data_5F4P # _model_server_result.job_id BbVuPYplaQxV1E4b20kzYA _model_server_result.datetime_utc '2024-10-18 02:26:55' _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 5f4p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 5F4P # _exptl.entry_id 5F4P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 446.906 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-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 5F4P _cell.length_a 67.378 _cell.length_b 127.517 _cell.length_c 192.945 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F4P _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,R _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 J 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 D CYS 54 1_555 A SG CYS 26 D CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 71 D CYS 119 1_555 A SG CYS 84 D CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 97 D CYS 218 1_555 A SG CYS 126 D CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 107 D CYS 228 1_555 A SG CYS 118 D CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 A SG CYS 175 D CYS 296 1_555 A SG CYS 194 D CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 A SG CYS 240 D CYS 378 1_555 A SG CYS 304 D CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf7 A SG CYS 247 D CYS 385 1_555 A SG CYS 277 D CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 B SG CYS 6 A CYS 54 1_555 B SG CYS 26 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 B SG CYS 71 A CYS 119 1_555 B SG CYS 84 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 B SG CYS 97 A CYS 218 1_555 B SG CYS 126 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf11 B SG CYS 107 A CYS 228 1_555 B SG CYS 118 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf12 B SG CYS 175 A CYS 296 1_555 B SG CYS 194 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf13 B SG CYS 240 A CYS 378 1_555 B SG CYS 304 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf14 B SG CYS 247 A CYS 385 1_555 B SG CYS 277 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? # _chem_comp.formula 'C21 H24 Cl F N6 O2' _chem_comp.formula_weight 446.906 _chem_comp.id 5VG _chem_comp.mon_nstd_flag . _chem_comp.name "~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-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 N28 C02 5VG doub 1 n n C26 C27 5VG doub 2 n y C26 C24 5VG sing 3 n y C27 C20 5VG sing 4 n y N03 C02 5VG sing 5 n n N03 C04 5VG sing 6 n n CL25 C24 5VG sing 7 n n C02 N01 5VG sing 8 n n C24 C22 5VG doub 9 n y C20 N19 5VG sing 10 n n C20 C21 5VG doub 11 n y C04 C05 5VG sing 12 n n N19 C17 5VG sing 13 n n C05 C06 5VG sing 14 n n C05 C13 5VG sing 15 n n O16 C15 5VG doub 16 n n C22 C21 5VG sing 17 n y C22 F23 5VG sing 18 n n C17 C15 5VG sing 19 n n C17 O18 5VG doub 20 n n C06 C07 5VG sing 21 n n C15 N14 5VG sing 22 n n N14 C13 5VG sing 23 n n C13 C12 5VG sing 24 n n C07 C12 5VG doub 25 n y C07 C08 5VG sing 26 n y C12 C11 5VG sing 27 n y C08 C09 5VG doub 28 n y C11 C10 5VG doub 29 n y C09 C10 5VG sing 30 n y C09 C00 5VG sing 31 n n C00 N 5VG sing 32 n n N C 5VG sing 33 n n C10 H1 5VG sing 34 n n C13 H2 5VG sing 35 n n C21 H3 5VG sing 36 n n C26 H4 5VG sing 37 n n N H5 5VG sing 38 n n C H7 5VG sing 39 n n C H8 5VG sing 40 n n C H9 5VG sing 41 n n C00 H10 5VG sing 42 n n C00 H11 5VG sing 43 n n N01 H12 5VG sing 44 n n N01 H13 5VG sing 45 n n N03 H14 5VG sing 46 n n C04 H15 5VG sing 47 n n C04 H16 5VG sing 48 n n C05 H17 5VG sing 49 n n C06 H18 5VG sing 50 n n C06 H19 5VG sing 51 n n C08 H20 5VG sing 52 n n C11 H21 5VG sing 53 n n N14 H22 5VG sing 54 n n N19 H23 5VG sing 55 n n C27 H24 5VG sing 56 n n N28 H25 5VG sing 57 n n # _atom_sites.entry_id 5F4P _atom_sites.fract_transf_matrix[1][1] 0.014842 _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] 0.007842 _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] 0.005183 _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 D 1 501 503 NAG NAG . D 2 NAG D 1 502 504 NAG NAG . E 2 NAG D 1 503 505 NAG NAG . F 2 NAG D 1 504 506 NAG NAG . G 2 NAG D 1 505 507 NAG NAG . H 2 NAG D 1 506 508 NAG NAG . I 3 5VG D 1 507 501 5VG LIG . J 3 5VG A 1 501 501 5VG LIG . K 2 NAG A 1 502 503 NAG NAG . L 2 NAG A 1 503 504 NAG NAG . M 2 NAG A 1 504 505 NAG NAG . N 2 NAG A 1 505 506 NAG NAG . O 2 NAG A 1 506 507 NAG NAG . P 2 NAG A 1 507 508 NAG NAG . Q 4 HOH D 1 601 6 HOH HOH . Q 4 HOH D 2 602 8 HOH HOH . Q 4 HOH D 3 603 9 HOH HOH . Q 4 HOH D 4 604 12 HOH HOH . Q 4 HOH D 5 605 10 HOH HOH . Q 4 HOH D 6 606 2 HOH HOH . R 4 HOH A 1 601 11 HOH HOH . R 4 HOH A 2 602 13 HOH HOH . R 4 HOH A 3 603 1 HOH HOH . R 4 HOH A 4 604 7 HOH HOH . R 4 HOH A 5 605 5 HOH HOH . R 4 HOH A 6 606 4 HOH HOH . R 4 HOH A 7 607 3 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 C10 5VG . . . J 3 -20.468 1.554 24.51 1 80.03 ? C10 5VG 501 A 1 HETATM 2 C C13 5VG . . . J 3 -20.904 -0.165 20.996 1 72.34 ? C13 5VG 501 A 1 HETATM 3 C C15 5VG . . . J 3 -22.127 -2.27 20.492 1 73 ? C15 5VG 501 A 1 HETATM 4 C C17 5VG . . . J 3 -22.333 -3.757 20.709 1 80.42 ? C17 5VG 501 A 1 HETATM 5 C C20 5VG . . . J 3 -23.69 -5.825 20.063 1 75.64 ? C20 5VG 501 A 1 HETATM 6 C C21 5VG . . . J 3 -23.632 -6.509 21.286 1 69.32 ? C21 5VG 501 A 1 HETATM 7 C C22 5VG . . . J 3 -23.929 -7.883 21.329 1 64.81 ? C22 5VG 501 A 1 HETATM 8 C C24 5VG . . . J 3 -24.29 -8.57 20.145 1 71.81 ? C24 5VG 501 A 1 HETATM 9 C C26 5VG . . . J 3 -24.35 -7.893 18.935 1 66.93 ? C26 5VG 501 A 1 HETATM 10 N N 5VG . . . J 3 -18.705 1.77 26.858 1 96.01 ? N 5VG 501 A 1 HETATM 11 C C 5VG . . . J 3 -18.397 2.622 27.935 1 87.83 ? C 5VG 501 A 1 HETATM 12 C C00 5VG . . . J 3 -18.339 2.409 25.632 1 86.41 ? C00 5VG 501 A 1 HETATM 13 CL CL25 5VG . . . J 3 -24.654 -10.24 20.185 1 92.83 ? CL25 5VG 501 A 1 HETATM 14 N N01 5VG . . . J 3 -22.494 2.389 18.559 1 72.02 ? N01 5VG 501 A 1 HETATM 15 C C02 5VG . . . J 3 -21.984 1.542 17.715 1 74.88 ? C02 5VG 501 A 1 HETATM 16 N N03 5VG . . . J 3 -20.684 0.919 17.991 1 70.39 ? N03 5VG 501 A 1 HETATM 17 C C04 5VG . . . J 3 -19.981 1.252 19.211 1 71.43 ? C04 5VG 501 A 1 HETATM 18 C C05 5VG . . . J 3 -19.771 0.019 20.048 1 69.68 ? C05 5VG 501 A 1 HETATM 19 C C06 5VG . . . J 3 -18.547 0.154 20.887 1 65.21 ? C06 5VG 501 A 1 HETATM 20 C C07 5VG . . . J 3 -19.03 0.698 22.215 1 76.4 ? C07 5VG 501 A 1 HETATM 21 C C08 5VG . . . J 3 -18.34 1.31 23.284 1 82.71 ? C08 5VG 501 A 1 HETATM 22 C C09 5VG . . . J 3 -19.079 1.74 24.447 1 82.15 ? C09 5VG 501 A 1 HETATM 23 C C11 5VG . . . J 3 -21.175 0.93 23.411 1 78.32 ? C11 5VG 501 A 1 HETATM 24 C C12 5VG . . . J 3 -20.447 0.507 22.283 1 73.12 ? C12 5VG 501 A 1 HETATM 25 N N14 5VG . . . J 3 -21.095 -1.564 21.208 1 72.34 ? N14 5VG 501 A 1 HETATM 26 O O16 5VG . . . J 3 -22.859 -1.661 19.689 1 65.58 ? O16 5VG 501 A 1 HETATM 27 O O18 5VG . . . J 3 -21.608 -4.375 21.504 1 71.81 ? O18 5VG 501 A 1 HETATM 28 N N19 5VG . . . J 3 -23.394 -4.417 19.963 1 81.56 ? N19 5VG 501 A 1 HETATM 29 C C27 5VG . . . J 3 -24.047 -6.502 18.896 1 67.7 ? C27 5VG 501 A 1 HETATM 30 N N28 5VG . . . J 3 -22.612 1.256 16.648 1 67.18 ? N28 5VG 501 A 1 HETATM 31 F F23 5VG . . . J 3 -23.87 -8.558 22.531 1 75.16 ? F23 5VG 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #