data_8YRK # _model_server_result.job_id FeDFsttpq7uLMy909t37mQ _model_server_result.datetime_utc '2025-07-26 06:04:44' _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 8yrk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":506}' # _entry.id 8YRK # _exptl.entry_id 8YRK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 435.257 _entity.id 12 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (11R,16S)-11-(3,5-dichloro-4-methoxyphenyl)-4,7-dioxa-12,14-diazatetracyclo[8.7.0.03,8.012,16]heptadeca-1,3(8),9-triene-13,15-dione _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 8YRK _cell.length_a 104.097 _cell.length_b 158.982 _cell.length_c 179.057 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YRK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA _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 ? 12 P N N ? 12 W 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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc5 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc7 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc8 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc9 H MG MG . A MG 502 1_555 Y O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc10 H MG MG . A MG 502 1_555 Y O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc11 H MG MG . A MG 502 1_555 Y O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc12 H MG MG . A MG 502 1_555 Y O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc13 I CA CA . A CA 503 1_555 Y O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc15 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc16 L MG MG . B MG 502 1_555 Z O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.869 ? metalc ? metalc17 L MG MG . B MG 502 1_555 Z O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc18 L MG MG . B MG 502 1_555 Z O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc19 L MG MG . B MG 502 1_555 Z O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc20 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? metalc ? metalc21 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc22 C O THR 41 C THR 41 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc23 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc24 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc25 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc26 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc27 Q O1G GTP . C GTP 501 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? metalc ? metalc28 Q O3G GTP . C GTP 501 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc29 Q O1B GTP . C GTP 501 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc30 R CA CA . C CA 502 1_555 AA O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc31 AA O HOH . C HOH 602 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc32 AA O HOH . C HOH 603 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc33 AA O HOH . C HOH 604 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc34 AA O HOH . C HOH 607 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc35 U O1B GDP . D GDP 502 1_555 V MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc36 V MG MG . D MG 503 1_555 BA O HOH . D HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc37 V MG MG . D MG 503 1_555 BA O HOH . D HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc38 V MG MG . D MG 503 1_555 BA O HOH . D HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? # _chem_comp.formula 'C20 H16 Cl2 N2 O5' _chem_comp.formula_weight 435.257 _chem_comp.id A1D62 _chem_comp.mon_nstd_flag . _chem_comp.name (11R,16S)-11-(3,5-dichloro-4-methoxyphenyl)-4,7-dioxa-12,14-diazatetracyclo[8.7.0.03,8.012,16]heptadeca-1,3(8),9-triene-13,15-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Tubulin polymerization-IN-41' # 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 O1 A1D62 sing 1 n n O1 C2 A1D62 sing 2 n n C2 C3 A1D62 doub 3 n y C3 CL1 A1D62 sing 4 n n C3 C4 A1D62 sing 5 n y C4 C5 A1D62 doub 6 n y C5 C6 A1D62 sing 7 n n C6 C7 A1D62 sing 8 n n C7 C8 A1D62 doub 9 n y C8 C9 A1D62 sing 10 n y C9 C10 A1D62 doub 11 n y C10 C11 A1D62 sing 12 n y C11 C12 A1D62 doub 13 n y C12 C13 A1D62 sing 14 n n C13 C14 A1D62 sing 15 n n C14 C15 A1D62 sing 16 n n C15 O2 A1D62 doub 17 n n C15 N1 A1D62 sing 18 n n N1 C16 A1D62 sing 19 n n C16 O3 A1D62 doub 20 n n C16 N2 A1D62 sing 21 n n C10 O4 A1D62 sing 22 n n O4 C17 A1D62 sing 23 n n C17 C18 A1D62 sing 24 n n C18 O5 A1D62 sing 25 n n C5 C19 A1D62 sing 26 n y C19 C20 A1D62 doub 27 n y C20 CL2 A1D62 sing 28 n n C2 C20 A1D62 sing 29 n y C6 N2 A1D62 sing 30 n n C7 C12 A1D62 sing 31 n y C14 N2 A1D62 sing 32 n n C9 O5 A1D62 sing 33 n n N1 H11 A1D62 sing 34 n n C4 H4 A1D62 sing 35 n n C6 H5 A1D62 sing 36 n n C8 H6 A1D62 sing 37 n n C13 H8 A1D62 sing 38 n n C13 H9 A1D62 sing 39 n n C17 H13 A1D62 sing 40 n n C17 H12 A1D62 sing 41 n n C1 H2 A1D62 sing 42 n n C1 H1 A1D62 sing 43 n n C1 H3 A1D62 sing 44 n n C11 H7 A1D62 sing 45 n n C14 H10 A1D62 sing 46 n n C18 H15 A1D62 sing 47 n n C18 H14 A1D62 sing 48 n n C19 H16 A1D62 sing 49 n n # _atom_sites.entry_id 8YRK _atom_sites.fract_transf_matrix[1][1] 0.009606 _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] 0.00629 _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] 0.005585 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 CL A 1 504 504 CL CL . K 9 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 10 MES B 1 503 503 MES MES . N 10 MES B 1 504 504 MES MES . O 11 GOL B 1 505 505 GOL GOL . P 12 A1D62 B 1 506 506 A1D62 LIG . Q 5 GTP C 1 501 501 GTP GTP . R 7 CA C 1 502 503 CA CA . S 13 EDO C 1 503 504 EDO EDO . T 6 MG D 1 501 502 MG MG . U 9 GDP D 1 502 501 GDP GDP . V 6 MG D 1 503 502 MG MG . W 12 A1D62 D 1 504 503 A1D62 LIG . X 14 ACP F 1 401 401 ACP ACP . Y 15 HOH A 1 601 2 HOH HOH . Y 15 HOH A 2 602 3 HOH HOH . Y 15 HOH A 3 603 4 HOH HOH . Y 15 HOH A 4 604 5 HOH HOH . Y 15 HOH A 5 605 1 HOH HOH . Z 15 HOH B 1 601 19 HOH HOH . Z 15 HOH B 2 602 8 HOH HOH . Z 15 HOH B 3 603 10 HOH HOH . Z 15 HOH B 4 604 6 HOH HOH . Z 15 HOH B 5 605 9 HOH HOH . Z 15 HOH B 6 606 7 HOH HOH . Z 15 HOH B 7 607 28 HOH HOH . Z 15 HOH B 8 608 29 HOH HOH . Z 15 HOH B 9 609 30 HOH HOH . AA 15 HOH C 1 601 26 