data_5F4U # _model_server_result.job_id p42t9vqWhfnQHkutspMRGw _model_server_result.datetime_utc '2024-10-18 02:33:33' _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 5f4u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":507}' # _entry.id 5F4U # _exptl.entry_id 5F4U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 488.946 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-[[carbamimidoyl(methyl)amino]methyl]-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide" _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 5F4U _cell.length_a 67.439 _cell.length_b 128.123 _cell.length_c 193.599 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F4U _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 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,G,H,I,J,K,L,M,N,O,P,Q _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 ? 3 I N N ? 3 Q 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 disulf ? disulf1 A SG CYS 6 A CYS 54 1_555 A SG CYS 26 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 A SG CYS 71 A CYS 119 1_555 A SG CYS 84 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 97 A CYS 218 1_555 A SG CYS 126 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 107 A CYS 228 1_555 A SG CYS 118 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 A SG CYS 175 A CYS 296 1_555 A SG CYS 194 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 A SG CYS 240 A CYS 378 1_555 A SG CYS 304 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 247 A CYS 385 1_555 A SG CYS 277 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 B SG CYS 6 B CYS 54 1_555 B SG CYS 26 B CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 B SG CYS 71 B CYS 119 1_555 B SG CYS 84 B CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 B SG CYS 97 B CYS 218 1_555 B SG CYS 126 B CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf11 B SG CYS 107 B CYS 228 1_555 B SG CYS 118 B CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 B SG CYS 175 B CYS 296 1_555 B SG CYS 194 B CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 B SG CYS 240 B CYS 378 1_555 B SG CYS 304 B CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf14 B SG CYS 247 B CYS 385 1_555 B SG CYS 277 B CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _chem_comp.formula 'C22 H26 Cl F N8 O2' _chem_comp.formula_weight 488.946 _chem_comp.id 5VH _chem_comp.mon_nstd_flag . _chem_comp.name "~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-[[carbamimidoyl(methyl)amino]methyl]-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide" _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 CAF CAG 5VH doub 1 n y CAF CAD 5VH sing 2 n y NBD CBC 5VH doub 3 n n CAG CAH 5VH sing 4 n y NBB CBC 5VH sing 5 n n NBB CBA 5VH sing 6 n n CBC NBE 5VH sing 7 n n CLAE CAD 5VH sing 8 n n CAD CAB 5VH doub 9 n y CBA CAZ 5VH sing 10 n n CAH NAI 5VH sing 11 n n CAH CAA 5VH doub 12 n y CAZ CAY 5VH sing 13 n n CAZ CAO 5VH sing 14 n n NAI CAJ 5VH sing 15 n n CAY CAX 5VH sing 16 n n OAM CAL 5VH doub 17 n n CAJ CAL 5VH sing 18 n n CAJ OAK 5VH doub 19 n n CAL NAN 5VH sing 20 n n CAB CAA 5VH sing 21 n y CAB FAC 5VH sing 22 n n NAN CAO 5VH sing 23 n n CAO CAP 5VH sing 24 n n CAX CAW 5VH doub 25 n y CAX CAP 5VH sing 26 n y CAW CAV 5VH sing 27 n y CAP CAQ 5VH doub 28 n y CAQ CAR 5VH sing 29 n y CAV CAR 5VH doub 30 n y CAR CAS 5VH sing 31 n n CAU NAT 5VH sing 32 n n CAS NAT 5VH sing 33 n n NAT CBF 5VH sing 34 n n CBF NBH 5VH doub 35 n n CBF NBG 5VH sing 36 n n CAA H1 5VH sing 37 n n CAF H2 5VH sing 38 n n CAG H3 5VH sing 39 n n NAI H4 5VH sing 40 n n NAN H5 5VH sing 41 n n CAO H6 5VH sing 42 n n CAQ H7 5VH sing 43 n n CAS H8 5VH sing 44 n n CAS H9 5VH sing 45 n n CAU H10 5VH sing 46 n n CAU H11 5VH sing 47 n n CAU H12 5VH sing 48 n n NBH