data_2PHB # _model_server_result.job_id XEGdhvP-XSGi9UQoIwpQMg _model_server_result.datetime_utc '2025-03-22 07:10:08' _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 2phb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":9001}' # _entry.id 2PHB # _exptl.entry_id 2PHB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.907 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R,4R)-N~1~-(4-CHLOROPHENYL)-N~2~-[2-FLUORO-4-(2-OXOPYRIDIN-1(2H)-YL)PHENYL]-4-METHOXYPYRROLIDINE-1,2-DICARBOXAMIDE _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 2PHB _cell.length_a 56.483 _cell.length_b 72.406 _cell.length_c 77.715 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PHB _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 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 # _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 D _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 7 A CYS 22 1_555 A SG CYS 12 A CYS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? disulf ? disulf2 A SG CYS 27 A CYS 42 1_555 A SG CYS 43 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? disulf ? disulf3 A SG CYS 108 A CYS 122 1_555 B SG CYS 45 B CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? disulf ? disulf4 A SG CYS 156 A CYS 168 1_555 A SG CYS 170 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.764 ? disulf ? disulf5 A SG CYS 181 A CYS 191 1_555 A SG CYS 209 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? disulf ? disulf6 B SG CYS 2 B CYS 1 1_555 B SG CYS 13 B CYS 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? disulf ? disulf7 B SG CYS 9 B CYS 8 1_555 B SG CYS 22 B CYS 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? disulf ? disulf8 B SG CYS 24 B CYS 23 1_555 B SG CYS 37 B CYS 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc1 A OD1 ASP 56 A ASP 70 1_555 C CA CA . A CA 9000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc2 A O ASN 58 A ASN 72 1_555 C CA CA . A CA 9000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc3 A O GLN 61 A GLN 75 1_555 C CA CA . A CA 9000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc4 A OE1 GLU 66 A GLU 80 1_555 C CA CA . A CA 9000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc5 C CA CA . A CA 9000 1_555 E O HOH . A HOH 9038 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? # _chem_comp.formula 'C24 H22 Cl F N4 O4' _chem_comp.formula_weight 484.907 _chem_comp.id 230 _chem_comp.mon_nstd_flag . _chem_comp.name (2R,4R)-N~1~-(4-CHLOROPHENYL)-N~2~-[2-FLUORO-4-(2-OXOPYRIDIN-1(2H)-YL)PHENYL]-4-METHOXYPYRROLIDINE-1,2-DICARBOXAMIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms PD-0348292 # 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 N1 C4 230 sing 1 n n N1 C7 230 sing 2 n n N1 HN1 230 sing 3 n n N3 C15 230 sing 4 n n N3 C14 230 sing 5 n n N3 C1 230 sing 6 n n C4 C3 230 doub 7 n y C4 C5 230 