HOH HOH . AA 15 HOH C 2 602 13 HOH HOH . AA 15 HOH C 3 603 12 HOH HOH . AA 15 HOH C 4 604 14 HOH HOH . AA 15 HOH C 5 605 15 HOH HOH . AA 15 HOH C 6 606 23 HOH HOH . AA 15 HOH C 7 607 11 HOH HOH . AA 15 HOH C 8 608 32 HOH HOH . AA 15 HOH C 9 609 27 HOH HOH . AA 15 HOH C 10 610 20 HOH HOH . AA 15 HOH C 11 611 21 HOH HOH . AA 15 HOH C 12 612 31 HOH HOH . BA 15 HOH D 1 601 16 HOH HOH . BA 15 HOH D 2 602 24 HOH HOH . BA 15 HOH D 3 603 17 HOH HOH . BA 15 HOH D 4 604 18 HOH HOH . BA 15 HOH D 5 605 33 HOH HOH . BA 15 HOH D 6 606 34 HOH HOH . CA 15 HOH E 1 201 22 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 N N1 A1D62 . . . P 12 19.708 70.405 42.47 1 75.22 ? N1 A1D62 506 B 1 HETATM 2 C C4 A1D62 . . . P 12 15.951 66.965 42.016 1 87.87 ? C4 A1D62 506 B 1 HETATM 3 C C5 A1D62 . . . P 12 17.231 66.944 41.468 1 60.98 ? C5 A1D62 506 B 1 HETATM 4 C C6 A1D62 . . . P 12 18.465 66.981 42.356 1 57.47 ? C6 A1D62 506 B 1 HETATM 5 C C7 A1D62 . . . P 12 18.263 66.225 43.673 1 54.35 ? C7 A1D62 506 B 1 HETATM 6 C C8 A1D62 . . . P 12 17.746 64.932 43.639 1 54.79 ? C8 A1D62 506 B 1 HETATM 7 C C10 A1D62 . . . P 12 17.842 64.816 46.038 1 57.02 ? C10 A1D62 506 B 1 HETATM 8 C C13 A1D62 . . . P 12 19.225 68.167 44.997 1 59 ? C13 A1D62 506 B 1 HETATM 9 C C15 A1D62 . . . P 12 19.235 70.338 43.745 1 72.23 ? C15 A1D62 506 B 1 HETATM 10 C C17 A1D62 . . . P 12 17.341 62.761 47.177 1 60.59 ? C17 A1D62 506 B 1 HETATM 11 C C20 A1D62 . . . P 12 16.267 66.842 39.267 1 89.51 ? C20 A1D62 506 B 1 HETATM 12 C C1 A1D62 . . . P 12 13.726 66.52 37.843 1 96.57 ? C1 A1D62 506 B 1 HETATM 13 C C11 A1D62 . . . P 12 18.424 66.074 46.088 1 61.05 ? C11 A1D62 506 B 1 HETATM 14 C C12 A1D62 . . . P 12 18.624 66.787 44.905 1 61.87 ? C12 A1D62 506 B 1 HETATM 15 C C14 A1D62 . . . P 12 18.58 68.986 43.932 1 70.84 ? C14 A1D62 506 B 1 HETATM 16 C C16 A1D62 . . . P 12 19.444 69.23 41.772 1 72.23 ? C16 A1D62 506 B 1 HETATM 17 C C18 A1D62 . . . P 12 16.707 62.261 45.938 1 49.44 ? C18 A1D62 506 B 1 HETATM 18 C C19 A1D62 . . . P 12 17.373 66.873 40.087 1 83.03 ? C19 A1D62 506 B 1 HETATM 19 C C2 A1D62 . . . P 12 14.989 66.861 39.814 1 107.03 ? C2 A1D62 506 B 1 HETATM 20 C C3 A1D62 . . . P 12 14.846 66.926 41.188 1 94.59 ? C3 A1D62 506 B 1 HETATM 21 C C9 A1D62 . . . P 12 17.538 64.229 44.817 1 55.56 ? C9 A1D62 506 B 1 HETATM 22 N N2 A1D62 . . . P 12 18.871 68.364 42.638 1 64.66 ? N2 A1D62 506 B 1 HETATM 23 O O1 A1D62 . . . P 12 13.755 66.841 39.226 1 88.4 ? O1 A1D62 506 B 1 HETATM 24 O O2 A1D62 . . . P 12 19.313 71.223 44.568 1 74.47 ? O2 A1D62 506 B 1 HETATM 25 O O3 A1D62 . . . P 12 19.765 68.984 40.622 1 66.69 ? O3 A1D62 506 B 1 HETATM 26 O O4 A1D62 . . . P 12 17.747 64.138 47.224 1 61.57 ? O4 A1D62 506 B 1 HETATM 27 O O5 A1D62 . . . P 12 16.985 62.975 44.719 1 50.78 ? O5 A1D62 506 B 1 HETATM 28 CL CL1 A1D62 . . . P 12 13.229 66.958 41.824 1 91.48 ? CL1 A1D62 506 B 1 HETATM 29 CL CL2 A1D62 . . . P 12 16.499 66.769 37.548 1 159.2 ? CL2 A1D62 506 B 1 # _model_server_stats.io_time_ms 240 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 357 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 29 #