data_1VZK # _model_server_result.job_id W-wyCMciWA_Dr-PRMiW10Q _model_server_result.datetime_utc '2025-03-04 23:05:24' _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 1vzk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1013}' # _entry.id 1VZK # _exptl.entry_id 1VZK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 360.436 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-(5-{4-[AMINO(IMINO)METHYL]PHENYL}-2-THIENYL)-1H-BENZIMIDAZOLE-6- CARBOXIMIDAMIDE DIHYDROCHLORIDE' _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 1VZK _cell.length_a 25.677 _cell.length_b 39.921 _cell.length_c 65.185 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VZK _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 PQS _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 2 _struct_asym.id C _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 metalc ? metalc1 D MG MG . A MG 1014 1_555 E O HOH . A HOH 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc2 D MG MG . A MG 1014 1_555 E O HOH . A HOH 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc3 D MG MG . A MG 1014 1_555 E O HOH . A HOH 2015 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc4 D MG MG . A MG 1014 1_555 E O HOH . A HOH 2016 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc5 D MG MG . A MG 1014 1_555 E O HOH . A HOH 2020 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc6 D MG MG . A MG 1014 1_555 F O HOH . B HOH 2019 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 12 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 11 B DC 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 10 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 9 B DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 DA 5 A DA 5 1_555 B N3 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 DA 5 A DA 5 1_555 B O4 DT 8 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 DA 6 A DA 6 1_555 B N3 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N6 DA 6 A DA 6 1_555 B O4 DT 7 B DT 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N3 DT 7 A DT 7 1_555 B N1 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O4 DT 7 A DT 7 1_555 B N6 DA 6 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N3 DT 8 A DT 8 1_555 B N1 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O4 DT 8 A DT 8 1_555 B N6 DA 5 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N3 DC 9 A DC 9 1_555 B N1 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N4 DC 9 A DC 9 1_555 B O6 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A O2 DC 9 A DC 9 1_555 B N2 DG 4 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N1 DG 10 A DG 10 1_555 B N3 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N2 DG 10 A DG 10 1_555 B O2 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A O6 DG 10 A DG 10 1_555 B N4 DC 3 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N3 DC 11 A DC 11 1_555 B N1 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N4 DC 11 A DC 11 1_555 B O6 