data_9IJT # _model_server_result.job_id NhsjsB-jcqGqyjDKVkCqTg _model_server_result.datetime_utc '2025-08-02 14:47:16' _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 9ijt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 9IJT # _exptl.entry_id 9IJT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 447.526 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2~{S})-1-[[4-methoxy-2-[(2-methyl-3-phenyl-phenyl)methoxy]pyrimidin-5-yl]methyl]piperidine-2-carboxylic 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 90 _cell.angle_gamma 90 _cell.entry_id 9IJT _cell.length_a 40.717 _cell.length_b 85.206 _cell.length_c 161.157 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9IJT _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,G,H,I,J _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 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 disulf ? disulf1 A SG CYS 24 A CYS 40 1_555 A SG CYS 98 A CYS 114 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 24 A CYS 40 1_555 A SG CYS 98 A CYS 114 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.022 ? disulf ? disulf3 B SG CYS 24 B CYS 40 1_555 B SG CYS 98 B CYS 114 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.021 ? disulf ? disulf4 B SG CYS 24 B CYS 40 1_555 B SG CYS 98 B CYS 114 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.999 ? disulf ? disulf5 C SG CYS 24 C CYS 40 1_555 C SG CYS 98 C CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? disulf ? disulf6 D SG CYS 24 D CYS 40 1_555 D SG CYS 98 D CYS 114 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 D SG CYS 24 D CYS 40 1_555 D SG CYS 98 D CYS 114 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.008 ? # _chem_comp.formula 'C26 H29 N3 O4' _chem_comp.formula_weight 447.526 _chem_comp.id A1L2P _chem_comp.mon_nstd_flag . _chem_comp.name '(2~{S})-1-[[4-methoxy-2-[(2-methyl-3-phenyl-phenyl)methoxy]pyrimidin-5-yl]methyl]piperidine-2-carboxylic 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 C32 C31 A1L2P doub 1 n y C32 C33 A1L2P sing 2 n y C31 C30 A1L2P sing 3 n y C33 C34 A1L2P doub 4 n y C26 C27 A1L2P doub 5 n y C26 C25 A1L2P sing 6 n y C30 C29 A1L2P doub 7 n y C34 C29 A1L2P sing 8 n y C27 C28 A1L2P sing 9 n y C25 C3 A1L2P doub 10 n y C12 C11 A1L2P doub 11 n y C12 N13 A1L2P sing 12 n y C29 C28 A1L2P sing 13 n n C28 C2 A1L2P doub 14 n y C3 C2 A1L2P sing 15 n y C3 C4 A1L2P sing 16 n n C11 C8 A1L2P sing 17 n y C11 C14 A1L2P sing 18 n n C2 C1 A1L2P sing 19 n n C8 N7 A1L2P doub 20 n y C8 O9 A1L2P sing 21 n n C6 N13 A1L2P doub 22 n y C6 N7 A1L2P sing 23 n y C6 O5 A1L2P sing 24 n n C22 C20 A1L2P sing 25 n n C22 O24 A1L2P doub 26 n n C22 O23 A1L2P sing 27 n n C18 C17 A1L2P sing 28 n n C18 C19 A1L2P sing 29 n n C17 C16 A1L2P sing 30 n n C19 C20 A1L2P sing 31 n n C16 N15 A1L2P sing 32 n n C20 N15 A1L2P sing 33 n n C10 O9 A1L2P sing 34 n n C14 N15 A1L2P sing 35 n n C4 O5 A1L2P sing 36 n n C32 H60 A1L2P sing 37 n n C31 H59 A1L2P sing 38 n n C33 H61 A1L2P sing 39 n n C26 H56 A1L2P sing 40 n n C30 H58 A1L2P sing 41 n n C34 H62 A1L2P sing 42 n n C27 H57 A1L2P sing 43 n n C25 H55 A1L2P sing 44 n n C12 H43 A1L2P sing 45 n n C18 H51 A1L2P sing 46 n n C18 H50 A1L2P sing 47 n n C17 H48 A1L2P sing 48 n n C17 H49 A1L2P sing 49 n n C19 H53 A1L2P sing 50 n n C19 H52 A1L2P sing 51 n n C16 H46 A1L2P sing 52 n n C16 H47 A1L2P sing 53 n n C20 H21 A1L2P sing 54 n n C1 H36 A1L2P sing 55 n n C1 H37 A1L2P sing 56 n n C1 H35 A1L2P sing 57 n n C10 H42 A1L2P sing 58 n n C10 H40 A1L2P sing 59 n n C10 H41 A1L2P sing 60 n n C14 H44 A1L2P sing 61 n n C14 H45 A1L2P sing 62 n n C4 H38 A1L2P sing 63 n n C4 H39 A1L2P sing 64 n n O23 H54 A1L2P sing 65 n n # _atom_sites.entry_id 9IJT _atom_sites.fract_transf_matrix[1][1] 0.02456 _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] 0.011736 _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] 0.006205 _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 E 2 A1L2P B 1 201 201 A1L2P UNL . F 2 A1L2P D 1 201 201 A1L2P UNL . G 3 HOH A 1 201 36 HOH HOH . G 3 HOH A 2 202 85 HOH HOH . G 3 HOH A 3 203 87 HOH HOH . G 3 HOH A 4 204 67 HOH HOH . G 3 HOH A 5 205 86 HOH HOH . G 3 HOH A 6 206 37 HOH HOH . G 3 HOH A 7 207 45 HOH HOH . G 3 HOH A 8 208 34 HOH HOH . G 3 HOH A 9 209 39 HOH HOH . G 3 HOH A 10 210 107 HOH HOH . G 3 HOH A 11 211 41 HOH HOH . G 3 HOH A 12 212 38 HOH HOH . G 3 HOH A 13 213 82 HOH HOH . G 3 HOH A 14 214 109 HOH HOH . G 3 HOH A 15 215 68 HOH HOH . G 3 HOH A 16 216 33 HOH HOH . G 3 HOH A 17 217 42 HOH HOH . G 3 HOH A 18 218 43 HOH HOH . G 3 HOH A 19 219 80 HOH HOH . G 3 HOH A 20 220 81 HOH HOH . G 3 HOH A 21 221 35 HOH HOH . G 3 HOH A 22 222 110 HOH HOH . G 3 HOH A 23 223 97 HOH HOH . G 3 HOH A 24 224 108 HOH HOH . G 3 HOH A 25 225 44 HOH HOH . G 3 HOH A 26 226 83 HOH HOH . G 3 HOH A 27 227 40 HOH HOH . G 3 HOH A 28 228 123 HOH HOH . G 3 HOH A 29 229 84 HOH HOH . H 3 HOH B 1 301 77 HOH HOH . H 3 HOH B 2 302 98 HOH HOH . H 3 HOH B 3 303 112 HOH HOH . H 3 HOH B 4 304 5 HOH HOH . H 3 HOH B 5 305 76 HOH HOH . H 3 HOH B 6 306 25 HOH HOH . H 3 HOH B 7 307 74 HOH HOH . H 3 HOH B 8 308 3 HOH HOH . H 3 HOH B 9 309 113 HOH HOH . H 3 HOH B 10 310 72 HOH HOH . H 3 HOH B 11 311 26 HOH HOH . H 3 HOH B 12 312 27 HOH HOH . H 3 HOH B 13 313 21 HOH HOH . H 3 HOH B 14 314 2 HOH HOH . H 3 HOH B 15 315 114 HOH HOH . H 3 HOH B 16 316 99 HOH HOH . H 3 HOH B 17 317 111 HOH HOH . H 3 HOH B 18 318 23 HOH HOH . H 3 HOH B 19 319 29 HOH HOH . H 3 HOH B 20 320 91 HOH HOH . H 3 HOH B 21 321 78 HOH HOH . H 3 HOH B 22 322 8 HOH HOH . H 3 HOH B 23 323 71 HOH HOH . H 3 HOH B 24 324 9 HOH HOH . H 3 HOH B 25 325 30 HOH HOH . H 3 HOH B 26 326 100 HOH HOH . H 3 HOH B 27 327 19 HOH HOH . H 3 HOH B 28 328 7 HOH HOH . H 3 HOH B 29 329 22 HOH HOH . H 3 HOH B 30 330 1 HOH HOH . H 3 HOH B 31 331 124 HOH HOH . H 3 HOH B 32 332 24 HOH HOH . H 3 HOH B 33 333 102 HOH HOH . H 3 HOH B 34 334 75 HOH HOH . H 3 HOH B 35 335 31 HOH HOH . H 3 HOH B 36 336 28 HOH HOH . H 3 HOH B 37 337 10 HOH HOH . H 3 HOH B 38 338 32 HOH HOH . H 3 HOH B 39 339 73 HOH HOH . H 3 HOH B 40 340 79 HOH HOH . I 3 HOH C 1 201 89 HOH HOH . I 3 HOH C 2 202 58 HOH HOH . I 3 HOH C 3 203 88 HOH HOH . I 3 HOH C 4 204 64 HOH HOH . I 3 HOH C 5 205 90 HOH HOH . I 3 HOH C 6 206 61 HOH HOH . I 3 HOH C 7 207 59 HOH HOH . I 3 HOH C 8 208 115 HOH HOH . I 3 HOH C 9 209 116 HOH HOH . I 3 HOH C 10 210 66 HOH HOH . I 3 HOH C 11 211 60 HOH HOH . I 3 HOH C 12 212 62 HOH HOH . I 3 HOH C 13 213 65 HOH HOH . I 3 HOH C 14 214 104 HOH HOH . I 3 HOH C 15 215 63 HOH HOH . J 3 HOH D 1 301 56 HOH HOH . J 3 HOH D 2 302 69 HOH HOH . J 3 HOH D 3 303 70 HOH HOH . J 3 HOH D 4 304 49 HOH HOH . J 3 HOH D 5 305 47 HOH HOH . J 3 HOH D 6 306 93 HOH HOH . J 3 HOH D 7 307 121 HOH HOH . J 3 HOH D 8 308 57 HOH HOH . J 3 HOH D 9 309 96 HOH HOH . J 3 HOH D 10 310 4 HOH HOH . J 3 HOH D 11 311 120 HOH HOH . J 3 HOH D 12 312 55 HOH HOH . J 3 HOH D 13 313 119 HOH HOH . J 3 HOH D 14 314 94 HOH HOH . J 3 HOH D 15 315 13 HOH HOH . J 3 HOH D 16 316 52 HOH HOH . J 3 HOH D 17 317 92 HOH HOH . J 3 HOH D 18 318 50 HOH HOH . J 3 HOH D 19 319 117 HOH HOH . J 3 HOH D 20 320 101 HOH HOH . J 3 HOH D 21 321 6 HOH HOH . J 3 HOH D 22 322 48 HOH HOH . J 3 HOH D 23 323 11 HOH HOH . J 3 HOH D 24 324 16 HOH HOH . J 3 HOH D 25 325 17 HOH HOH . J 3 HOH D 26 326 18 HOH HOH . J 3 HOH D 27 327 51 HOH HOH . J 3 HOH D 28 328 14 HOH HOH . J 3 HOH D 29 329 105 HOH HOH . J 3 HOH D 30 330 95 HOH HOH . J 3 HOH D 31 331 106 HOH HOH . J 3 HOH D 32 332 46 HOH HOH . J 3 HOH D 33 333 53 HOH HOH . J 3 HOH D 34 334 15 HOH HOH . J 3 HOH D 35 335 122 HOH HOH . J 3 HOH D 36 336 118 HOH HOH . J 3 HOH D 37 337 20 HOH HOH . J 3 HOH D 38 338 54 HOH HOH . J 3 HOH D 39 339 103 HOH HOH . J 3 HOH D 40 340 12 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 C32 A1L2P . . . E 2 12.626 11.395 22.447 1 35.38 0 C32 A1L2P 201 B 1 HETATM 2 C C31 A1L2P . . . E 2 12.138 11.806 21.228 1 36.11 0 C31 A1L2P 201 B 1 HETATM 3 C C33 A1L2P . . . E 2 11.827 10.715 23.359 1 32.82 0 C33 A1L2P 201 B 1 HETATM 4 C C26 A1L2P . . . E 2 7.119 9.443 20.049 1 42.23 0 C26 A1L2P 201 B 1 HETATM 5 C C30 A1L2P . . . E 2 10.83 11.558 20.898 1 36.45 0 C30 A1L2P 201 B 1 HETATM 6 C C34 A1L2P . . . E 2 10.519 10.461 23.015 1 34.27 0 C34 A1L2P 201 B 1 HETATM 7 C C27 A1L2P . . . E 2 8.41 9.762 20.408 1 39.23 0 C27 A1L2P 201 B 1 HETATM 8 C C25 A1L2P . . . E 2 6.062 10.002 20.728 1 42.18 0 C25 A1L2P 201 B 1 HETATM 9 C C12 A1L2P . . . E 2 0.839 10.293 23.822 1 59.69 0 C12 A1L2P 201 B 1 HETATM 10 C C29 A1L2P . . . E 2 10.023 10.873 21.791 1 35.73 0 C29 A1L2P 201 B 1 HETATM 11 C C28 A1L2P . . . E 2 8.644 10.6 21.445 1 37.33 0 C28 A1L2P 201 B 1 HETATM 12 C C3 A1L2P . . . E 2 6.277 10.885 21.764 1 40.58 0 C3 A1L2P 201 B 1 HETATM 13 C C11 A1L2P . . . E 2 0.626 11.565 24.314 1 62.03 0 C11 A1L2P 201 B 1 HETATM 14 C C2 A1L2P . . . E 2 7.573 11.18 22.128 1 37.72 0 C2 A1L2P 201 B 1 HETATM 15 C C8 A1L2P . . . E 2 1.646 12.471 24.112 1 55.7 0 C8 A1L2P 201 B 1 HETATM 16 C C6 A1L2P . . . E 2 2.878 10.92 23.044 1 50.51 0 C6 A1L2P 201 B 1 HETATM 17 C C22 A1L2P . . . E 2 -0.605 10.695 28.42 1 78.56 0 C22 A1L2P 201 B 1 HETATM 18 C C18 A1L2P . . . E 2 -2.508 13.149 27.178 1 83.97 0 C18 A1L2P 201 B 1 HETATM 19 C C17 A1L2P . . . E 2 -3.179 11.818 26.901 1 85.34 0 C17 A1L2P 201 B 1 HETATM 20 C C19 A1L2P . . . E 2 -1.071 13.038 27.671 1 80.1 0 C19 A1L2P 201 B 1 HETATM 21 C C16 A1L2P . . . E 2 -2.329 10.752 26.208 1 84.19 0 C16 A1L2P 201 B 1 HETATM 22 C C20 A1L2P . . . E 2 -0.389 11.722 27.348 1 77.95 0 C20 A1L2P 201 B 1 HETATM 23 C C1 A1L2P . . . E 2 7.855 12.131 23.229 1 34.06 0 C1 A1L2P 201 B 1 HETATM 24 C C10 A1L2P . . . E 2 2.6 14.32 24.986 1 51.68 0 C10 A1L2P 201 B 1 HETATM 25 C C14 A1L2P . . . E 2 -0.63 11.948 25.017 1 69.77 0 C14 A1L2P 201 B 1 HETATM 26 C C4 A1L2P . . . E 2 5.078 11.474 22.466 1 43.08 0 C4 A1L2P 201 B 1 HETATM 27 N N13 A1L2P . . . E 2 1.957 9.95 23.17 1 54.28 0 N13 A1L2P 201 B 1 HETATM 28 N N7 A1L2P . . . E 2 2.798 12.177 23.484 1 50.6 0 N7 A1L2P 201 B 1 HETATM 29 N N15 A1L2P . . . E 2 -0.896 11.077 26.156 1 76.67 0 N15 A1L2P 201 B 1 HETATM 30 O O24 A1L2P . . . E 2 0.058 9.681 28.518 1 75.56 0 O24 A1L2P 201 B 1 HETATM 31 O O23 A1L2P . . . E 2 -1.654 10.995 29.227 1 82.51 0 O23 A1L2P 201 B 1 HETATM 32 O O9 A1L2P . . . E 2 1.375 13.724 24.594 1 50.17 0 O9 A1L2P 201 B 1 HETATM 33 O O5 A1L2P . . . E 2 4.015 10.514 22.381 1 47.73 0 O5 A1L2P 201 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #