data_5A0B # _model_server_result.job_id l-ahuEWEuPVuIB8N4jyJdQ _model_server_result.datetime_utc '2024-11-26 20:59:34' _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 5a0b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1001}' # _entry.id 5A0B # _exptl.entry_id 5A0B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 550.575 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4R)-4-(4-cyanophenyl)-6-methyl-2-oxidanylidene-3-[2-oxidanylidene-2-(4-propan-2-ylpiperazin-1-yl)ethyl]-1-[3-(trifluoromethyl)phenyl]-4H-pyrimidine-5-carbonitrile _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 5A0B _cell.length_a 77.459 _cell.length_b 77.459 _cell.length_c 149.625 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5A0B _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63 2 2' # _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,G _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf2 A SG CYS 122 A CYS 136 1_555 A SG CYS 179 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? disulf ? disulf3 A SG CYS 152 A CYS 168 1_555 A SG CYS 158 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf4 A SG CYS 169 A CYS 191 1_555 A SG CYS 194 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? covale ? covale1 A ND2 ASN 95 A ASN 109 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale2 A ND2 ASN 144 A ASN 159 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale3 B O6 NAG . B NAG 1 1_555 B C1 FUC . B FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale4 C O6 NAG . C NAG 1 1_555 C C1 FUC . C FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? # _chem_comp.formula 'C29 H29 F3 N6 O2' _chem_comp.formula_weight 550.575 _chem_comp.id JJX _chem_comp.mon_nstd_flag . _chem_comp.name (4R)-4-(4-cyanophenyl)-6-methyl-2-oxidanylidene-3-[2-oxidanylidene-2-(4-propan-2-ylpiperazin-1-yl)ethyl]-1-[3-(trifluoromethyl)phenyl]-4H-pyrimidine-5-carbonitrile _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 C33 C34 JJX sing 205 n n C33 N31 JJX sing 206 n n C34 N35 JJX sing 207 n n N35 C38 JJX sing 208 n n N35 C36 JJX sing 209 n n C38 C40 JJX sing 210 n n C38 C39 JJX sing 211 n n C36 C37 JJX sing 212 n n C37 N31 JJX sing 213 n n N31 C30 JJX sing 214 n n C30 O32 JJX doub 215 n n C30 C29 JJX sing 216 n n C29 N12 JJX sing 217 n n N12 C11 JJX sing 218 n n N12 C7 JJX sing 219 n n C11 O21 JJX doub 220 n n C11 N10 JJX sing 221 n n C7 C3 JJX sing 222 n n C7 C8 JJX sing 223 n n C3 C2 JJX sing 224 n y C3 C4 JJX doub 225 n y C2 C1 JJX doub 226 n y C1 C6 JJX sing 227 n y C6 C19 JJX sing 228 n n C6 C5 JJX doub 229 n y C19 N20 JJX trip 230 n n C5 C4 JJX sing 231 n y C8 C27 JJX sing 232 n n C8 C9 JJX doub 233 n n C27 N28 JJX trip 234 n n C9 C22 JJX sing 235 n n C9 N10 JJX sing 236 n n N10 C13 JJX sing 237 n n C13 C18 JJX sing 238 n y C13 C14 JJX doub 239 n y C18 C17 JJX doub 240 n y C14 C15 JJX sing 241 n y C15 C16 JJX doub 242 n y C16 C17 JJX sing 243 n y C17 C23 JJX sing 244 n n C23 F25 JJX sing 245 n n C23 F26 JJX sing 246 n n C23 F24 JJX sing 247 n n C33 H331 JJX sing 248 n n C33 H332 JJX sing 249 n n C34 H341 JJX sing 250 n n C34 H342 JJX sing 251 n n C38 H38 JJX sing 252 n n C36 H361 JJX sing 253 n n C36 H362 JJX sing 254 n n C40 H401 JJX