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A O2 DC 11 A DC 11 1_555 B N2 DG 2 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N1 DG 12 A DG 12 1_555 B N3 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N2 DG 12 A DG 12 1_555 B O2 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A O6 DG 12 A DG 12 1_555 B N4 DC 1 B DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C19 H16 N6 S' _chem_comp.formula_weight 360.436 _chem_comp.id D1B _chem_comp.mon_nstd_flag . _chem_comp.name '2-(5-{4-[AMINO(IMINO)METHYL]PHENYL}-2-THIENYL)-1H-BENZIMIDAZOLE-6- CARBOXIMIDAMIDE DIHYDROCHLORIDE' _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 S2 D1B sing 1 n y C1 C5 D1B doub 2 n y C1 C15 D1B sing 3 n y S2 C3 D1B sing 4 n y C3 C4 D1B doub 5 n y C3 C6 D1B sing 6 n y C4 C5 D1B sing 7 n y C4 H4 D1B sing 8 n n C5 H5 D1B sing 9 n n C6 N7 D1B doub 10 n y C6 N10 D1B sing 11 n y N7 C8 D1B sing 12 n y C8 C9 D1B doub 13 n y C8 C11 D1B sing 14 n y C9 N10 D1B sing 15 n y C9 C14 D1B sing 16 n y N10 H10 D1B sing 17 n n C11 C12 D1B doub 18 n y C11 H11 D1B sing 19 n n C12 C13 D1B sing 20 n y C12 H12 D1B sing 21 n n C13 C14 D1B doub 22 n y C13 C21 D1B sing 23 n n C14 H14 D1B sing 24 n n C15 C16 D1B sing 25 n y C15 C20 D1B doub 26 n y C16 C17 D1B doub 27 n y C16 H16 D1B sing 28 n n C17 C18 D1B sing 29 n y C17 H17 D1B sing 30 n n C18 C19 D1B doub 31 n y C18 C24 D1B sing 32 n n C19 C20 D1B sing 33 n y C19 H19 D1B sing 34 n n C20 H20 D1B sing 35 n n C21 N22 D1B sing 36 n n C21 N23 D1B doub 37 z n N22 H221 D1B sing 38 n n N22 H222 D1B sing 39 n n N23 H23 D1B sing 40 n n C24 N25 D1B doub 41 n n C24 N26 D1B sing 42 n n N25 H25 D1B sing 43 n n N26 H261 D1B sing 44 n n N26 H262 D1B sing 45 n n # _atom_sites.entry_id 1VZK _atom_sites.fract_transf_matrix[1][1] 0.038945 _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] 0.025049 _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] 0.015341 _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 D1B A 1 1013 1013 D1B D1B . D 3 MG A 1 1014 1014 MG MG . E 4 HOH A 1 2001 2001 HOH HOH . E 4 HOH A 2 2002 2002 HOH HOH . E 4 HOH A 3 2003 2003 HOH HOH . E 4 HOH A 4 2004 2004 HOH HOH . E 4 HOH A 5 2005 2005 HOH HOH . E 4 HOH A 6 2006 2006 HOH HOH . E 4 HOH A 7 2007 2007 HOH HOH . E 4 HOH A 8 2008 2008 HOH HOH . E 4 HOH A 9 2009 2009 HOH HOH . E 4 HOH A 10 2010 2010 HOH HOH . E 4 HOH A 11 2011 2011 HOH HOH . E 4 HOH A 12 2012 2012 HOH HOH . E 4 HOH A 13 2013 2013 HOH HOH . E 4 HOH A 14 2014 2014 HOH HOH . E 4 HOH A 15 2015 2015 HOH HOH . E 4 HOH A 16 2016 2016 HOH HOH . E 4 HOH A 17 2017 2017 HOH HOH . E 4 HOH A 18 2018 2018 HOH HOH . E 4 HOH A 19 2019 2019 HOH HOH . E 4 HOH A 20 2020 2020 HOH HOH . E 4 HOH A 21 2021 2021 HOH HOH . E 4 HOH A 22 2022 2022 HOH HOH . E 4 HOH A 23 2023 2023 HOH HOH . E 4 HOH A 24 2024 2024 HOH HOH . E 4 HOH A 25 2025 2025 HOH HOH . E 4 HOH A 26 2026 2026 HOH HOH . E 4 HOH A 27 2027 2027 HOH HOH . E 4 HOH A 28 2028 2028 HOH HOH . E 4 HOH A 29 2029 2029 HOH HOH . E 4 HOH A 30 2030 2030 HOH HOH . E 4 HOH A 31 2031 2031 HOH HOH . E 4 HOH A 32 2032 2032 HOH HOH . E 4 HOH A 33 2033 2033 HOH HOH . E 4 HOH A 34 2034 2034 HOH HOH . F 4 HOH B 1 2001 2001 HOH HOH . F 4 HOH B 2 2002 2002 HOH HOH . F 4 HOH B 3 2003 2003 HOH HOH . F 4 HOH B 4 2004 2004 HOH HOH . F 4 HOH B 5 2005 2005 HOH HOH . F 4 HOH B 6 2006 2006 HOH HOH . F 4 HOH B 7 2007 2007 HOH HOH . F 4 HOH B 8 2008 2008 HOH HOH . F 4 HOH B 9 2009 2009 HOH HOH . F 4 HOH B 10 2010 2010 HOH HOH . F 4 HOH B 11 2011 2011 HOH HOH . F 4 HOH B 12 2012 2012 HOH HOH . F 4 HOH B 13 2013 2013 HOH HOH . F 4 HOH B 14 2014 2014 HOH HOH . F 4 HOH B 15 2015 2015 HOH HOH . F 4 HOH B 16 2016 2016 HOH HOH . F 4 HOH B 17 2017 2017 HOH HOH . F 4 HOH B 18 2018 2018 HOH HOH . F 4 HOH B 19 2019 2019 HOH HOH . F 4 HOH B 20 2020 2020 HOH HOH . F 4 HOH B 21 2021 2021 HOH HOH . F 4 HOH B 22 2022 2022 HOH HOH . F 4 HOH B 23 2023 2023 HOH HOH . F 4 HOH B 24 2024 2024 HOH HOH . F 4 HOH B 25 2025 2025 HOH HOH . F 4 HOH B 26 2026 2026 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 C1 D1B . . . C 2 10.496 24.748 5.157 1 31.79 ? C1 D1B 1013 A 1 HETATM 2 S S2 D1B . . . C 2 10.864 23.585 6.359 1 35.65 ? S2 D1B 1013 A 1 HETATM 3 C C3 D1B . . . C 2 9.389 23.888 7.152 1 27.19 ? C3 D1B 1013 A 1 HETATM 4 C C4 D1B . . . C 2 8.63 24.836 6.525 1 30.5 ? C4 D1B 1013 A 1 HETATM 5 C C5 D1B . . . C 2 9.257 25.331 5.383 1 29.6 ? C5 D1B 1013 A 1 HETATM 6 C C6 D1B . . . C 2 9.085 23.091 8.411 1 26.48 ? C6 D1B 1013 A 1 HETATM 7 N N7 D1B . . . C 2 7.915 23.088 8.95 1 25.61 ? N7 D1B 1013 A 1 HETATM 8 C C8 D1B . . . C 2 8.036 22.254 10.053 1 24.26 ? C8 D1B 1013 A 1 HETATM 9 C C9 D1B . . . C 2 9.336 21.768 10.129 1 23.04 ? C9 D1B 1013 A 1 HETATM 10 N N10 D1B . . . C 2 10.087 22.283 9.062 1 25.52 ? N10 D1B 1013 A 1 HETATM 11 C C11 D1B . . . C 2 7.068 21.894 11.004 1 24.4 ? C11 D1B 1013 A 1 HETATM 12 C C12 D1B . . . C 2 7.446 21.032 12.031 1 24.32 ? C12 D1B 1013 A 1 HETATM 13 C C13 D1B . . . C 2 8.771 20.509 12.143 1 22.33 ? C13 D1B 1013 A 1 HETATM 14 C C14 D1B . . . C 2 9.725 20.895 11.157 1 13.88 ? C14 D1B 1013 A 1 HETATM 15 C C15 D1B . . . C 2 11.385 25.03 4.074 1 34.5 ? C15 D1B 1013 A 1 HETATM 16 C C16 D1B . . . C 2 11.202 26.187 3.292 1 34.73 ? C16 D1B 1013 A 1 HETATM 17 C C17 D1B . . . C 2 12.056 26.461 2.235 1 38.52 ? C17 D1B 1013 A 1 HETATM 18 C C18 D1B . . . C 2 13.127 25.595 1.9 1 38.66 ? C18 D1B 1013 A 1 HETATM 19 C C19 D1B . . . C 2 13.28 24.434 2.689 1 36.85 ? C19 D1B 1013 A 1 HETATM 20 C C20 D1B . . . C 2 12.427 24.157 3.757 1 32.96 ? C20 D1B 1013 A 1 HETATM 21 C C21 D1B . . . C 2 9.137 19.637 13.184 1 23.33 ? C21 D1B 1013 A 1 HETATM 22 N N22 D1B . . . C 2 10.401 19.498 13.6 1 23.36 ? N22 D1B 1013 A 1 HETATM 23 N N23 D1B . . . C 2 8.266 18.856 13.836 1 30.96 ? N23 D1B 1013 A 1 HETATM 24 C C24 D1B . . . C 2 13.975 25.899 0.815 1 38.5 ? C24 D1B 1013 A 1 HETATM 25 N N25 D1B . . . C 2 14.368 24.954 -0.052 1 38.92 ? N25 D1B 1013 A 1 HETATM 26 N N26 D1B . . . C 2 14.418 27.125 0.535 1 34.46 ? N26 D1B 1013 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 26 #