data_6S9X # _model_server_result.job_id Qo5Hy32dSgGv8xvhYEbzaQ _model_server_result.datetime_utc '2025-01-03 00:42:16' _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 6s9x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6S9X # _exptl.entry_id 6S9X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 654.757 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ~{N}-[3-[1-[[4-[5-[(4-hydroxyphenyl)methyl]-6-oxidanylidene-2-phenyl-1~{H}-pyrazin-3-yl]phenyl]methyl]piperidin-4-yl]-2-oxidanylidene-1~{H}-benzimidazol-5-yl]propanamide _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 90 _cell.entry_id 6S9X _cell.length_a 70.46 _cell.length_b 71.33 _cell.length_c 91.56 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6S9X _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 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 _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 2 _struct_asym.id B _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 60 A CYS 60 1_555 A SG CYS 77 A CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? covale ? covale1 A SG CYS 310 A CYS 310 1_555 B CBL L1W . A L1W 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.827 ? # _chem_comp.formula 'C39 H38 N6 O4' _chem_comp.formula_weight 654.757 _chem_comp.id L1W _chem_comp.mon_nstd_flag . _chem_comp.name ~{N}-[3-[1-[[4-[5-[(4-hydroxyphenyl)methyl]-6-oxidanylidene-2-phenyl-1~{H}-pyrazin-3-yl]phenyl]methyl]piperidin-4-yl]-2-oxidanylidene-1~{H}-benzimidazol-5-yl]propanamide _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 CBL CBK L1W sing 173 n n CBF CBE L1W doub 174 n y CBF CBG L1W sing 175 n y CBE CBC L1W sing 176 n y CBK CBJ L1W sing 177 n n NBI CBJ L1W sing 178 n n NBI CBG L1W sing 179 n n CBJ OBM L1W doub 180 n n CBG CBH L1W doub 181 n y CBC NBB L1W sing 182 n n CBC CBD L1W doub 183 n y NBB CBA L1W sing 184 n n CBH CBD L1W sing 185 n y CBD NAZ L1W sing 186 n n CBA NAZ L1W sing 187 n n CBA OBN L1W doub 188 n n NAZ CAW L1W sing 189 n n CAX CAW L1W sing 190 n n CAX CAY L1W sing 191 n n CAW CAV L1W sing 192 n n CAY NAT L1W sing 193 n n CAV CAU L1W sing 194 n n NAT CAU L1W sing 195 n n NAT CAS L1W sing 196 n n CAS CAP L1W sing 197 n n CAQ CAP L1W doub 198 n y CAQ CAR L1W sing 199 n y CAP CAO L1W sing 200 n y CAR CAH L1W doub 201 n y CAO CAN L1W doub 202 n y CBS CBR L1W doub 203 n y CBS CBT L1W sing 204 n y OBW CBT L1W sing 205 n n CAH CAN L1W sing 206 n y CAH CAE L1W sing 207 n n CBR CBQ L1W sing 208 n y CBT CBU L1W doub 209 n y CAM CAL L1W doub 210 n y CAM CAG L1W sing 211 n y CAL CAK L1W sing 212 n y CAE NAF L1W sing 213 n n CAE CAD L1W doub 214 n n NAF CAA L1W doub 215 n n CBQ CBV L1W doub 216 n y CBQ CBP L1W sing 217 n n CBU CBV L1W sing 218 n y CAD CAG L1W sing 219 n n CAD NAC L1W sing 220 n n CAG CAI L1W doub 