data_4HDC
#
_model_server_result.job_id            -HIYuU_8dlZMCooxgPZRLA 
_model_server_result.datetime_utc      '2025-03-26 14:57:51' 
_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          4hdc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    4HDC 
#
_exptl.entry_id    4HDC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              526.024 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '2-(3-chlorophenoxy)-4-{(1R)-3-methyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]butyl}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          101.44 
_cell.angle_gamma         90 
_cell.entry_id            4HDC 
_cell.length_a            46.53 
_cell.length_b            90.736 
_cell.length_c            48.346 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4HDC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 
#
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           'C28 H32 Cl N3 O5' 
_chem_comp.formula_weight    526.024 
_chem_comp.id                13Y 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '2-(3-chlorophenoxy)-4-{(1R)-3-methyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]butyl}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
O31 C30 13Y doub 1 n n 
N32 C30 13Y sing 2 n n 
N32 C34 13Y sing 3 n n 
C30 C29 13Y sing 4 n n 
O35 C34 13Y doub 5 n n 
C34 N27 13Y sing 6 n n 
C29 C36 13Y sing 7 n n 
C29 C28 13Y doub 8 n n 
CL1 C2 13Y sing 9 n n 
N27 C28 13Y sing 10 n n 
N27 C25 13Y sing 11 n n 
C3 C2 13Y doub 12 n y 
C3 C4 13Y sing 13 n y 
C2 C7 13Y sing 14 n y 
C25 C26 13Y sing 15 n n 
C25 C24 13Y sing 16 n n 
C4 C5 13Y doub 17 n y 
C7 C6 13Y doub 18 n y 
C26 N20 13Y sing 19 n n 
C19 C17 13Y sing 20 n n 
C24 C23 13Y sing 21 n n 
C5 C6 13Y sing 22 n y 
C6 O8 13Y sing 23 n n 
C16 C17 13Y sing 24 n n 
C16 C15 13Y sing 25 n n 
N20 C15 13Y sing 26 n n 
N20 C22 13Y sing 27 n n 
C17 C18 13Y sing 28 n n 
C23 C22 13Y sing 29 n n 
O8 C9 13Y sing 30 n n 
C14 C9 13Y doub 31 n y 
C14 C13 13Y sing 32 n y 
C15 C13 13Y sing 33 n n 
C9 C10 13Y sing 34 n y 
C13 C12 13Y doub 35 n y 
C10 C11 13Y doub 36 n y 
C10 C37 13Y sing 37 n n 
C12 C11 13Y sing 38 n y 
O39 C37 13Y doub 39 n n 
C37 O38 13Y sing 40 n n 
C4 H1 13Y sing 41 n n 
C5 H2 13Y sing 42 n n 
C3 H3 13Y sing 43 n n 
C7 H4 13Y sing 44 n n 
C11 H5 13Y sing 45 n n 
C12 H6 13Y sing 46 n n 
C14 H7 13Y sing 47 n n 
C15 H8 13Y sing 48 n n 
C16 H9 13Y sing 49 n n 
C16 H10 13Y sing 50 n n 
C17 H11 13Y sing 51 n n 
C18 H12 13Y sing 52 n n 
C18 H13 13Y sing 53 n n 
C18 H14 13Y sing 54 n n 
C19 H15 13Y sing 55 n n 
C19 H16 13Y sing 56 n n 
C19 H17 13Y sing 57 n n 
C22 H19 13Y sing 58 n n 
C22 H20 13Y sing 59 n n 
C23 H21 13Y sing 60 n n 
C23 H22 13Y sing 61 n n 
C24 H23 13Y sing 62 n n 
C24 H24 13Y sing 63 n n 
C25 H25 13Y sing 64 n n 
C26 H26 13Y sing 65 n n 
C26 H27 13Y sing 66 n n 
C28 H28 13Y sing 67 n n 
N32 H29 13Y sing 68 n n 
C36 H30 13Y sing 69 n n 
C36 H31 13Y sing 70 n n 
C36 H32 13Y sing 71 n n 
O38 H33 13Y sing 72 n n 
#
_atom_sites.entry_id                     4HDC 
_atom_sites.fract_transf_matrix[1][1]    0.021492 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004349 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011021 
_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]    0.021103 
_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 13Y A 1 301 1 13Y 13Y . 
D 2 13Y B 1 301 1 13Y 13Y . 
E 3 HOH A 1 401 2 HOH HOH . 
E 3 HOH A 2 402 3 HOH HOH . 
E 3 HOH A 3 403 4 HOH HOH . 
E 3 HOH A 4 404 5 HOH HOH . 
E 3 HOH A 5 405 7 HOH HOH . 
E 3 HOH A 6 406 9 HOH HOH . 
E 3 HOH A 7 407 12 HOH HOH . 
