data_5A8X # _model_server_result.job_id sIntns8RaKR0KNDncyRvyg _model_server_result.datetime_utc '2024-11-28 01:17:41' _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 5a8x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1001}' # _entry.id 5A8X # _exptl.entry_id 5A8X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 453.436 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ethyl (5R)-5-(4-cyanophenyl)-7-methyl-8-[3-(trifluoromethyl)phenyl]-1,5-dihydroimidazo[1,2-a]pyrimidin-4-ium-6-carboxylate' _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 5A8X _cell.length_a 73.795 _cell.length_b 73.795 _cell.length_c 70.01 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5A8X _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 FUC _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O6 _pdbx_entity_branch_link.leaving_atom_id_2 HO6 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 401 NAG 2 n B FUC 2 B 2 FUC A 402 FUC 2 n C NAG 1 C 1 NAG A 411 NAG 2 n C FUC 2 C 2 FUC A 412 FUC # 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 26 A CYS 42 1_555 A SG CYS 42 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 122 A CYS 136 1_555 A SG CYS 179 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 152 A CYS 168 1_555 A SG CYS 158 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 169 A CYS 191 1_555 A SG CYS 194 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? covale ? covale1 A ND2 ASN 95 A ASN 109 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale2 A ND2 ASN 144 A ASN 159 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 B O6 NAG . B NAG 1 1_555 B C1 FUC . B FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _chem_comp.formula 'C24 H20 F3 N4 O2 1' _chem_comp.formula_weight 453.436 _chem_comp.id IUY _chem_comp.mon_nstd_flag . _chem_comp.name 'ethyl (5R)-5-(4-cyanophenyl)-7-methyl-8-[3-(trifluoromethyl)phenyl]-1,5-dihydroimidazo[1,2-a]pyrimidin-4-ium-6-carboxylate' _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 C1 C2 IUY sing 196 n n C1 C3 IUY doub 197 n n C1 C12 IUY sing 198 n n C2 C6 IUY sing 199 n n C2 N19 IUY sing 200 n n C3 N4 IUY sing 201 n n C3 C5 IUY sing 202 n n N4 C20 IUY sing 203 n n N4 C24 IUY sing 204 n n C6 C7 IUY doub 205 n y C6 C11 IUY sing 206 n y C7 C8 IUY sing 207 n y C8 C9 IUY doub 208 n y C9 C10 IUY sing 209 n y C9 C17 IUY sing 210 n n C10 C11 IUY doub 211 n y C12 O13 IUY doub 212 n n C12 O14 IUY sing 213 n n O14 C15 IUY sing 214 n n C15 C16 IUY sing 215 n n C17 N18 IUY trip 216 n n N19 C20 IUY doub 217 n y N19 C23 IUY sing 218 n y C20 N21 IUY sing 219 n y