221 n y CAK CAJ L1W doub 222 n y CAA CBP L1W sing 223 n n CAA CAB L1W sing 224 n n NAC CAB L1W sing 225 n n CAB OBO L1W doub 226 n n CAI CAJ L1W sing 227 n y CAI H2 L1W sing 228 n n CAJ H3 L1W sing 229 n n CAK H4 L1W sing 230 n n CAL H5 L1W sing 231 n n CAM H6 L1W sing 232 n n CAN H7 L1W sing 233 n n CAO H8 L1W sing 234 n n CAQ H9 L1W sing 235 n n CAR H10 L1W sing 236 n n CAS H11 L1W sing 237 n n CAS H12 L1W sing 238 n n CAU H13 L1W sing 239 n n CAU H14 L1W sing 240 n n CAV H15 L1W sing 241 n n CAV H16 L1W sing 242 n n CAW H17 L1W sing 243 n n CAX H18 L1W sing 244 n n CAX H19 L1W sing 245 n n CAY H20 L1W sing 246 n n CAY H21 L1W sing 247 n n CBE H22 L1W sing 248 n n CBF H23 L1W sing 249 n n CBH H24 L1W sing 250 n n CBK H25 L1W sing 251 n n CBK H26 L1W sing 252 n n CBL H27 L1W sing 253 n n CBL H28 L1W sing 254 n n CBL H29 L1W sing 255 n n CBP H30 L1W sing 256 n n CBP H31 L1W sing 257 n n CBR H32 L1W sing 258 n n CBS H33 L1W sing 259 n n CBU H34 L1W sing 260 n n CBV H35 L1W sing 261 n n NBB H37 L1W sing 262 n n NBI H38 L1W sing 263 n n OBW H39 L1W sing 264 n n NAC H1 L1W sing 265 n n # _atom_sites.entry_id 6S9X _atom_sites.fract_transf_matrix[1][1] 0.014192 _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] 0.014019 _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] 0.010922 _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 L1W A 1 501 501 L1W DRG . C 3 HOH A 1 601 7 HOH HOH . C 3 HOH A 2 602 8 HOH HOH . C 3 HOH A 3 603 4 HOH HOH . C 3 HOH A 4 604 9 HOH HOH . C 3 HOH A 5 605 17 HOH HOH . C 3 HOH A 6 606 5 HOH HOH . C 3 HOH A 7 607 18 HOH HOH . C 3 HOH A 8 608 11 HOH HOH . C 3 HOH A 9 609 16 HOH HOH . C 3 HOH A 10 610 10 HOH HOH . C 3 HOH A 11 611 2 HOH HOH . C 3 HOH A 12 612 6 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 CAA L1W . . . B 2 1.503 -0.275 15.351 1 81.08 ? CAA L1W 501 A 1 HETATM 2 C CAB L1W . . . B 2 2.446 -0.628 16.304 1 75.32 ? CAB L1W 501 A 1 HETATM 3 C CAD L1W . . . B 2 4.042 0.781 15.196 1 70.93 ? CAD L1W 501 A 1 HETATM 4 C CAE L1W . . . B 2 3.063 1.123 14.239 1 70.45 ? CAE L1W 501 A 1 HETATM 5 C CAG L1W . . . B 2 5.359 1.241 15.221 1 58.38 ? CAG L1W 501 A 1 HETATM 6 C CAH L1W . . . B 2 3.332 2.006 13.177 1 69.66 ? CAH L1W 501 A 1 HETATM 7 C CAI L1W . . . B 2 5.817 1.902 16.354 1 52.77 ? CAI L1W 501 A 1 HETATM 8 C CAJ L1W . . . B 2 7.127 2.365 16.419 1 51.44 ? CAJ L1W 501 A 1 HETATM 9 C CAK L1W . . . B 2 7.989 2.154 15.351 1 61.35 ? CAK L1W 501 A 1 HETATM 10 C CAL L1W . . . B 2 7.535 1.485 14.219 1 56.06 ? CAL L1W 501 A 1 HETATM 11 C CAM L1W . . . B 2 6.226 1.022 14.154 1 54.09 ? CAM L1W 501 A 1 HETATM 12 C CAN L1W . . . B 2 3.913 3.252 13.402 1 70.86 ? CAN L1W 501 A 1 HETATM 13 C CAO L1W . . . B 2 4.187 4.114 12.348 1 80.63 ? CAO L1W 501 A 1 HETATM 14 C CAP L1W . . . B 2 3.873 3.768 11.039 1 73.91 ? CAP L1W 501 A 1 HETATM 15 C CAQ L1W . . . B 2 3.294 2.526 10.796 1 69.2 ? CAQ L1W 501 A 1 HETATM 16 C CAR L1W . . . B 2 3.024 1.658 11.861 1 68.59 ? CAR L1W 501 A 1 HETATM 17 C CAS L1W . . . B 2 4.178 4.659 10.002 1 75.03 ? CAS L1W 501 A 1 HETATM 18 C CAU L1W . . . B 2 2.269 6.026 9.648 1 75.88 ? CAU L1W 501 A 1 HETATM 19 C CAV L1W . . . B 2 1.151 6.436 8.704 1 77.28 ? CAV L1W 501 A 1 HETATM 20 C CAW L1W . . . B 2 1.723 6.894 7.359 1 80.76 ? CAW L1W 501 A 1 HETATM 21 C CAX L1W . . . B 2 2.597 5.794 6.798 1 77.62 ? CAX L1W 501 A 1 HETATM 22 C CAY L1W . . . B 2 3.668 5.454 7.822 1 75.94 ? CAY L1W 501 A 1 HETATM 23 C CBA L1W . . . B 2 -0.526 6.713 6.159 1 93.95 ? CBA L1W 501 A 1 HETATM 24 C CBC L1W . . . B 2 -0.421 8.377 4.84 1 96.59 ? CBC L1W 501 A 1 HETATM 25 C CBD L1W . . . B 2 0.718 8.339 5.547 1 94.85 ? CBD L1W 501 A 1 HETATM 26 C CBE L1W . . . B 2 -0.642 9.312 3.92 1 106.97 ? CBE L1W 501 A 1 HETATM 27 C CBF L1W . . . B 2 0.308 10.285 3.668 1 104.55 ? CBF L1W 501 A 1 HETATM 28 C CBG L1W . . . B 2 1.482 10.265 4.404 1 100.96 ? CBG L1W 501 A 1 HETATM 29 C CBH L1W . . . B 2 1.671 9.255 5.346 1 95.39 ? CBH L1W 501 A 1 HETATM 30 C CBJ L1W . . . B 2 2.161 12.477 4.414 1 113.94 ? CBJ L1W 501 A 1 HETATM 31 C CBK L1W . . . B 2 3.286 13.429 4.004 1 116.39 ? CBK L1W 501 A 1 HETATM 32 C CBL L1W . . . B 2 3.331 13.471 2.455 1 117.69 ? CBL L1W 501 A 1 HETATM 33 C CBP L1W . . . B 2 0.247 -0.876 15.511 1 81.88 ? CBP L1W 501 A 1 HETATM 34 C CBQ L1W . . . B 2 -0.821 -0.351 14.787 1 86.32 ? CBQ L1W 501 A 1 HETATM 35 C CBR L1W . . . B 2 -0.877 -0.413 13.4 1 92.52 ? CBR L1W 501 A 1 HETATM 36 C CBS L1W . . . B 2 -1.978 0.103 12.723 1 97.12 ? CBS L1W 501 A 1 HETATM 37 C CBT L1W . . . B 2 -3.037 0.664 13.426 1 97.01 ? CBT L1W 501 A 1 HETATM 38 C CBU L1W . . . B 2 -2.991 0.711 14.814 1 84.74 ? CBU L1W 501 A 1 HETATM 39 C CBV L1W . . . B 2 -1.888 0.197 15.488 1 82.57 ? CBV L1W 501 A 1 HETATM 40 N NAC L1W . . . B 2 3.72 -0.095 16.227 1 65.58 ? NAC L1W 501 A 1 HETATM 41 N NAF L1W . . . B 2 1.829 0.575 14.349 1 71.88 ? NAF L1W 501 A 1 HETATM 42 N NAT L1W . . . B 2 3.077 4.946 9.07 1 77.88 ? NAT L1W 501 A 1 HETATM 43 N NAZ L1W . . . B 2 0.651 7.297 6.385 1 90.75 ? NAZ L1W 501 A 1 HETATM 44 N NBB L1W . . . B 2 -1.192 7.367 5.224 1 87.04 ? NBB L1W 501 A 1 HETATM 45 N NBI L1W . . . B 2 2.412 11.186 4.15 1 106.37 ? NBI L1W 501 A 1 HETATM 46 O OBM L1W . . . B 2 1.139 12.902 4.949 1 116.17 ? OBM L1W 501 A 1 HETATM 47 O OBN L1W . . . B 2 -0.976 5.72 6.729 1 97.86 ? OBN L1W 501 A 1 HETATM 48 O OBO L1W . . . B 2 2.165 -1.406 17.216 1 85.36 ? OBO L1W 501 A 1 HETATM 49 O OBW L1W . . . B 2 -4.113 1.166 12.762 1 103.76 ? OBW L1W 501 A 1 # _model_server_stats.io_time_ms 76 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 49 #