E 3 HOH A 8 408 16 HOH HOH . 
E 3 HOH A 9 409 17 HOH HOH . 
E 3 HOH A 10 410 18 HOH HOH . 
E 3 HOH A 11 411 20 HOH HOH . 
E 3 HOH A 12 412 21 HOH HOH . 
E 3 HOH A 13 413 25 HOH HOH . 
E 3 HOH A 14 414 29 HOH HOH . 
E 3 HOH A 15 415 34 HOH HOH . 
E 3 HOH A 16 416 36 HOH HOH . 
E 3 HOH A 17 417 38 HOH HOH . 
E 3 HOH A 18 418 40 HOH HOH . 
E 3 HOH A 19 419 41 HOH HOH . 
E 3 HOH A 20 420 45 HOH HOH . 
E 3 HOH A 21 421 46 HOH HOH . 
E 3 HOH A 22 422 49 HOH HOH . 
E 3 HOH A 23 423 50 HOH HOH . 
E 3 HOH A 24 424 54 HOH HOH . 
E 3 HOH A 25 425 55 HOH HOH . 
E 3 HOH A 26 426 56 HOH HOH . 
E 3 HOH A 27 427 58 HOH HOH . 
E 3 HOH A 28 428 60 HOH HOH . 
E 3 HOH A 29 429 62 HOH HOH . 
E 3 HOH A 30 430 63 HOH HOH . 
E 3 HOH A 31 431 66 HOH HOH . 
E 3 HOH A 32 432 67 HOH HOH . 
E 3 HOH A 33 433 68 HOH HOH . 
E 3 HOH A 34 434 69 HOH HOH . 
E 3 HOH A 35 435 74 HOH HOH . 
E 3 HOH A 36 436 75 HOH HOH . 
E 3 HOH A 37 437 77 HOH HOH . 
E 3 HOH A 38 438 80 HOH HOH . 
E 3 HOH A 39 439 81 HOH HOH . 
E 3 HOH A 40 440 85 HOH HOH . 
E 3 HOH A 41 441 86 HOH HOH . 
E 3 HOH A 42 442 87 HOH HOH . 
E 3 HOH A 43 443 91 HOH HOH . 
E 3 HOH A 44 444 92 HOH HOH . 
E 3 HOH A 45 445 95 HOH HOH . 
E 3 HOH A 46 446 97 HOH HOH . 
E 3 HOH A 47 447 98 HOH HOH . 
E 3 HOH A 48 448 103 HOH HOH . 
E 3 HOH A 49 449 107 HOH HOH . 
E 3 HOH A 50 450 108 HOH HOH . 
E 3 HOH A 51 451 110 HOH HOH . 
E 3 HOH A 52 452 111 HOH HOH . 
E 3 HOH A 53 453 112 HOH HOH . 
E 3 HOH A 54 454 115 HOH HOH . 
E 3 HOH A 55 455 116 HOH HOH . 
E 3 HOH A 56 456 117 HOH HOH . 
E 3 HOH A 57 457 118 HOH HOH . 
E 3 HOH A 58 458 119 HOH HOH . 
E 3 HOH A 59 459 123 HOH HOH . 
E 3 HOH A 60 460 125 HOH HOH . 
E 3 HOH A 61 461 126 HOH HOH . 
E 3 HOH A 62 462 127 HOH HOH . 
E 3 HOH A 63 463 128 HOH HOH . 
E 3 HOH A 64 464 131 HOH HOH . 
E 3 HOH A 65 465 132 HOH HOH . 
E 3 HOH A 66 466 136 HOH HOH . 
E 3 HOH A 67 467 137 HOH HOH . 
E 3 HOH A 68 468 138 HOH HOH . 
E 3 HOH A 69 469 141 HOH HOH . 
E 3 HOH A 70 470 143 HOH HOH . 
E 3 HOH A 71 471 144 HOH HOH . 
E 3 HOH A 72 472 149 HOH HOH . 
E 3 HOH A 73 473 152 HOH HOH . 
E 3 HOH A 74 474 155 HOH HOH . 
E 3 HOH A 75 475 156 HOH HOH . 
E 3 HOH A 76 476 161 HOH HOH . 
E 3 HOH A 77 477 162 HOH HOH . 
F 3 HOH B 1 401 1 HOH HOH . 
F 3 HOH B 2 402 6 HOH HOH . 
F 3 HOH B 3 403 8 HOH HOH . 
F 3 HOH B 4 404 10 HOH HOH . 
F 3 HOH B 5 405 11 HOH HOH . 
F 3 HOH B 6 406 13 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 19 HOH HOH . 
F 3 HOH B 10 410 22 HOH HOH . 
F 3 HOH B 11 411 23 HOH HOH . 
F 3 HOH B 12 412 24 HOH HOH . 
F 3 HOH B 13 413 26 HOH HOH . 
F 3 HOH B 14 414 27 HOH HOH . 
F 3 HOH B 15 415 28 HOH HOH . 
F 3 HOH B 16 416 30 HOH HOH . 
F 3 HOH B 17 417 31 HOH HOH . 
F 3 HOH B 18 418 32 HOH HOH . 
F 3 HOH B 19 419 33 HOH HOH . 
F 3 HOH B 20 420 35 HOH HOH . 
F 3 HOH B 21 421 37 HOH HOH . 
F 3 HOH B 22 422 39 HOH HOH . 
F 3 HOH B 23 423 42 HOH HOH . 
F 3 HOH B 24 424 43 HOH HOH . 
F 3 HOH B 25 425 44 HOH HOH . 
F 3 HOH B 26 426 47 HOH HOH . 
F 3 HOH B 27 427 48 HOH HOH . 
F 3 HOH B 28 428 51 HOH HOH . 
F 3 HOH B 29 429 52 HOH HOH . 
F 3 HOH B 30 430 53 HOH HOH . 
F 3 HOH B 31 431 57 HOH HOH . 
F 3 HOH B 32 432 59 HOH HOH . 
F 3 HOH B 33 433 61 HOH HOH . 
F 3 HOH B 34 434 64 HOH HOH . 
F 3 HOH B 35 435 65 HOH HOH . 
F 3 HOH B 36 436 70 HOH HOH . 
F 3 HOH B 37 437 71 HOH HOH . 
F 3 HOH B 38 438 72 HOH HOH . 
F 3 HOH B 39 439 73 HOH HOH . 
F 3 HOH B 40 440 76 HOH HOH . 
F 3 HOH B 41 441 78 HOH HOH . 
F 3 HOH B 42 442 79 HOH HOH . 
F 3 HOH B 43 443 82 HOH HOH . 
F 3 HOH B 44 444 83 HOH HOH . 
F 3 HOH B 45 445 84 HOH HOH . 
F 3 HOH B 46 446 88 HOH HOH . 
F 3 HOH B 47 447 89 HOH HOH . 
F 3 HOH B 48 448 90 HOH HOH . 
F 3 HOH B 49 449 93 HOH HOH . 
F 3 HOH B 50 450 94 HOH HOH . 
F 3 HOH B 51 451 96 HOH HOH . 
F 3 HOH B 52 452 99 HOH HOH . 
F 3 HOH B 53 453 100 HOH HOH . 
F 3 HOH B 54 454 101 HOH HOH . 
F 3 HOH B 55 455 102 HOH HOH . 
F 3 HOH B 56 456 104 HOH HOH . 
F 3 HOH B 57 457 105 HOH HOH . 
F 3 HOH B 58 458 106 HOH HOH . 
F 3 HOH B 59 459 109 HOH HOH . 
F 3 HOH B 60 460 113 HOH HOH . 
F 3 HOH B 61 461 114 HOH HOH . 
F 3 HOH B 62 462 120 HOH HOH . 
F 3 HOH B 63 463 121 HOH HOH . 
F 3 HOH B 64 464 122 HOH HOH . 
F 3 HOH B 65 465 124 HOH HOH . 
F 3 HOH B 66 466 129 HOH HOH . 
F 3 HOH B 67 467 130 HOH HOH . 
F 3 HOH B 68 468 133 HOH HOH . 
F 3 HOH B 69 469 134 HOH HOH . 
F 3 HOH B 70 470 135 HOH HOH . 
F 3 HOH B 71 471 139 HOH HOH . 
F 3 HOH B 72 472 140 HOH HOH . 
F 3 HOH B 73 473 142 HOH HOH . 
F 3 HOH B 74 474 145 HOH HOH . 
F 3 HOH B 75 475 146 HOH HOH . 
F 3 HOH B 76 476 147 HOH HOH . 
F 3 HOH B 77 477 148 HOH HOH . 
F 3 HOH B 78 478 150 HOH HOH . 
F 3 HOH B 79 479 151 HOH HOH . 
F 3 HOH B 80 480 153 HOH HOH . 
F 3 HOH B 81 481 154 HOH HOH . 
F 3 HOH B 82 482 157 HOH HOH . 
F 3 HOH B 83 483 158 HOH HOH . 
F 3 HOH B 84 484 159 HOH HOH . 
F 3 HOH B 85 485 160 HOH HOH . 
F 3 HOH B 86 486 163 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 C2 13Y . . . C 2 18.621 -0.564 2.455 1 27.59 ? C2 13Y 301 A 1 
HETATM 2 C C4 13Y . . . C 2 16.894 -1.897 3.445 1 28.48 ? C4 13Y 301 A 1 
HETATM 3 C C5 13Y . . . C 2 16.796 -0.963 4.475 1 28.96 ? C5 13Y 301 A 1 
HETATM 4 C C6 13Y . . . C 2 17.602 0.185 4.492 1 25.76 ? C6 13Y 301 A 1 
HETATM 5 CL CL1 13Y . . . C 2 19.699 -0.268 1.16 1 27.34 ? CL1 13Y 301 A 1 
HETATM 6 C C3 13Y . . . C 2 17.829 -1.712 2.444 1 26.49 ? C3 13Y 301 A 1 
HETATM 7 C C7 13Y . . . C 2 18.518 0.398 3.46 1 27.05 ? C7 13Y 301 A 1 
HETATM 8 O O8 13Y . . . C 2 17.522 1.125 5.508 1 25.14 ? O8 13Y 301 A 1 
HETATM 9 C C9 13Y . . . C 2 16.378 1.398 6.183 1 28.34 ? C9 13Y 301 A 1 
HETATM 10 C C10 13Y . . . C 2 16.226 1.06 7.554 1 30.72 ? C10 13Y 301 A 1 
HETATM 11 C C11 13Y . . . C 2 15.073 1.467 8.246 1 29.5 ? C11 13Y 301 A 1 
HETATM 12 C C12 13Y . . . C 2 14.079 2.161 7.577 1 30.28 ? C12 13Y 301 A 1 
HETATM 13 C C13 13Y . . . C 2 14.216 2.482 6.222 1 30.18 ? C13 13Y 301 A 1 
HETATM 14 C C14 13Y . . . C 2 15.372 2.106 5.541 1 29.12 ? C14 13Y 301 A 1 
HETATM 15 C C15 13Y . . . C 2 13.105 3.274 5.543 1 32.94 ? C15 13Y 301 A 1 
HETATM 16 C C16 13Y . . . C 2 13.497 4.444 4.611 1 38.84 ? C16 13Y 301 A 1 
HETATM 17 C C17 13Y . . . C 2 14.567 5.397 5.162 1 44.3 ? C17 13Y 301 A 1 
HETATM 18 C C18 13Y . . . C 2 13.986 6.303 6.257 1 45.49 ? C18 13Y 301 A 1 
HETATM 19 C C19 13Y . . . C 2 15.132 6.224 3.993 1 46.28 ? C19 13Y 301 A 1 
HETATM 20 N N20 13Y . . . C 2 12.021 2.472 4.933 1 30.89 ? N20 13Y 301 A 1 
HETATM 21 C C22 13Y . . . C 2 11.272 1.653 5.937 1 26.56 ? C22 13Y 301 A 1 
HETATM 22 C C23 13Y . . . C 2 10.015 1.055 5.323 1 24.51 ? C23 13Y 301 A 1 
HETATM 23 C C24 13Y . . . C 2 10.422 0.158 4.143 1 24.61 ? C24 13Y 301 A 1 
HETATM 24 C C25 13Y . . . C 2 11.231 0.984 3.118 1 24.66 ? C25 13Y 301 A 1 
HETATM 25 C C26 13Y . . . C 2 12.452 1.594 3.811 1 24.65 ? C26 13Y 301 A 1 
HETATM 26 N N27 13Y . . . C 2 11.656 0.237 1.91 1 25.01 ? N27 13Y 301 A 1 
HETATM 27 C C28 13Y . . . C 2 12.181 -1.04 2.06 1 24.34 ? C28 13Y 301 A 1 
HETATM 28 C C29 13Y . . . C 2 12.648 -1.761 1.018 1 19.62 ? C29 13Y 301 A 1 
HETATM 29 C C30 13Y . . . C 2 12.58 -1.177 -0.299 1 23.03 ? C30 13Y 301 A 1 
HETATM 30 O O31 13Y . . . C 2 12.933 -1.742 -1.351 1 25.8 ? O31 13Y 301 A 1 
HETATM 31 N N32 13Y . . . C 2 12.032 0.091 -0.346 1 18.58 ? N32 13Y 301 A 1 
HETATM 32 C C34 13Y . . . C 2 11.582 0.833 0.68 1 23.35 ? C34 13Y 301 A 1 
HETATM 33 O O35 13Y . . . C 2 11.143 1.96 0.509 1 26.06 ? O35 13Y 301 A 1 
HETATM 34 C C36 13Y . . . C 2 13.211 -3.147 1.174 1 19.29 ? C36 13Y 301 A 1 
HETATM 35 C C37 13Y . . . C 2 17.258 0.284 8.262 1 33.35 ? C37 13Y 301 A 1 
HETATM 36 O O38 13Y . . . C 2 17.737 0.688 9.327 1 31.05 ? O38 13Y 301 A 1 
HETATM 37 O O39 13Y . . . C 2 17.637 -0.865 7.732 1 32.27 ? O39 13Y 301 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           37 
#