sing 255 n n C40 H402 JJX sing 256 n n C40 H403 JJX sing 257 n n C39 H391 JJX sing 258 n n C39 H392 JJX sing 259 n n C39 H393 JJX sing 260 n n C37 H371 JJX sing 261 n n C37 H372 JJX sing 262 n n C29 H291 JJX sing 263 n n C29 H292 JJX sing 264 n n C7 H7 JJX sing 265 n n C2 H2 JJX sing 266 n n C4 H4 JJX sing 267 n n C1 H1 JJX sing 268 n n C5 H5 JJX sing 269 n n C22 H221 JJX sing 270 n n C22 H222 JJX sing 271 n n C22 H223 JJX sing 272 n n C18 H18 JJX sing 273 n n C14 H14 JJX sing 274 n n C15 H15 JJX sing 275 n n C16 H16 JJX sing 276 n n # _atom_sites.entry_id 5A0B _atom_sites.fract_transf_matrix[1][1] 0.01291 _atom_sites.fract_transf_matrix[1][2] 0.007454 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014907 _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] 0.006683 _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 JJX A 1 1001 1001 JJX JJX . F 5 DMS A 1 1002 1002 DMS DMS . G 6 HOH A 1 2001 2001 HOH HOH . G 6 HOH A 2 2002 2002 HOH HOH . G 6 HOH A 3 2003 2003 HOH HOH . G 6 HOH A 4 2004 2004 HOH HOH . G 6 HOH A 5 2005 2005 HOH HOH . G 6 HOH A 6 2006 2006 HOH HOH . G 6 HOH A 7 2007 2007 HOH HOH . G 6 HOH A 8 2008 2008 HOH HOH . G 6 HOH A 9 2009 2009 HOH HOH . G 6 HOH A 10 2010 2010 HOH HOH . G 6 HOH A 11 2011 2011 HOH HOH . G 6 HOH A 12 2012 2012 HOH HOH . G 6 HOH A 13 2013 2013 HOH HOH . G 6 HOH A 14 2014 2014 HOH HOH . G 6 HOH A 15 2015 2015 HOH HOH . G 6 HOH A 16 2016 2016 HOH HOH . G 6 HOH A 17 2017 2017 HOH HOH . G 6 HOH A 18 2018 2018 HOH HOH . G 6 HOH A 19 2019 2019 HOH HOH . G 6 HOH A 20 2020 2020 HOH HOH . G 6 HOH A 21 2021 2021 HOH HOH . G 6 HOH A 22 2022 2022 HOH HOH . G 6 HOH A 23 2023 2023 HOH HOH . G 6 HOH A 24 2024 2024 HOH HOH . G 6 HOH A 25 2025 2025 HOH HOH . G 6 HOH A 26 2026 2026 HOH HOH . G 6 HOH A 27 2027 2027 HOH HOH . G 6 HOH A 28 2028 2028 HOH HOH . G 6 HOH A 29 2029 2029 HOH HOH . G 6 HOH A 30 2030 2030 HOH HOH . G 6 HOH A 31 2031 2031 HOH HOH . G 6 HOH A 32 2032 2032 HOH HOH . G 6 HOH A 33 2033 2033 HOH HOH . G 6 HOH A 34 2034 2034 HOH HOH . G 6 HOH A 35 2035 2035 HOH HOH . G 6 HOH A 36 2036 2036 HOH HOH . G 6 HOH A 37 2037 2037 HOH HOH . G 6 HOH A 38 2038 2038 HOH HOH . G 6 HOH A 39 2039 2039 HOH HOH . G 6 HOH A 40 2040 2040 HOH HOH . G 6 HOH A 41 2041 2041 HOH HOH . G 6 HOH A 42 2042 2042 HOH HOH . G 6 HOH A 43 2043 2043 HOH HOH . G 6 HOH A 44 2044 2044 HOH HOH . G 6 HOH A 45 2045 2045 HOH HOH . G 6 HOH A 46 2046 2046 HOH HOH . G 6 HOH A 47 2047 2047 HOH HOH . G 6 HOH A 48 2048 2048 HOH HOH . G 6 HOH A 49 2049 2049 HOH HOH . G 6 HOH A 50 2050 2050 HOH HOH . G 6 HOH A 51 2051 2051 HOH HOH . G 6 HOH A 52 2052 2052 HOH HOH . G 6 HOH A 53 2053 2053 HOH HOH . G 6 HOH A 54 2054 2054 HOH HOH . G 6 HOH A 55 2055 2055 HOH HOH . G 6 HOH A 56 2056 2056 HOH HOH . G 6 HOH A 57 2057 2057 HOH HOH . G 6 HOH A 58 2058 2058 HOH HOH . G 6 HOH A 59 2059 2059 HOH HOH . G 6 HOH A 60 2060 2060 HOH HOH . G 6 HOH A 61 2061 2061 HOH HOH . G 6 HOH A 62 2062 2062 HOH HOH . G 6 HOH A 63 2063 2063 HOH HOH . G 6 HOH A 64 2064 2064 HOH HOH . G 6 HOH A 65 2065 2065 HOH HOH . G 6 HOH A 66 2066 2066 HOH HOH . G 6 HOH A 67 2067 2067 HOH HOH . G 6 HOH A 68 2068 2068 HOH HOH . G 6 HOH A 69 2069 2069 HOH HOH . G 6 HOH A 70 2070 2070 HOH