sing 8 n y C5 C6 230 doub 9 n y C5 F1 230 sing 10 n n C6 C1 230 sing 11 n y C6 H6 230 sing 12 n n C7 O1 230 doub 13 n n C7 C21 230 sing 14 n n C8 C9 230 sing 15 n y C8 CL1 230 sing 16 n n C8 C13 230 doub 17 n y C10 C9 230 doub 18 n y C10 C11 230 sing 19 n y C10 H10 230 sing 20 n n C13 C12 230 sing 21 n y C13 H13 230 sing 22 n n C15 C16 230 sing 23 n n C15 O2 230 doub 24 n n C17 C16 230 doub 25 n n C17 C18 230 sing 26 n n C17 H17 230 sing 27 n n C20 C21 230 sing 28 n n C20 C19 230 sing 29 n n C20 H201 230 sing 30 n n C20 H202 230 sing 31 n n C21 N4 230 sing 32 n n C21 H21 230 sing 33 n n C22 N4 230 sing 34 n n C22 C19 230 sing 35 n n C22 H221 230 sing 36 n n C22 H222 230 sing 37 n n C24 O3 230 sing 38 n n C24 H241 230 sing 39 n n C24 H242 230 sing 40 n n C24 H243 230 sing 41 n n C1 C2 230 doub 42 n y C2 C3 230 sing 43 n y C2 H2 230 sing 44 n n C3 H3 230 sing 45 n n C9 H9 230 sing 46 n n C11 N2 230 sing 47 n n C11 C12 230 doub 48 n y C12 H12 230 sing 49 n n N2 C23 230 sing 50 n n N2 HN2 230 sing 51 n n C14 C18 230 doub 52 n n C14 H14 230 sing 53 n n C16 H16 230 sing 54 n n C18 H18 230 sing 55 n n C19 O3 230 sing 56 n n C19 H19 230 sing 57 n n N4 C23 230 sing 58 n n C23 O4 230 doub 59 n n # _atom_sites.entry_id 2PHB _atom_sites.fract_transf_matrix[1][1] 0.017704 _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] 0.013811 _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] 0.012868 _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 C 3 CA A 1 9000 9000 CA CA . D 4 230 A 1 9001 9001 230 230 . E 5 HOH A 1 9002 2 HOH HOH . E 5 HOH A 2 9003 3 HOH HOH . E 5 HOH A 3 9004 4 HOH HOH . E 5 HOH A 4 9005 5 HOH HOH . E 5 HOH A 5 9006 6 HOH HOH . E 5 HOH A 6 9007 8 HOH HOH . E 5 HOH A 7 9008 9 HOH HOH . E 5 HOH A 8 9009 10 HOH HOH . E 5 HOH A 9 9010 11 HOH HOH . E 5 HOH A 10 9011 12 HOH HOH . E 5 HOH A 11 9012 13 HOH HOH . E 5 HOH A 12 9013 14 HOH HOH . E 5 HOH A 13 9014 16 HOH HOH . E 5 HOH A 14 9015 18 HOH HOH . E 5 HOH A 15 9016 19 HOH HOH . E 5 HOH A 16 9017 20 HOH HOH . E 5 HOH A 17 9018 21 HOH HOH . E 5 HOH A 18 9019 22 HOH HOH . E 5 HOH A 19 9020 23 HOH HOH . E 5 HOH A 20 9021 24 HOH HOH . E 5 HOH A 21 9022 25 HOH HOH . E 5 HOH A 22 9023 26 HOH HOH . E 5 HOH A 23 9024 27 HOH HOH . E 5 HOH A 24 9025 28 HOH HOH . E 5 HOH A 25 9026 30 HOH HOH . E 5 HOH A 26 9027 31 HOH HOH . E 5 HOH A 27 9028 32 HOH HOH . E 5 HOH A 28 9029 33 HOH HOH . E 5 HOH A 29 9030 34 HOH HOH . E 5 HOH A 30 9031 35 HOH HOH . E 5 HOH A 31 9032 36 HOH HOH . E 5 HOH A 32 9033 37 HOH HOH . E 5 HOH A 33 9034 38 HOH HOH . E 5 HOH A 34 9035 39 HOH HOH . E 5 HOH A 35 9036 42 HOH HOH . E 5 HOH A 36 9037 43 HOH HOH . E 5 HOH A 37 9038 44 HOH HOH . E 5 HOH A 38 9039 46 HOH HOH . E 5 HOH A 39 9040 47 HOH HOH . E 5 HOH A 40 9041 48 HOH HOH . E 5 HOH A 41 9042 49 HOH HOH . E 5 HOH A 42 9043 1 HOH HOH . F 5 HOH B 1 51 7 HOH HOH . F 5 HOH B 2 52 15 