data_9F39 # _model_server_result.job_id DatwdgUwjW4EvT6DI4kUqA _model_server_result.datetime_utc '2025-02-22 02:02:50' _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 9f39 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 9F39 # _exptl.entry_id 9F39 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 489.565 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R,3R)-3-[[(2S)-3-cyclopropyl-2-[3-(2-methylpropanoylamino)-2-oxidanylidene-pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide _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 102.445 _cell.angle_gamma 90 _cell.entry_id 9F39 _cell.length_a 113.702 _cell.length_b 53.197 _cell.length_c 44.856 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9F39 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _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 _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' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -9.666573 0 43.802033 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 145 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 145 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C13 _struct_conn.ptnr2_label_comp_id A1H9Y _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id A1H9Y _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _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 1.796 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C24 H35 N5 O6' _chem_comp.formula_weight 489.565 _chem_comp.id A1H9Y _chem_comp.mon_nstd_flag . _chem_comp.name (2R,3R)-3-[[(2S)-3-cyclopropyl-2-[3-(2-methylpropanoylamino)-2-oxidanylidene-pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide _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 A1H9Y sing 1 n n C2 C3 A1H9Y doub 2 n n C3 C4 A1H9Y sing 3 n n C4 N1 A1H9Y sing 4 n n N1 C5 A1H9Y sing 5 n n C1 C5 A1H9Y doub 6 n n N1 C6 A1H9Y sing 7 n n C3 N2 A1H9Y sing 8 n n C6 C7 A1H9Y sing 9 n n C7 N3 A1H9Y sing 10 n n N3 C8 A1H9Y sing 11 n n C6 C9 A1H9Y sing 12 n n C9 C10 A1H9Y sing 13 n n C10 C11 A1H9Y sing 14 n n C11 C12 A1H9Y sing 15 n n C10 C12 A1H9Y sing 16 n n C7 O1 A1H9Y doub 17 n n C4 O2 A1H9Y doub 18 n n C8 C13 A1H9Y sing 19 n n C8 C14 A1H9Y sing 20 n n C13 C15 A1H9Y sing 21 n n C14 C16 A1H9Y sing 22 n n C16 C17 A1H9Y sing 23 n n C17 C18 A1H9Y sing 24 n n C18 N4 A1H9Y sing 25 n n N4 C19 A1H9Y sing 26 n n C16 C19 A1H9Y sing 27 n n C19 O3 A1H9Y doub 28 n n N2 C20 A1H9Y sing 29 n n C20 C21 A1H9Y sing 30 n n C21 C22 A1H9Y sing 31 n n C21 C23 A1H9Y sing 32 n n C15 N5 A1H9Y sing 33 n n N5 C24 A1H9Y sing 34 n n C20 O4 A1H9Y doub 35 n n C15 O5 A1H9Y doub 36 n n C13 O6 A1H9Y sing 37 n n N3 H6 A1H9Y sing 38 n n C5 H3 A1H9Y sing 39 n n C6 H4 A1H9Y sing 40 n n C8 H7 A1H9Y sing 41 n n C10 H10 A1H9Y sing 42 n n C13 H15 A1H9Y sing 43 n n C17 H19 A1H9Y sing 44 n n C17 H20 A1H9Y sing 45 n n C21 H24 A1H9Y sing 46 n n C22 H26 A1H9Y sing 47 n n C22 H25 A1H9Y sing 48 n n C22 H27 A1H9Y sing 49 n n C24 H34 A1H9Y sing 50 n n C24 H33 A1H9Y sing 51 n n C24 H32 A1H9Y sing 52 n n C1 H1 A1H9Y sing 53 n n C2 H2 A1H9Y sing 54 n n N2 H5 A1H9Y sing 55 n n C9 H9 A1H9Y sing 56 n n C9 H8 A1H9Y sing 57 n n C11 H11 A1H9Y sing 58 n n C11 H12 A1H9Y sing 59 n n C12 H13 A1H9Y sing 60 n n C12 H14 A1H9Y sing 61 n n C14 H16 A1H9Y sing 62 n n C14 H17 A1H9Y sing 63 n n C16 H18 A1H9Y sing 64 n n C18 H21 A1H9Y sing 65 n n C18 H22 A1H9Y sing 66 n n N4 H23 A1H9Y sing 67 n n C23 H30 A1H9Y sing 68 n n C23 H29 A1H9Y sing 69 n n C23 H28 A1H9Y sing 70 n n N5 H31 A1H9Y sing 71 n n O6 H35 A1H9Y sing 72 n n # _atom_sites.entry_id 9F39 _atom_sites.fract_transf_matrix[1][1] 0.008795 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001941 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018798 _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] 0.02283 _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 A1H9Y A 1 401 401 A1H9Y LIG . C 3 HOH A 1 501 2 HOH HOH . C 3 HOH A 2 502 8 HOH HOH . C 3 HOH A 3 503 10 HOH HOH . C 3 HOH A 4 504 24 HOH HOH . C 3 HOH A 5 505 19 HOH HOH . C 3 HOH A 6 506 5 HOH HOH . C 3 HOH A 7 507 20 HOH HOH . C 3 HOH A 8 508 15 HOH HOH . C 3 HOH A 9 509 6 HOH HOH . C 3 HOH A 10 510 30 HOH HOH . C 3 HOH A 11 511 11 HOH HOH . C 3 HOH A 12 512 28 HOH HOH . C 3 HOH A 13 513 3 HOH HOH . C 3 HOH A 14 514 25 HOH HOH . C 3 HOH A 15 515 18 HOH HOH . C 3 HOH A 16 516 26 HOH HOH . C 3 HOH A 17 517 4 HOH HOH . C 3 HOH A 18 518 1 HOH HOH . C 3 HOH A 19 519 13 HOH HOH . C 3 HOH A 20 520 22 HOH HOH . C 3 HOH A 21 521 33 HOH HOH . C 3 HOH A 22 522 31 HOH HOH . C 3 HOH A 23 523 29 HOH HOH . C 3 HOH A 24 524 32 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 A1H9Y . . . B 2 -15.38 -25.936 -1.001 1 46.06 0 N1 A1H9Y 401 A 1 HETATM 2 N N3 A1H9Y . . . B 2 -13.543 -27.536 1.628 1 46.03 0 N3 A1H9Y 401 A 1 HETATM 3 C C4 A1H9Y . . . B 2 -15.614 -24.64 -0.56 1 53.02 0 C4 A1H9Y 401 A 1 HETATM 4 C C5 A1H9Y . . . B 2 -15.294 -26.243 -2.334 1 49.83 0 C5 A1H9Y 401 A 1 HETATM 5 C C6 A1H9Y . . . B 2 -15.248 -26.999 0.003 1 42.33 0 C6 A1H9Y 401 A 1 HETATM 6 C C7 A1H9Y . . . B 2 -13.793 -27.327 0.325 1 42.2 0 C7 A1H9Y 401 A 1 HETATM 7 C C8 A1H9Y . . . B 2 -12.484 -28.344 2.24 1 47.59 0 C8 A1H9Y 401 A 1 HETATM 8 C C10 A1H9Y . . . B 2 -17.545 -27.957 -0.153 1 41.81 0 C10 A1H9Y 401 A 1 HETATM 9 C C13 A1H9Y . . . B 2 -12.695 -29.824 1.825 1 48.43 0 C13 A1H9Y 401 A 1 HETATM 10 C C15 A1H9Y . . . B 2 -11.425 -30.674 1.715 1 45.24 0 C15 A1H9Y 401 A 1 HETATM 11 C C17 A1H9Y . . . B 2 -9.775 -25.594 1.536 1 46.8 0 C17 A1H9Y 401 A 1 HETATM 12 C C20 A1H9Y . . . B 2 -16.62 -21.307 -1.697 1 67.31 0 C20 A1H9Y 401 A 1 HETATM 13 C C21 A1H9Y . . . B 2 -16.592 -19.979 -0.964 1 70.41 0 C21 A1H9Y 401 A 1 HETATM 14 C C22 A1H9Y . . . B 2 -17.942 -19.7 -0.312 1 67.59 0 C22 A1H9Y 401 A 1 HETATM 15 C C24 A1H9Y . . . B 2 -10.331 -32.457 0.439 1 46.52 0 C24 A1H9Y 401 A 1 HETATM 16 C C1 A1H9Y . . . B 2 -15.443 -25.298 -3.282 1 52.46 0 C1 A1H9Y 401 A 1 HETATM 17 C C2 A1H9Y . . . B 2 -15.681 -23.97 -2.912 1 53.91 0 C2 A1H9Y 401 A 1 HETATM 18 C C3 A1H9Y . . . B 2 -15.794 -23.639 -1.592 1 58.43 0 C3 A1H9Y 401 A 1 HETATM 19 N N2 A1H9Y . . . B 2 -16.026 -22.357 -1.064 1 63.44 0 N2 A1H9Y 401 A 1 HETATM 20 C C9 A1H9Y . . . B 2 -16.081 -28.225 -0.377 1 40.69 0 C9 A1H9Y 401 A 1 HETATM 21 C C11 A1H9Y . . . B 2 -18.343 -27.18 -1.154 1 41.5 0 C11 A1H9Y 401 A 1 HETATM 22 C C12 A1H9Y . . . B 2 -18.593 -28.641 -0.977 1 41.47 0 C12 A1H9Y 401 A 1 HETATM 23 O O1 A1H9Y . . . B 2 -12.992 -27.52 -0.575 1 43.97 0 O1 A1H9Y 401 A 1 HETATM 24 O O2 A1H9Y . . . B 2 -15.696 -24.405 0.643 1 55.17 0 O2 A1H9Y 401 A 1 HETATM 25 C C14 A1H9Y . . . B 2 -11.107 -27.73 1.962 1 48.16 0 C14 A1H9Y 401 A 1 HETATM 26 C C16 A1H9Y . . . B 2 -11.018 -26.22 2.174 1 45.42 0 C16 A1H9Y 401 A 1 HETATM 27 C C18 A1H9Y . . . B 2 -9.178 -24.695 2.612 1 45.38 0 C18 A1H9Y 401 A 1 HETATM 28 N N4 A1H9Y . . . B 2 -9.9 -25.047 3.824 1 44.57 0 N4 A1H9Y 401 A 1 HETATM 29 C C19 A1H9Y . . . B 2 -10.987 -25.774 3.627 1 42.97 0 C19 A1H9Y 401 A 1 HETATM 30 O O3 A1H9Y . . . B 2 -11.855 -25.999 4.464 1 42.22 0 O3 A1H9Y 401 A 1 HETATM 31 C C23 A1H9Y . . . B 2 -16.197 -18.86 -1.923 1 73.22 0 C23 A1H9Y 401 A 1 HETATM 32 N N5 A1H9Y . . . B 2 -11.42 -31.541 0.711 1 46.9 0 N5 A1H9Y 401 A 1 HETATM 33 O O4 A1H9Y . . . B 2 -17.135 -21.416 -2.813 1 74.87 0 O4 A1H9Y 401 A 1 HETATM 34 O O5 A1H9Y . . . B 2 -10.523 -30.585 2.538 1 42.47 0 O5 A1H9Y 401 A 1 HETATM 35 O O6 A1H9Y . . . B 2 -13.403 -29.913 0.598 1 44.91 0 O6 A1H9Y 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 35 #