HOH . G 6 HOH A 71 2071 2071 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 C33 JJX . . . E 4 -5.614 -1.869 26.052 1 23.99 ? C33 JJX 1001 A 1 HETATM 2 C C34 JJX . . . E 4 -5.762 -0.878 27.22 1 26.7 ? C34 JJX 1001 A 1 HETATM 3 N N35 JJX . . . E 4 -4.755 0.192 27.019 1 30.32 ? N35 JJX 1001 A 1 HETATM 4 C C38 JJX . . . E 4 -4.593 0.942 28.319 1 34.17 ? C38 JJX 1001 A 1 HETATM 5 C C40 JJX . . . E 4 -5.756 1.906 28.66 1 32.93 ? C40 JJX 1001 A 1 HETATM 6 C C39 JJX . . . E 4 -3.249 1.682 28.335 1 35.85 ? C39 JJX 1001 A 1 HETATM 7 C C36 JJX . . . E 4 -5.069 0.973 25.766 1 24.87 ? C36 JJX 1001 A 1 HETATM 8 C C37 JJX . . . E 4 -4.964 0.022 24.511 1 22.51 ? C37 JJX 1001 A 1 HETATM 9 N N31 JJX . . . E 4 -5.802 -1.182 24.731 1 21.22 ? N31 JJX 1001 A 1 HETATM 10 C C30 JJX . . . E 4 -6.707 -1.63 23.831 1 20.44 ? C30 JJX 1001 A 1 HETATM 11 O O32 JJX . . . E 4 -6.823 -1.003 22.767 1 21.2 ? O32 JJX 1001 A 1 HETATM 12 C C29 JJX . . . E 4 -7.604 -2.909 24.109 1 20.62 ? C29 JJX 1001 A 1 HETATM 13 N N12 JJX . . . E 4 -8.553 -3.032 22.96 1 21.67 ? N12 JJX 1001 A 1 HETATM 14 C C11 JJX . . . E 4 -8.333 -4.066 22.032 1 18.5 ? C11 JJX 1001 A 1 HETATM 15 O O21 JJX . . . E 4 -7.41 -4.85 22.269 1 20.99 ? O21 JJX 1001 A 1 HETATM 16 C C7 JJX . . . E 4 -9.686 -2.106 22.844 1 20.13 ? C7 JJX 1001 A 1 HETATM 17 C C3 JJX . . . E 4 -10.65 -2.611 23.986 1 20.3 ? C3 JJX 1001 A 1 HETATM 18 C C2 JJX . . . E 4 -11.236 -1.693 24.87 1 21.12 ? C2 JJX 1001 A 1 HETATM 19 C C1 JJX . . . E 4 -12.049 -2.105 25.954 1 19.68 ? C1 JJX 1001 A 1 HETATM 20 C C6 JJX . . . E 4 -12.292 -3.454 26.148 1 18.98 ? C6 JJX 1001 A 1 HETATM 21 C C19 JJX . . . E 4 -13.119 -3.84 27.25 1 21.01 ? C19 JJX 1001 A 1 HETATM 22 N N20 JJX . . . E 4 -13.775 -4.154 28.124 1 20.94 ? N20 JJX 1001 A 1 HETATM 23 C C5 JJX . . . E 4 -11.743 -4.417 25.266 1 18.86 ? C5 JJX 1001 A 1 HETATM 24 C C4 JJX . . . E 4 -10.923 -3.978 24.208 1 21.5 ? C4 JJX 1001 A 1 HETATM 25 C C8 JJX . . . E 4 -10.344 -2.144 21.493 1 17.91 ? C8 JJX 1001 A 1 HETATM 26 C C27 JJX . . . E 4 -11.37 -1.191 21.242 1 21.56 ? C27 JJX 1001 A 1 HETATM 27 N N28 JJX . . . E 4 -12.202 -0.433 21.031 1 21.09 ? N28 JJX 1001 A 1 HETATM 28 C C9 JJX . . . E 4 -10.111 -3.221 20.631 1 21.12 ? C9 JJX 1001 A 1 HETATM 29 C C22 JJX . . . E 4 -10.907 -3.33 19.343 1 20.06 ? C22 JJX 1001 A 1 HETATM 30 N N10 JJX . . . E 4 -9.084 -4.171 20.887 1 19.94 ? N10 JJX 1001 A 1 HETATM 31 C C13 JJX . . . E 4 -8.926 -5.29 20.028 1 21.7 ? C13 JJX 1001 A 1 HETATM 32 C C18 JJX . . . E 4 -9.714 -6.44 20.32 1 19.54 ? C18 JJX 1001 A 1 HETATM 33 C C14 JJX . . . E 4 -8.068 -5.308 18.928 1 21.13 ? C14 JJX 1001 A 1 HETATM 34 C C15 JJX . . . E 4 -8.002 -6.481 18.14 1 15.47 ? C15 JJX 1001 A 1 HETATM 35 C C16 JJX . . . E 4 -8.764 -7.607 18.46 1 16.91 ? C16 JJX 1001 A 1 HETATM 36 C C17 JJX . . . E 4 -9.643 -7.598 19.527 1 17.47 ? C17 JJX 1001 A 1 HETATM 37 C C23 JJX . . . E 4 -10.419 -8.906 19.871 1 18.87 ? C23 JJX 1001 A 1 HETATM 38 F F25 JJX . . . E 4 -10.701 -9.629 18.759 1 17.33 ? F25 JJX 1001 A 1 HETATM 39 F F26 JJX . . . E 4 -11.484 -8.654 20.646 1 19.7 ? F26 JJX 1001 A 1 HETATM 40 F F24 JJX . . . E 4 -9.613 -9.618 20.642 1 15.6 ? F24 JJX 1001 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #