data_2VA6 # _model_server_result.job_id nwfuPYfg4-uHv6YHQ1gBRA _model_server_result.datetime_utc '2024-12-21 16:49:29' _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 2va6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1504}' # _entry.id 2VA6 # _exptl.entry_id 2VA6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.389 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "(6S)-2-amino-6-(3'-methoxybiphenyl-3-yl)-3,6-dimethyl-5,6-dihydropyrimidin-4(3H)-one" _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 2VA6 _cell.length_a 102.971 _cell.length_b 102.971 _cell.length_c 167.28 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VA6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PQS _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_555 x,x-y,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 27.88 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 218 A CYS 155 1_555 A SG CYS 422 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 A SG CYS 280 A CYS 217 1_555 A SG CYS 445 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf3 A SG CYS 332 A CYS 269 1_555 A SG CYS 382 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? # _chem_comp.formula 'C19 H21 N3 O2' _chem_comp.formula_weight 323.389 _chem_comp.id H24 _chem_comp.mon_nstd_flag . _chem_comp.name "(6S)-2-amino-6-(3'-methoxybiphenyl-3-yl)-3,6-dimethyl-5,6-dihydropyrimidin-4(3H)-one" _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 O2 H24 sing 129 n n O2 C3 H24 sing 130 n n C3 C4 H24 sing 131 n y C3 C8 H24 doub 132 n y C4 C5 H24 doub 133 n y C5 C6 H24 sing 134 n y C6 C7 H24 doub 135 n y C7 C8 H24 sing 136 n y C7 C9 H24 sing 137 n y C9 C10 H24 sing 138 n y C9 C26 H24 doub 139 n y C10 C11 H24 doub 140 n y C11 C12 H24 sing 141 n y C12 C13 H24 doub 142 n y C13 C26 H24 sing 143 n y C13 C14 H24 sing 144 n n C14 C15 H24 sing 145 n n C14 C18 H24 sing 146 n n C14 N25 H24 sing 147 n n C18 C19 H24 sing 148 n n C19 O20 H24 doub 149 n n C19 N21 H24 sing 150 n n N21 C22 H24 sing 151 n n N21 C23 H24 sing 152 n n C23 N25 H24 doub 153 n n C23 N24 H24 sing 154 n n C1 H1C1 H24 sing 155 n n C1 H1C2 H24 sing 156 n n C1 H1C3 H24 sing 157 n n C4 H4 H24 sing 158 n n C8 H8 H24 sing 159 n n C5 H5 H24 sing 160 n n C6 H6 H24 sing 161 n n C10 H10 H24 sing 162 n n C26 H26 H24 sing 163 n n C11 H11 H24 sing 164 n n C12 H12 H24 sing 165 n n C15 H151 H24 sing 166 n n C15 H152 H24 sing 167 n n C15 H153 H24 sing 168 n n C18 H181 H24 sing 169 n n C18 H182 H24 sing 170 n n C22 H221 H24 sing 171 n n C22 H222 H24 sing 172 n n C22 H223 H24 sing 173 n n N24 H241 H24 sing 174 n n N24 H242 H24 sing 175 n n # _atom_sites.entry_id 2VA6 _atom_sites.fract_transf_matrix[1][1] 0.009711 _atom_sites.fract_transf_matrix[1][2] 0.005607 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011214 _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] 0.005978 _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 B 2 IOD A 1 1501 1501 IOD IOD . C 2 IOD A 1 1502 1502 IOD IOD . D 2 IOD A 1 1503 1503 IOD IOD . E 3 H24 A 1 1504 1504 H24 H24 . F 4 HOH A 1 2001 2001 HOH HOH . F 4 HOH A 2 2002 2002 HOH HOH . F 4 HOH A 3 2003 2003 HOH HOH . F 4 HOH A 4 2004 2004 HOH HOH . F 4 HOH A 5 2005 2005 HOH HOH . F 4 HOH A 6 2006 2006 HOH HOH . F 4 HOH A 7 2007 2007 HOH HOH . F 4 HOH A 8 2008 2008 HOH HOH . F 4 HOH A 9 2009 2009 HOH HOH . F 4 HOH A 10 2010 2010 HOH HOH . F 4 HOH A 11 2011 2011 HOH HOH . F 4 HOH A 12 2012 2012 HOH HOH . F 4 HOH A 13 2013 2013 HOH HOH . F 4 HOH A 14 2014 2014 HOH HOH . F 4 HOH A 15 2015 2015 HOH HOH . F 4 HOH A 16 2016 2016 HOH HOH . F 4 HOH A 17 2017 2017 HOH HOH . F 4 HOH A 18 2018 2018 HOH HOH . F 4 HOH A 19 2019 2019 HOH HOH . F 4 HOH A 20 2020 2020 HOH HOH . F 4 HOH A 21 2021 2021 HOH HOH . F 4 HOH A 22 2022 2022 HOH HOH . F 4 HOH A 23 2023 2023 HOH HOH . F 4 HOH A 24 2024 2024 HOH HOH . F 4 HOH A 25 2025 2025 HOH HOH . F 4 HOH A 26 2026 2026 HOH HOH . F 4 HOH A 27 2027 2027 HOH HOH . F 4 HOH A 28 2028 2028 HOH HOH . F 4 HOH A 29 2029 2029 HOH HOH . F 4 HOH A 30 2030 2030 HOH HOH . F 4 HOH A 31 2031 2031 HOH HOH . F 4 HOH A 32 2032 2032 HOH HOH . F 4 HOH A 33 2033 2033 HOH HOH . F 4 HOH A 34 2034 2034 HOH HOH . F 4 HOH A 35 2035 2035 HOH HOH . F 4 HOH A 36 2036 2036 HOH HOH . F 4 HOH A 37 2037 2037 HOH HOH . F 4 HOH A 38 2038 2038 HOH HOH . F 4 HOH A 39 2039 2039 HOH HOH . F 4 HOH A 40 2040 2040 HOH HOH . F 4 HOH A 41 2041 2041 HOH HOH . F 4 HOH A 42 2042 2042 HOH HOH . F 4 HOH A 43 2043 2043 HOH HOH . F 4 HOH A 44 2044 2044 HOH HOH . F 4 HOH A 45 2045 2045 HOH HOH . F 4 HOH A 46 2046 2046 HOH HOH . F 4 HOH A 47 2047 2047 HOH HOH . F 4 HOH A 48 2048 2048 HOH HOH . F 4 HOH A 49 2049 2049 HOH HOH . F 4 HOH A 50 2050 2050 HOH HOH . F 4 HOH A 51 2051 2051 HOH HOH . F 4 HOH A 52 2052 2052 HOH HOH . F 4 HOH A 53 2053 2053 HOH HOH . F 4 HOH A 54 2054 2054 HOH HOH . F 4 HOH A 55 2055 2055 HOH HOH . F 4 HOH A 56 2056 2056 HOH HOH . F 4 HOH A 57 2057 2057 HOH HOH . F 4 HOH A 58 2058 2058 HOH HOH . F 4 HOH A 59 2059 2059 HOH HOH . F 4 HOH A 60 2060 2060 HOH HOH . F 4 HOH A 61 2061 2061 HOH HOH . F 4 HOH A 62 2062 2062 HOH HOH . F 4 HOH A 63 2063 2063 HOH HOH . F 4 HOH A 64 2064 2064 HOH HOH . F 4 HOH A 65 2065 2065 HOH HOH . F 4 HOH A 66 2066 2066 HOH HOH . F 4 HOH A 67 2067 2067 HOH HOH . F 4 HOH A 68 2068 2068 HOH HOH . F 4 HOH A 69 2069 2069 HOH HOH . F 4 HOH A 70 2070 2070 HOH HOH . F 4 HOH A 71 2071 2071 HOH HOH . F 4 HOH A 72 2072 2072 HOH HOH . F 4 HOH A 73 2073 2073 HOH HOH . F 4 HOH A 74 2074 2074 HOH HOH . F 4 HOH A 75 2075 2075 HOH HOH . F 4 HOH A 76 2076 2076 HOH HOH . F 4 HOH A 77 2077 2077 HOH HOH . F 4 HOH A 78 2078 2078 HOH HOH . F 4 HOH A 79 2079 2079 HOH HOH . F 4 HOH A 80 2080 2080 HOH HOH . F 4 HOH A 81 2081 2081 HOH HOH . F 4 HOH A 82 2082 2082 HOH HOH . F 4 HOH A 83 2083 2083 HOH HOH . F 4 HOH A 84 2084 2084 HOH HOH . F 4 HOH A 85 2085 2085 HOH HOH . F 4 HOH A 86 2086 2086 HOH HOH . F 4 HOH A 87 2087 2087 HOH HOH . F 4 HOH A 88 2088 2088 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 H24 . . . E 3 71.395 46.195 1.077 1 36.37 ? C1 H24 1504 A 1 HETATM 2 O O2 H24 . . . E 3 71.202 47.196 2.094 1 49.5 ? O2 H24 1504 A 1 HETATM 3 C C3 H24 . . . E 3 71.916 47.071 3.259 1 48.47 ? C3 H24 1504 A 1 HETATM 4 C C4 H24 . . . E 3 72.954 46.164 3.437 1 50.82 ? C4 H24 1504 A 1 HETATM 5 C C5 H24 . . . E 3 73.611 46.087 4.644 1 50.91 ? C5 H24 1504 A 1 HETATM 6 C C6 H24 . . . E 3 73.224 46.895 5.695 1 52.86 ? C6 H24 1504 A 1 HETATM 7 C C7 H24 . . . E 3 72.182 47.81 5.545 1 51.27 ? C7 H24 1504 A 1 HETATM 8 C C8 H24 . . . E 3 71.52 47.875 4.322 1 49.81 ? C8 H24 1504 A 1 HETATM 9 C C9 H24 . . . E 3 71.747 48.641 6.704 1 46.48 ? C9 H24 1504 A 1 HETATM 10 C C10 H24 . . . E 3 72.688 49.1 7.614 1 45.84 ? C10 H24 1504 A 1 HETATM 11 C C11 H24 . . . E 3 72.298 49.825 8.716 1 42.86 ? C11 H24 1504 A 1 HETATM 12 C C12 H24 . . . E 3 70.965 50.073 8.946 1 42.94 ? C12 H24 1504 A 1 HETATM 13 C C13 H24 . . . E 3 69.997 49.618 8.063 1 40.2 ? C13 H24 1504 A 1 HETATM 14 C C14 H24 . . . E 3 68.526 49.924 8.388 1 45.04 ? C14 H24 1504 A 1 HETATM 15 C C15 H24 . . . E 3 68.364 51.404 8.751 1 44.84 ? C15 H24 1504 A 1 HETATM 16 C C18 H24 . . . E 3 68.083 49.093 9.598 1 45.61 ? C18 H24 1504 A 1 HETATM 17 C C19 H24 . . . E 3 67.707 47.688 9.236 1 46.3 ? C19 H24 1504 A 1 HETATM 18 O O20 H24 . . . E 3 68.103 46.732 9.879 1 49.28 ? O20 H24 1504 A 1 HETATM 19 N N21 H24 . . . E 3 66.955 47.551 8.118 1 46.19 ? N21 H24 1504 A 1 HETATM 20 C C22 H24 . . . E 3 66.406 46.22 7.817 1 30.78 ? C22 H24 1504 A 1 HETATM 21 C C23 H24 . . . E 3 66.832 48.643 7.204 1 43.63 ? C23 H24 1504 A 1 HETATM 22 N N24 H24 . . . E 3 65.873 48.629 6.274 1 40.16 ? N24 H24 1504 A 1 HETATM 23 N N25 H24 . . . E 3 67.647 49.674 7.217 1 44.77 ? N25 H24 1504 A 1 HETATM 24 C C26 H24 . . . E 3 70.397 48.889 6.949 1 37.94 ? C26 H24 1504 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 24 #