH HOH . 
E 3 HOH A 12 412 24 HOH HOH . 
E 3 HOH A 13 413 27 HOH HOH . 
E 3 HOH A 14 414 28 HOH HOH . 
E 3 HOH A 15 415 29 HOH HOH . 
E 3 HOH A 16 416 30 HOH HOH . 
E 3 HOH A 17 417 31 HOH HOH . 
E 3 HOH A 18 418 35 HOH HOH . 
E 3 HOH A 19 419 36 HOH HOH . 
E 3 HOH A 20 420 41 HOH HOH . 
E 3 HOH A 21 421 43 HOH HOH . 
E 3 HOH A 22 422 46 HOH HOH . 
E 3 HOH A 23 423 48 HOH HOH . 
E 3 HOH A 24 424 49 HOH HOH . 
E 3 HOH A 25 425 50 HOH HOH . 
E 3 HOH A 26 426 51 HOH HOH . 
E 3 HOH A 27 427 52 HOH HOH . 
E 3 HOH A 28 428 53 HOH HOH . 
E 3 HOH A 29 429 54 HOH HOH . 
E 3 HOH A 30 430 56 HOH HOH . 
E 3 HOH A 31 431 57 HOH HOH . 
E 3 HOH A 32 432 60 HOH HOH . 
E 3 HOH A 33 433 61 HOH HOH . 
E 3 HOH A 34 434 62 HOH HOH . 
E 3 HOH A 35 435 63 HOH HOH . 
E 3 HOH A 36 436 64 HOH HOH . 
E 3 HOH A 37 437 67 HOH HOH . 
E 3 HOH A 38 438 68 HOH HOH . 
E 3 HOH A 39 439 69 HOH HOH . 
E 3 HOH A 40 440 70 HOH HOH . 
E 3 HOH A 41 441 71 HOH HOH . 
E 3 HOH A 42 442 73 HOH HOH . 
E 3 HOH A 43 443 74 HOH HOH . 
E 3 HOH A 44 444 75 HOH HOH . 
E 3 HOH A 45 445 78 HOH HOH . 
E 3 HOH A 46 446 80 HOH HOH . 
E 3 HOH A 47 447 85 HOH HOH . 
E 3 HOH A 48 448 87 HOH HOH . 
E 3 HOH A 49 449 88 HOH HOH . 
E 3 HOH A 50 450 91 HOH HOH . 
E 3 HOH A 51 451 92 HOH HOH . 
E 3 HOH A 52 452 93 HOH HOH . 
E 3 HOH A 53 453 95 HOH HOH . 
E 3 HOH A 54 454 98 HOH HOH . 
E 3 HOH A 55 455 101 HOH HOH . 
E 3 HOH A 56 456 104 HOH HOH . 
E 3 HOH A 57 457 108 HOH HOH . 
E 3 HOH A 58 458 109 HOH HOH . 
E 3 HOH A 59 459 113 HOH HOH . 
E 3 HOH A 60 460 114 HOH HOH . 
E 3 HOH A 61 461 118 HOH HOH . 
E 3 HOH A 62 462 119 HOH HOH . 
E 3 HOH A 63 463 120 HOH HOH . 
E 3 HOH A 64 464 121 HOH HOH . 
E 3 HOH A 65 465 123 HOH HOH . 
E 3 HOH A 66 466 124 HOH HOH . 
E 3 HOH A 67 467 126 HOH HOH . 
E 3 HOH A 68 468 127 HOH HOH . 
E 3 HOH A 69 469 130 HOH HOH . 
E 3 HOH A 70 470 133 HOH HOH . 
E 3 HOH A 71 471 136 HOH HOH . 
E 3 HOH A 72 472 137 HOH HOH . 
E 3 HOH A 73 473 141 HOH HOH . 
E 3 HOH A 74 474 144 HOH HOH . 
E 3 HOH A 75 475 145 HOH HOH . 
E 3 HOH A 76 476 147 HOH HOH . 
E 3 HOH A 77 477 148 HOH HOH . 
E 3 HOH A 78 478 149 HOH HOH . 
E 3 HOH A 79 479 150 HOH HOH . 
E 3 HOH A 80 480 153 HOH HOH . 
E 3 HOH A 81 481 154 HOH HOH . 
E 3 HOH A 82 482 156 HOH HOH . 
E 3 HOH A 83 483 157 HOH HOH . 
E 3 HOH A 84 484 158 HOH HOH . 
E 3 HOH A 85 485 159 HOH HOH . 
E 3 HOH A 86 486 160 HOH HOH . 
E 3 HOH A 87 487 161 HOH HOH . 
F 3 HOH B 1 401 3 HOH HOH . 
F 3 HOH B 2 402 4 HOH HOH . 
F 3 HOH B 3 403 5 HOH HOH . 
F 3 HOH B 4 404 7 HOH HOH . 
F 3 HOH B 5 405 8 HOH HOH . 
F 3 HOH B 6 406 11 HOH HOH . 
F 3 HOH B 7 407 14 HOH HOH . 
F 3 HOH B 8 408 15 HOH HOH . 
F 3 HOH B 9 409 16 HOH HOH . 
F 3 HOH B 10 410 19 HOH HOH . 
F 3 HOH B 11 411 20 HOH HOH . 
F 3 HOH B 12 412 23 HOH HOH . 
F 3 HOH B 13 413 25 HOH HOH . 
F 3 HOH B 14 414 26 HOH HOH . 
F 3 HOH B 15 415 32 HOH HOH . 
F 3 HOH B 16 416 33 HOH HOH . 
F 3 HOH B 17 417 34 HOH HOH . 
F 3 HOH B 18 418 37 HOH HOH . 
F 3 HOH B 19 419 38 HOH HOH . 
F 3 HOH B 20 420 39 HOH HOH . 
F 3 HOH B 21 421 40 HOH HOH . 
F 3 HOH B 22 422 42 HOH HOH . 
F 3 HOH B 23 423 44 HOH HOH . 
F 3 HOH B 24 424 45 HOH HOH . 
F 3 HOH B 25 425 47 HOH HOH . 
F 3 HOH B 26 426 55 HOH HOH . 
F 3 HOH B 27 427 58 HOH HOH . 
F 3 HOH B 28 428 59 HOH HOH . 
F 3 HOH B 29 429 65 HOH HOH . 
F 3 HOH B 30 430 66 HOH HOH . 
F 3 HOH B 31 431 72 HOH HOH . 
F 3 HOH B 32 432 76 HOH HOH . 
F 3 HOH B 33 433 77 HOH HOH . 
F 3 HOH B 34 434 79 HOH HOH . 
F 3 HOH B 35 435 81 HOH HOH . 
F 3 HOH B 36 436 82 HOH HOH . 
F 3 HOH B 37 437 83 HOH HOH . 
F 3 HOH B 38 438 84 HOH HOH . 
F 3 HOH B 39 439 86 HOH HOH . 
F 3 HOH B 40 440 89 HOH HOH . 
F 3 HOH B 41 441 90 HOH HOH . 
F 3 HOH B 42 442 94 HOH HOH . 
F 3 HOH B 43 443 96 HOH HOH . 
F 3 HOH B 44 444 97 HOH HOH . 
F 3 HOH B 45 445 99 HOH HOH . 
F 3 HOH B 46 446 100 HOH HOH . 
F 3 HOH B 47 447 102 HOH HOH . 
F 3 HOH B 48 448 105 HOH HOH . 
F 3 HOH B 49 449 106 HOH HOH . 
F 3 HOH B 50 450 107 HOH HOH . 
F 3 HOH B 51 451 110 HOH HOH . 
F 3 HOH B 52 452 111 HOH HOH . 
F 3 HOH B 53 453 112 HOH HOH . 
F 3 HOH B 54 454 115 HOH HOH . 
F 3 HOH B 55 455 116 HOH HOH . 
F 3 HOH B 56 456 117 HOH HOH . 
F 3 HOH B 57 457 122 HOH HOH . 
F 3 HOH B 58 458 125 HOH HOH . 
F 3 HOH B 59 459 128 HOH HOH . 
F 3 HOH B 60 460 129 HOH HOH . 
F 3 HOH B 61 461 131 HOH HOH . 
F 3 HOH B 62 462 132 HOH HOH . 
F 3 HOH B 63 463 134 HOH HOH . 
F 3 HOH B 64 464 138 HOH HOH . 
F 3 HOH B 65 465 139 HOH HOH . 
F 3 HOH B 66 466 140 HOH HOH . 
F 3 HOH B 67 467 142 HOH HOH . 
F 3 HOH B 68 468 143 HOH HOH . 
F 3 HOH B 69 469 146 HOH HOH . 
F 3 HOH B 70 470 151 HOH HOH . 
F 3 HOH B 71 471 152 HOH HOH . 
F 3 HOH B 72 472 155 HOH HOH . 
F 3 HOH B 73 473 162 HOH HOH . 
F 3 HOH B 74 474 163 HOH HOH . 
F 3 HOH B 75 475 164 HOH HOH . 
F 3 HOH B 76 476 165 HOH HOH . 
F 3 HOH B 77 477 166 HOH HOH . 
F 3 HOH B 78 478 167 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 C26 0Y5 . . . C 2 10.436 -1.849 26.976 1 21.25 ? C26 0Y5 301 A 1 
HETATM 2 C C19 0Y5 . . . C 2 8.593 1.312 31.547 1 30.66 ? C19 0Y5 301 A 1 
HETATM 3 C C27 0Y5 . . . C 2 11.458 -1.733 26.056 1 22.28 ? C27 0Y5 301 A 1 
HETATM 4 C C18 0Y5 . . . C 2 7.545 1.97 30.952 1 30.26 ? C18 0Y5 301 A 1 
HETATM 5 C C25 0Y5 . . . C 2 10.262 -0.836 27.907 1 26.43 ? C25 0Y5 301 A 1 
HETATM 6 C C22 0Y5 . . . C 2 8.788 2.143 28.904 1 26.73 ? C22 0Y5 301 A 1 
HETATM 7 C C29 0Y5 . . . C 2 12.116 0.376 26.98 1 24.87 ? C29 0Y5 301 A 1 
HETATM 8 C C20 0Y5 . . . C 2 9.744 1.076 30.828 1 29.16 ? C20 0Y5 301 A 1 
HETATM 9 C C17 0Y5 . . . C 2 7.627 2.363 29.626 1 29.65 ? C17 0Y5 301 A 1 
HETATM 10 C C28 0Y5 . . . C 2 12.299 -0.631 26.046 1 25.53 ? C28 0Y5 301 A 1 
HETATM 11 C C24 0Y5 . . . C 2 11.099 0.268 27.895 1 26.72 ? C24 0Y5 301 A 1 
HETATM 12 C C21 0Y5 . . . C 2 9.845 1.495 29.507 1 27.29 ? C21 0Y5 301 A 1 
HETATM 13 C C3 0Y5 . . . C 2 6.044 -1.157 25.422 1 23.02 ? C3 0Y5 301 A 1 
HETATM 14 C C2 0Y5 . . . C 2 6.521 -1.892 24.406 1 19.19 ? C2 0Y5 301 A 1 
HETATM 15 C C8 0Y5 . . . C 2 6.417 -1.284 23.052 1 19.56 ? C8 0Y5 301 A 1 
HETATM 16 C C5 0Y5 . . . C 2 5.429 0.753 24.069 1 21.11 ? C5 0Y5 301 A 1 
HETATM 17 C C34 0Y5 . . . C 2 10.83 0.444 31.579 1 33.84 ? C34 0Y5 301 A 1 
HETATM 18 C C12 0Y5 . . . C 2 3.558 0.692 28.57 1 23.56 ? C12 0Y5 301 A 1 
HETATM 19 C C11 0Y5 . . . C 2 4.037 -0.05 27.324 1 22.4 ? C11 0Y5 301 A 1 
HETATM 20 C C13 0Y5 . . . C 2 4.724 1.361 29.275 1 22.25 ? C13 0Y5 301 A 1 
HETATM 21 C C15 0Y5 . . . C 2 6.052 1.477 27.255 1 23.06 ? C15 0Y5 301 A 1 
HETATM 22 C C10 0Y5 . . . C 2 4.96 0.81 26.449 1 20.09 ? C10 0Y5 301 A 1 
HETATM 23 C C1 0Y5 . . . C 2 7.103 -3.262 24.552 1 18.9 ? C1 0Y5 301 A 1 
HETATM 24 C C16 0Y5 . . . C 2 6.464 3.061 28.995 1 26.89 ? C16 0Y5 301 A 1 
HETATM 25 C C30 0Y5 . . . C 2 13.378 -0.488 25.029 1 27.24 ? C30 0Y5 301 A 1 
HETATM 26 N N7 0Y5 . . . C 2 5.86 -0.009 23.008 1 19.11 ? N7 0Y5 301 A 1 
HETATM 27 N N4 0Y5 . . . C 2 5.503 0.118 25.303 1 20.19 ? N4 0Y5 301 A 1 
HETATM 28 N N14 0Y5 . . . C 2 5.432 2.255 28.339 1 24.47 ? N14 0Y5 301 A 1 
HETATM 29 O O9 0Y5 . . . C 2 6.81 -1.88 22.062 1 20.7 ? O9 0Y5 301 A 1 
HETATM 30 O O6 0Y5 . . . C 2 5.037 1.913 23.92 1 21.94 ? O6 0Y5 301 A 1 
HETATM 31 O O35 0Y5 . . . C 2 11.256 0.912 32.625 1 36.8 ? O35 0Y5 301 A 1 
HETATM 32 O O36 0Y5 . . . C 2 11.271 -0.693 30.991 1 34.72 ? O36 0Y5 301 A 1 
HETATM 33 O O23 0Y5 . . . C 2 11.009 1.336 28.776 1 27.47 ? O23 0Y5 301 A 1 
HETATM 34 F F31 0Y5 . . . C 2 12.985 -0.836 23.773 1 24.17 ? F31 0Y5 301 A 1 
HETATM 35 F F32 0Y5 . . . C 2 13.817 0.783 24.862 1 27.03 ? F32 0Y5 301 A 1 
HETATM 36 F F33 0Y5 . . . C 2 14.468 -1.226 25.32 1 27.09 ? F33 0Y5 301 A 1 
#
_model_server_stats.io_time_ms              50 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           36 
#