H13 5VH sing 49 n n NBG H14 5VH sing 50 n n NBG H15 5VH sing 51 n n CAV H16 5VH sing 52 n n CAW H17 5VH sing 53 n n CAY H18 5VH sing 54 n n CAY H19 5VH sing 55 n n CAZ H20 5VH sing 56 n n CBA H21 5VH sing 57 n n CBA H22 5VH sing 58 n n NBB H23 5VH sing 59 n n NBE H24 5VH sing 60 n n NBE H25 5VH sing 61 n n NBD H26 5VH sing 62 n n # _atom_sites.entry_id 5F4U _atom_sites.fract_transf_matrix[1][1] 0.014828 _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] 0.007805 _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] 0.005165 _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 2 NAG A 1 501 503 NAG NAG . D 2 NAG A 1 502 504 NAG NAG . E 2 NAG A 1 503 505 NAG NAG . F 2 NAG A 1 504 506 NAG NAG . G 2 NAG A 1 505 507 NAG NAG . H 2 NAG A 1 506 508 NAG NAG . I 3 5VH A 1 507 1 5VH DRG . J 2 NAG B 1 501 502 NAG NAG . K 2 NAG B 1 502 503 NAG NAG . L 2 NAG B 1 503 504 NAG NAG . M 2 NAG B 1 504 505 NAG NAG . N 2 NAG B 1 505 506 NAG NAG . O 2 NAG B 1 506 507 NAG NAG . P 2 NAG B 1 507 508 NAG NAG . Q 3 5VH B 1 508 2 5VH DRG . # 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 5VH . . . I 3 -12.025 -54.177 17.923 1 20 ? CAA 5VH 507 A 1 HETATM 2 C CAB 5VH . . . I 3 -11.663 -52.844 17.764 1 20 ? CAB 5VH 507 A 1 HETATM 3 F FAC 5VH . . . I 3 -11.958 -51.937 18.734 1 20 ? FAC 5VH 507 A 1 HETATM 4 C CAD 5VH . . . I 3 -10.997 -52.438 16.613 1 20 ? CAD 5VH 507 A 1 HETATM 5 CL CLAE 5VH . . . I 3 -10.547 -50.783 16.416 1 20 ? CLAE 5VH 507 A 1 HETATM 6 C CAF 5VH . . . I 3 -10.694 -53.363 15.621 1 20 ? CAF 5VH 507 A 1 HETATM 7 C CAG 5VH . . . I 3 -11.056 -54.695 15.78 1 20 ? CAG 5VH 507 A 1 HETATM 8 C CAH 5VH . . . I 3 -11.721 -55.101 16.931 1 20 ? CAH 5VH 507 A 1 HETATM 9 N NAI 5VH . . . I 3 -12.071 -56.388 17.085 1 20 ? NAI 5VH 507 A 1 HETATM 10 C CAJ 5VH . . . I 3 -13.339 -56.678 17.519 1 20 ? CAJ 5VH 507 A 1 HETATM 11 O OAK 5VH . . . I 3 -14.166 -55.805 17.801 1 20 ? OAK 5VH 507 A 1 HETATM 12 C CAL 5VH . . . I 3 -13.848 -58.149 17.692 1 20 ? CAL 5VH 507 A 1 HETATM 13 O OAM 5VH . . . I 3 -13.044 -59.033 17.401 1 20 ? OAM 5VH 507 A 1 HETATM 14 N NAN 5VH . . . I 3 -15.085 -58.502 18.129 1 20 ? NAN 5VH 507 A 1 HETATM 15 C CAO 5VH . . . I 3 -15.665 -59.84 18.318 1 20 ? CAO 5VH 507 A 1 HETATM 16 C CAP 5VH . . . I 3 -16.746 -59.773 19.201 1 20 ? CAP 5VH 507 A 1 HETATM 17 C CAQ 5VH . . . I 3 -16.739 -59.724 20.533 1 20 ? CAQ 5VH 507 A 1 HETATM 18 C CAR 5VH . . . I 3 -17.926 -59.659 21.246 1 20 ? CAR 5VH 507 A 1 HETATM 19 C CAS 5VH . . . I 3 -17.918 -59.608 22.636 1 20 ? CAS 5VH 507 A 1 HETATM 20 N NAT 5VH . . . I 3 -17.904 -60.974 23.177 1 20 ? NAT 5VH 507 A 1 HETATM 21 C CAU 5VH . . . I 3 -17.981 -62.129 22.268 1 20 ? CAU 5VH 507 A 1 HETATM 22 C CBF 5VH . . . I 3 -17.821 -61.214 24.501 1 20 ? CBF 5VH 507 A 1 HETATM 23 N NBH 5VH . . . I 3 -17.809 -62.466 24.991 1 20 ? NBH 5VH 507 A 1 HETATM 24 N NBG 5VH . . . I 3 -17.749 -60.186 25.361 1 20 ? NBG 5VH 507 A 1 HETATM 25 C CAV 5VH . . . I 3 -19.12 -59.65 20.547 1 20 ? CAV 5VH 507 A 1 HETATM 26 C CAW 5VH . . . I 3 -19.074 -59.704 19.162 1 20 ? CAW 5VH 507 A 1 HETATM 27 C CAX 5VH . . . I 3 -17.909 -59.762 18.519 1 20 ? CAX 5VH 507 A 1 HETATM 28 C CAY 5VH . . . I 3 -17.666 -59.822 17.145 1 20 ? CAY 5VH 507 A 1 HETATM 29 C CAZ 5VH . . . I 3 -16.258 -60.328 17.027 1 20 ? CAZ 5VH 507 A 1 HETATM 30 C CBA 5VH . . . I 3 -16.06 -61.371 16.736 1 20 ? CBA 5VH 507 A 1 HETATM 31 N NBB 5VH . . . I 3 -14.549 -61.523 16.134 1 20 ? NBB 5VH 507 A 1 HETATM 32 C CBC 5VH . . . I 3 -13.403 -62.419 16.14 1 20 ? CBC 5VH 507 A 1 HETATM 33 N NBE 5VH . . . I 3 -13.243 -62.79 17.226 1 20 ? NBE 5VH 507 A 1 HETATM 34 N NBD 5VH . . . I 3 -11.958 -62.625 15.765 1 20 ? NBD 5VH 507 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 230 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 34 #