HOH HOH . F 5 HOH B 3 53 17 HOH HOH . F 5 HOH B 4 54 29 HOH HOH . F 5 HOH B 5 55 40 HOH HOH . F 5 HOH B 6 56 41 HOH HOH . F 5 HOH B 7 57 45 HOH HOH . F 5 HOH B 8 58 50 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 230 . . . D 4 6.527 6.136 21.575 1 42.84 ? N1 230 9001 A 1 HETATM 2 N N3 230 . . . D 4 8.3 2.076 18.027 1 44.71 ? N3 230 9001 A 1 HETATM 3 C C4 230 . . . D 4 6.973 5.176 20.689 1 43.02 ? C4 230 9001 A 1 HETATM 4 C C5 230 . . . D 4 6.639 3.785 20.935 1 43.02 ? C5 230 9001 A 1 HETATM 5 C C6 230 . . . D 4 7.067 2.736 20.068 1 43.75 ? C6 230 9001 A 1 HETATM 6 C C7 230 . . . D 4 5.644 7.131 21.325 1 44.88 ? C7 230 9001 A 1 HETATM 7 C C8 230 . . . D 4 12.104 7.685 26.263 1 33.48 ? C8 230 9001 A 1 HETATM 8 C C10 230 . . . D 4 10.378 8.555 24.769 1 35.84 ? C10 230 9001 A 1 HETATM 9 C C13 230 . . . D 4 11.118 6.958 27.033 1 34.85 ? C13 230 9001 A 1 HETATM 10 C C15 230 . . . D 4 7.603 1.77 16.819 1 45.6 ? C15 230 9001 A 1 HETATM 11 C C17 230 . . . D 4 9.329 0.026 16.321 1 46.16 ? C17 230 9001 A 1 HETATM 12 C C20 230 . . . D 4 3.886 7.607 22.871 1 44.93 ? C20 230 9001 A 1 HETATM 13 C C21 230 . . . D 4 5.321 8.063 22.535 1 44.83 ? C21 230 9001 A 1 HETATM 14 C C22 230 . . . D 4 5.21 7.241 24.896 1 46.31 ? C22 230 9001 A 1 HETATM 15 C C24 230 . . . D 4 3.066 4.763 24.01 0 47.6 ? C24 230 9001 A 1 HETATM 16 C C1 230 . . . D 4 7.858 3.066 18.903 1 44.14 ? C1 230 9001 A 1 HETATM 17 C C2 230 . . . D 4 8.197 4.451 18.644 1 41.8 ? C2 230 9001 A 1 HETATM 18 C C3 230 . . . D 4 7.765 5.495 19.518 1 42.83 ? C3 230 9001 A 1 HETATM 19 F F1 230 . . . D 4 5.908 3.456 22.007 1 44.27 ? F1 230 9001 A 1 HETATM 20 O O1 230 . . . D 4 5.1 7.331 20.251 1 46.91 ? O1 230 9001 A 1 HETATM 21 C C9 230 . . . D 4 11.742 8.475 25.149 1 33.45 ? C9 230 9001 A 1 HETATM 22 C C11 230 . . . D 4 9.338 7.827 25.516 1 36.93 ? C11 230 9001 A 1 HETATM 23 C C12 230 . . . D 4 9.731 7.039 26.646 1 34.17 ? C12 230 9001 A 1 HETATM 24 CL CL1 230 . . . D 4 13.76 7.597 26.686 1 33.17 ? CL1 230 9001 A 1 HETATM 25 N N2 230 . . . D 4 7.98 7.834 25.205 1 39.68 ? N2 230 9001 A 1 HETATM 26 C C14 230 . . . D 4 9.573 1.324 18.409 1 43.85 ? C14 230 9001 A 1 HETATM 27 C C16 230 . . . D 4 8.168 0.682 15.936 1 45.86 ? C16 230 9001 A 1 HETATM 28 C C18 230 . . . D 4 10.065 0.339 17.586 1 46.18 ? C18 230 9001 A 1 HETATM 29 O O2 230 . . . D 4 6.568 2.32 16.422 1 46.64 ? O2 230 9001 A 1 HETATM 30 C C19 230 . . . D 4 3.825 7.097 24.317 1 45.55 ? C19 230 9001 A 1 HETATM 31 N N4 230 . . . D 4 6.032 7.801 23.825 1 45.18 ? N4 230 9001 A 1 HETATM 32 O O3 230 . . . D 4 3.614 5.711 24.105 1 48.29 ? O3 230 9001 A 1 HETATM 33 C C23 230 . . . D 4 7.39 8.091 23.966 1 43.59 ? C23 230 9001 A 1 HETATM 34 O O4 230 . . . D 4 8.016 8.567 23.001 1 43.52 ? O4 230 9001 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 408 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 34 #