N21 C22 IUY sing 220 n y C22 C23 IUY doub 221 n y C24 C25 IUY doub 222 n y C24 C29 IUY sing 223 n y C25 C26 IUY sing 224 n y C26 C27 IUY doub 225 n y C27 C28 IUY sing 226 n y C28 C29 IUY doub 227 n y C28 C30 IUY sing 228 n n C30 F31 IUY sing 229 n n C30 F32 IUY sing 230 n n C30 F33 IUY sing 231 n n C2 H2 IUY sing 232 n n C5 H5 IUY sing 233 n n C5 H5A IUY sing 234 n n C5 H5B IUY sing 235 n n C7 H7 IUY sing 236 n n C8 H8 IUY sing 237 n n C10 H10 IUY sing 238 n n C11 H11 IUY sing 239 n n C15 H15 IUY sing 240 n n C15 H15A IUY sing 241 n n C16 H16 IUY sing 242 n n C16 H16A IUY sing 243 n n C16 H16B IUY sing 244 n n N21 HN21 IUY sing 245 n n C22 H22 IUY sing 246 n n C23 H23 IUY sing 247 n n C25 H25 IUY sing 248 n n C26 H26 IUY sing 249 n n C27 H27 IUY sing 250 n n C29 H29 IUY sing 251 n n # _atom_sites.entry_id 5A8X _atom_sites.fract_transf_matrix[1][1] 0.013551 _atom_sites.fract_transf_matrix[1][2] 0.007824 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015647 _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] 0.014284 _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 3 NAG A 1 403 403 NAG NAG . E 4 IUY A 1 1001 1001 IUY IUY . F 5 HOH A 1 2001 2001 HOH HOH . F 5 HOH A 2 2002 2002 HOH HOH . F 5 HOH A 3 2003 2003 HOH HOH . F 5 HOH A 4 2004 2004 HOH HOH . F 5 HOH A 5 2005 2005 HOH HOH . F 5 HOH A 6 2006 2006 HOH HOH . F 5 HOH A 7 2007 2007 HOH HOH . F 5 HOH A 8 2008 2008 HOH HOH . F 5 HOH A 9 2009 2009 HOH HOH . F 5 HOH A 10 2010 2010 HOH HOH . F 5 HOH A 11 2011 2011 HOH HOH . F 5 HOH A 12 2012 2012 HOH HOH . F 5 HOH A 13 2013 2013 HOH HOH . F 5 HOH A 14 2014 2014 HOH HOH . F 5 HOH A 15 2015 2015 HOH HOH . F 5 HOH A 16 2016 2016 HOH HOH . F 5 HOH A 17 2017 2017 HOH HOH . F 5 HOH A 18 2018 2018 HOH HOH . F 5 HOH A 19 2019 2019 HOH HOH . F 5 HOH A 20 2020 2020 HOH HOH . F 5 HOH A 21 2021 2021 HOH HOH . F 5 HOH A 22 2022 2022 HOH HOH . F 5 HOH A 23 2023 2023 HOH HOH . F 5 HOH A 24 2024 2024 HOH HOH . F 5 HOH A 25 2025 2025 HOH HOH . F 5 HOH A 26 2026 2026 HOH HOH . F 5 HOH A 27 2027 2027 HOH HOH . F 5 HOH A 28 2028 2028 HOH HOH . F 5 HOH A 29 2029 2029 HOH HOH . F 5 HOH A 30 2030 2030 HOH HOH . F 5 HOH A 31 2031 2031 HOH HOH . F 5 HOH A 32 2032 2032 HOH HOH . F 5 HOH A 33 2033 2033 HOH HOH . F 5 HOH A 34 2034 2034 HOH HOH . F 5 HOH A 35 2035 2035 HOH HOH . F 5 HOH A 36 2036 2036 HOH HOH . F 5 HOH A 37 2037 2037 HOH HOH . F 5 HOH A 38 2038 2038 HOH HOH . F 5 HOH A 39 2039 2039 HOH HOH . F 5 HOH A 40 2040 2040 HOH HOH . F 5 HOH A 41 2041 2041 HOH HOH . F 5 HOH A 42 2042 2042 HOH HOH . F 5 HOH A 43 2043 2043 HOH HOH . F 5 HOH A 44 2044 2044 HOH HOH . F 5 HOH A 45 2045 2045 HOH HOH . F 5 HOH A 46 2046 2046 HOH HOH . F 5 HOH A 47 2047 2047 HOH HOH . F 5 HOH A 48 2048 2048 HOH HOH . F 5 HOH A 49 2049 2049 HOH HOH . F 5 HOH A 50 2050 2050 HOH HOH . F 5 HOH A 51 2051 2051 HOH HOH . F 5 HOH A 52 2052 2052 HOH HOH . F 5 HOH A 53 2053 2053 HOH HOH . F 5 HOH A 54 2054 2054 HOH HOH . F 5 HOH A 55 2055 2055 HOH HOH . F 5 HOH A 56 2056 2056 HOH HOH . F 5 HOH A 57 2057 2057 HOH HOH . F 5 HOH A 58 2058 2058 HOH HOH . F 5 HOH A 59 2059 2059 HOH HOH . F 5 HOH A 60 2060 2060 HOH HOH . F 5 HOH A 61 2061 2061 HOH HOH . F 5 HOH A 62 2062 2062 HOH HOH . F 5 HOH A 63 2063 2063 HOH HOH . F 5 HOH A 64 2064 2064 HOH HOH . F 5 HOH A 65 2065 2065 HOH HOH . F 5 HOH A 66 2066 2066 HOH HOH . F 5 HOH A 67 2067 2067 HOH HOH . F 5 HOH A 68 2068 2068 HOH HOH . F 5 HOH A 69 2069 2069 HOH HOH . F 5 HOH A 70 2070 2070 HOH HOH . F 5 HOH A 71 2071 2071 HOH HOH . F 5 HOH A 72 2072 2072 HOH HOH . F 5 HOH A 73 2073 2073 HOH HOH . F 5 HOH A 74 2074 2074 HOH HOH . F 5 HOH A 75 2075 2075 HOH HOH . F 5 HOH A 76 2076 2076 HOH HOH . F 5 HOH A 77 2077 2077 HOH HOH . F 5 HOH A 78 2078 2078 HOH HOH . F 5 HOH A 79 2079 2079 HOH HOH . F 5 HOH A 80 2080 2080 HOH HOH . F 5 HOH A 81 2081 2081 HOH HOH . F 5 HOH A 82 2082 2082 HOH HOH . F 5 HOH A 83 2083 2083 HOH HOH . F 5 HOH A 84 2084 2084 HOH HOH . F 5 HOH A 85 2085 2085 HOH HOH . F 5 HOH A 86 2086 2086 HOH HOH . F 5 HOH A 87 2087 2087 HOH HOH . F 5 HOH A 88 2088 2088 HOH HOH . F 5 HOH A 89 2089 2089 HOH HOH . F 5 HOH A 90 2090 2090 HOH HOH . F 5 HOH A 91 2091 2091 HOH HOH . F 5 HOH A 92 2092 2092 HOH HOH . F 5 HOH A 93 2093 2093 HOH HOH . F 5 HOH A 94 2094 2094 HOH HOH . F 5 HOH A 95 2095 2095 HOH HOH . F 5 HOH A 96 2096 2096 HOH HOH . F 5 HOH A 97 2097 2097 HOH HOH . F 5 HOH A 98 2098 2098 HOH HOH . F 5 HOH A 99 2099 2099 HOH HOH . F 5 HOH A 100 2100 2100 HOH HOH . F 5 HOH A 101 2101 2101 HOH HOH . F 5 HOH A 102 2102 2102 HOH HOH . F 5 HOH A 103 2103 2103 HOH HOH . F 5 HOH A 104 2104 2104 HOH HOH . F 5 HOH A 105 2105 2105 HOH HOH . F 5 HOH A 106 2106 2106 HOH HOH . F 5 HOH A 107 2107 2107 HOH HOH . F 5 HOH A 108 2108 2108 HOH HOH . F 5 HOH A 109 2109 2109 HOH HOH . F 5 HOH A 110 2110 2110 HOH HOH . F 5 HOH A 111 2111 2111 HOH HOH . F 5 HOH A 112 2112 2112 HOH HOH . F 5 HOH A 113 2113 2113 HOH HOH . F 5 HOH A 114 2114 2114 HOH HOH . F 5 HOH A 115 2115 2115 HOH HOH . F 5 HOH A 116 2116 2116 HOH HOH . F 5 HOH A 117 2117 2117 HOH HOH . F 5 HOH A 118 2118 2118 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 C1 IUY . . . E 4 27.715 -21.667 4.436 1 10.31 ? C1 IUY 1001 A 1 HETATM 2 C C2 IUY . . . E 4 28.674 -22.469 5.289 1 10.41 ? C2 IUY 1001 A 1 HETATM 3 C C3 IUY . . . E 4 27.401 -22.016 3.151 1 9.56 ? C3 IUY 1001 A 1 HETATM 4 N N4 IUY . . . E 4 27.917 -23.15 2.547 1 9.24 ? N4 IUY 1001 A 1 HETATM 5 C C5 IUY . . . E 4 26.427 -21.176 2.345 1 8.52 ? C5 IUY 1001 A 1 HETATM 6 C C6 IUY . . . E 4 27.946 -23.293 6.345 1 10.62 ? C6 IUY 1001 A 1 HETATM 7 C C7 IUY . . . E 4 28.144 -23.072 7.713 1 9.53 ? C7 IUY 1001 A 1 HETATM 8 C C8 IUY . . . E 4 27.471 -23.84 8.664 1 10.87 ? C8 IUY 1001 A 1 HETATM 9 C C9 IUY . . . E 4 26.595 -24.868 8.238 1 10.16 ? C9 IUY 1001 A 1 HETATM 10 C C10 IUY . . . E 4 26.416 -25.101 6.875 1 9.17 ? C10 IUY 1001 A 1 HETATM 11 C C11 IUY . . . E 4 27.09 -24.328 5.934 1 9.47 ? C11 IUY 1001 A 1 HETATM 12 C C12 IUY . . . E 4 27.164 -20.512 5.063 1 12.44 ? C12 IUY 1001 A 1 HETATM 13 O O13 IUY . . . E 4 26.363 -19.768 4.499 1 10.51 ? O13 IUY 1001 A 1 HETATM 14 O O14 IUY . . . E 4 27.516 -20.241 6.347 1 13.47 ? O14 IUY 1001 A 1 HETATM 15 C C15 IUY . . . E 4 26.709 -19.279 7.05 1 13.81 ? C15 IUY 1001 A 1 HETATM 16 C C16 IUY . . . E 4 27.033 -19.288 8.559 1 11.4 ? C16 IUY 1001 A 1 HETATM 17 C C17 IUY . . . E 4 25.915 -25.692 9.184 1 10.35 ? C17 IUY 1001 A 1 HETATM 18 N N18 IUY . . . E 4 25.388 -26.364 9.933 1 11.16 ? N18 IUY 1001 A 1 HETATM 19 N N19 IUY . . . E 4 29.354 -23.47 4.455 1 12.21 ? N19 IUY 1001 A 1 HETATM 20 C C20 IUY . . . E 4 28.965 -23.793 3.18 1 10.92 ? C20 IUY 1001 A 1 HETATM 21 N N21 IUY . . . E 4 29.722 -24.743 2.724 1 10.97 ? N21 IUY 1001 A 1 HETATM 22 C C22 IUY . . . E 4 30.618 -25.088 3.674 1 11.85 ? C22 IUY 1001 A 1 HETATM 23 C C23 IUY . . . E 4 30.394 -24.312 4.766 1 12.78 ? C23 IUY 1001 A 1 HETATM 24 C C24 IUY . . . E 4 27.459 -23.708 1.335 1 10.06 ? C24 IUY 1001 A 1 HETATM 25 C C25 IUY . . . E 4 28.079 -23.378 0.128 1 7.42 ? C25 IUY 1001 A 1 HETATM 26 C C26 IUY . . . E 4 27.644 -23.914 -1.063 1 7.37 ? C26 IUY 1001 A 1 HETATM 27 C C27 IUY . . . E 4 26.583 -24.808 -1.054 1 8.06 ? C27 IUY 1001 A 1 HETATM 28 C C28 IUY . . . E 4 25.955 -25.171 0.133 1 9.15 ? C28 IUY 1001 A 1 HETATM 29 C C29 IUY . . . E 4 26.395 -24.634 1.333 1 9.4 ? C29 IUY 1001 A 1 HETATM 30 C C30 IUY . . . E 4 24.811 -26.162 0.132 1 9.58 ? C30 IUY 1001 A 1 HETATM 31 F F31 IUY . . . E 4 24.053 -26.102 -1.02 1 11.95 ? F31 IUY 1001 A 1 HETATM 32 F F32 IUY . . . E 4 25.306 -27.454 0.241 1 10.37 ? F32 IUY 1001 A 1 HETATM 33 F F33 IUY . . . E 4 23.968 -25.895 1.185 1 11.33 ? F33 IUY 1001 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 356 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 33 #