data_1CYZ # _model_server_result.job_id Ws65UxYEQx_zXbvMVPaFVQ _model_server_result.datetime_utc '2024-10-19 13:20:45' _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 1cyz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":12}' # _entry.id 1CYZ # _exptl.entry_id 1CYZ _exptl.method 'SOLUTION NMR' # _entity.details ? _entity.formula_weight 486.508 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM' _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 1CYZ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1CYZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 ? 2 C N N ? 2 D 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 hydrog WATSON-CRICK hydrog1 A N1 DG 1 A DG 1 1_555 B N3 DC 10 B DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 1 A DG 1 1_555 B O2 DC 10 B DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 1 A DG 1 1_555 B N4 DC 10 B DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DA 2 A DA 2 1_555 B N3 DT 9 B DT 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 DA 2 A DA 2 1_555 B O4 DT 9 B DT 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DA 3 A DA 3 1_555 B N3 DT 8 B DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N6 DA 3 A DA 3 1_555 B O4 DT 8 B DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N3 DC 4 A DC 4 1_555 B N1 DG 7 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N4 DC 4 A DC 4 1_555 B O6 DG 7 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O2 DC 4 A DC 4 1_555 B N2 DG 7 B DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog11 A N3 DT 5 A DT 5 1_555 B O6 DG 6 B DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog12 A O2 DT 5 A DT 5 1_555 B N1 DG 6 B DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog13 A N1 DG 6 A DG 6 1_555 B O2 DT 5 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog14 A O6 DG 6 A DG 6 1_555 B N3 DT 5 B DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 DG 7 A DG 7 1_555 B N3 DC 4 B DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N2 DG 7 A DG 7 1_555 B O2 DC 4 B DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O6 DG 7 A DG 7 1_555 B N4 DC 4 B DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N3 DT 8 A DT 8 1_555 B N1 DA 3 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O4 DT 8 A DT 8 1_555 B N6 DA 3 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N3 DT 9 A DT 9 1_555 B N1 DA 2 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O4 DT 9 A DT 9 1_555 B N6 DA 2 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N3 DC 10 A DC 10 1_555 B N1 DG 1 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N4 DC 10 A DC 10 1_555 B O6 DG 1 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O2 DC 10 A DC 10 1_555 B N2 DG 1 B DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C20 H28 N11 O4 1' _chem_comp.formula_weight 486.508 _chem_comp.id AR1 _chem_comp.mon_nstd_flag . _chem_comp.name '(2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'TRI-IMIDAZOLE DNA MINOR GROOVE BINDER;AR-1-144' # 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 CA OA AR1 doub 1 n n CA N1 AR1 sing 2 n n CA HA AR1 sing 3 n n N1 C11 AR1 sing 4 n n N1 HN1 AR1 sing 5 n n C11 N21 AR1 sing 6 n y C11 C51 AR1 doub 7 n y N21 C31 AR1 doub 8 n y C31 N41 AR1 sing 9 n y C31 C1 AR1 sing 10 n n N41 CN1 AR1 sing 11 n n N41 C51 AR1 sing 12 n y CN1 HN11 AR1 sing 13 n n CN1 HN12 AR1 sing 14 n n CN1 HN13 AR1 sing 15 n n C51 H51 AR1 sing 16 n n C1 O1 AR1 doub 17 n n C1 N2 AR1 sing 18 n n N2 C12 AR1 sing 19 n n N2 HN2 AR1 sing 20 n n C12 N22 AR1 sing 21 n y C12 C52 AR1 doub 22 n y N22 C32 AR1 doub 23 n y C32 N42 AR1 sing 24 n y C32 C2 AR1 sing 25 n n N42 CN2 AR1 sing 26 n n N42 C52 AR1 sing 27 n y CN2 HN21 AR1 sing 28 n n CN2 HN22 AR1 sing 29 n n CN2 HN23 AR1 sing 30 n n C52 H52 AR1 sing 31 n n C2 O2 AR1 doub 32 n n C2 N3 AR1 sing 33 n n N3 C13 AR1 sing 34 n n N3 HN3 AR1 sing 35 n n C13 N23 AR1 sing 36 n y C13 C53 AR1 doub 37 n y N23 C33 AR1 doub 38 n y C33 N43 AR1 sing 39 n y C33 C3 AR1 sing 40 n n N43 CN3 AR1 sing 41 n n N43 C53 AR1 sing 42 n y CN3 HN31 AR1 sing 43 n n CN3 HN32 AR1 sing 44 n n CN3 HN33 AR1 sing 45 n n C53 H53 AR1 sing 46 n n C3 O3 AR1 doub 47 n n C3 NT AR1 sing 48 n n NT C1T AR1 sing 49 n n NT HT AR1 sing 50 n n C1T C2T AR1 sing 51 n n C1T H1T1 AR1 sing 52 n n C1T H1T2 AR1 sing 53 n n C2T N3T AR1 sing 54 n n C2T H2T1 AR1 sing 55 n n C2T H2T2 AR1 sing 56 n n N3T CNT AR1 sing 57 n n N3T CMT AR1 sing 58 n n N3T HNT AR1 sing 59 n n CNT HNT1 AR1 sing 60 n n CNT HNT2 AR1 sing 61 n n CNT HNT3 AR1 sing 62 n n CMT HMT1 AR1 sing 63 n n CMT HMT2 AR1 sing 64 n n CMT HMT3 AR1 sing 65 n n # _atom_sites.entry_id 1CYZ _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 AR1 A 1 12 12 AR1 AR1 . D 2 AR1 B 1 26 26 AR1 AR1 . # 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 CA AR1 . . . C 2 9.7 3.529 9.439 1 0.24 ? CA AR1 12 A 1 HETATM 2 O OA AR1 . . . C 2 10.202 3.923 8.388 1 0.28 ? OA AR1 12 A 1 HETATM 3 N N1 AR1 . . . C 2 10.277 2.692 10.306 1 0.21 ? N1 AR1 12 A 1 HETATM 4 C C11 AR1 . . . C 2 11.598 2.149 10.179 1 0.22 ? C11 AR1 12 A 1 HETATM 5 N N21 AR1 . . . C 2 12.198 1.413 11.128 1 0.22 ? N21 AR1 12 A 1 HETATM 6 C C31 AR1 . . . C 2 13.471 1.164 10.763 1 0.25 ? C31 AR1 12 A 1 HETATM 7 N N41 AR1 . . . C 2 13.669 1.761 9.549 1 0.26 ? N41 AR1 12 A 1 HETATM 8 C CN1 AR1 . . . C 2 14.923 1.786 8.777 1 0.3 ? CN1 AR1 12 A 1 HETATM 9 C C51 AR1 . . . C 2 12.489 2.354 9.188 1 0.25 ? C51 AR1 12 A 1 HETATM 10 C C1 AR1 . . . C 2 14.46 0.428 11.575 1 0.25 ? C1 AR1 12 A 1 HETATM 11 O O1 AR1 . . . C 2 15.634 0.365 11.223 1 0.27 ? O1 AR1 12 A 1 HETATM 12 N N2 AR1 . . . C 2 13.942 -0.284 12.595 1 0.24 ? N2 AR1 12 A 1 HETATM 13 C C12 AR1 . . . C 2 14.649 -1.198 13.439 1 0.22 ? C12 AR1 12 A 1 HETATM 14 N N22 AR1 . . . C 2 14.061 -2.003 14.349 1 0.23 ? N22 AR1 12 A 1 HETATM 15 C C32 AR1 . . . C 2 14.996 -2.661 15.046 1 0.22 ? C32 AR1 12 A 1 HETATM 16 N N42 AR1 . . . C 2 16.208 -2.26 14.541 1 0.21 ? N42 AR1 12 A 1 HETATM 17 C CN2 AR1 . . . C 2 17.527 -2.737 14.962 1 0.22 ? CN2 AR1 12 A 1 HETATM 18 C C52 AR1 . . . C 2 15.976 -1.355 13.545 1 0.22 ? C52 AR1 12 A 1 HETATM 19 C C2 AR1 . . . C 2 14.739 -3.46 16.258 1 0.22 ? C2 AR1 12 A 1 HETATM 20 O O2 AR1 . . . C 2 15.681 -3.76 16.983 1 0.21 ? O2 AR1 12 A 1 HETATM 21 N N3 AR1 . . . C 2 13.49 -3.935 16.444 1 0.22 ? N3 AR1 12 A 1 HETATM 22 C C13 AR1 . . . C 2 13.1 -4.807 17.523 1 0.21 ? C13 AR1 12 A 1 HETATM 23 N N23 AR1 . . . C 2 11.905 -5.435 17.637 1 0.2 ? N23 AR1 12 A 1 HETATM 24 C C33 AR1 . . . C 2 11.843 -6.074 18.812 1 0.21 ? C33 AR1 12 A 1 HETATM 25 N N43 AR1 . . . C 2 13.016 -5.831 19.469 1 0.22 ? N43 AR1 12 A 1 HETATM 26 C CN3 AR1 . . . C 2 13.374 -6.266 20.828 1 0.23 ? CN3 AR1 12 A 1 HETATM 27 C C53 AR1 . . . C 2 13.786 -5.063 18.654 1 0.22 ? C53 AR1 12 A 1 HETATM 28 C C3 AR1 . . . C 2 10.778 -6.968 19.271 1 0.22 ? C3 AR1 12 A 1 HETATM 29 O O3 AR1 . . . C 2 10.919 -7.534 20.351 1 0.26 ? O3 AR1 12 A 1 HETATM 30 N NT AR1 . . . C 2 9.76 -7.236 18.433 1 0.22 ? NT AR1 12 A 1 HETATM 31 C C1T AR1 . . . C 2 8.752 -8.236 18.772 1 0.27 ? C1T AR1 12 A 1 HETATM 32 C C2T AR1 . . . C 2 7.675 -7.648 19.742 1 0.29 ? C2T AR1 12 A 1 HETATM 33 N N3T AR1 . . . C 2 8.026 -8.006 21.15 1 0.28 ? N3T AR1 12 A 1 HETATM 34 C CNT AR1 . . . C 2 7.636 -7.023 22.175 1 0.31 ? CNT AR1 12 A 1 HETATM 35 C CMT AR1 . . . C 2 7.653 -9.376 21.552 1 0.38 ? CMT AR1 12 A 1 HETATM 36 H HA AR1 . . . C 2 8.732 3.908 9.756 1 0.27 ? HA AR1 12 A 1 HETATM 37 H HN1 AR1 . . . C 2 9.757 2.488 11.14 1 0.21 ? HN1 AR1 12 A 1 HETATM 38 H HN11 AR1 . . . C 2 15.662 2.388 9.308 1 0.97 ? HN11 AR1 12 A 1 HETATM 39 H HN12 AR1 . . . C 2 14.746 2.222 7.793 1 1.02 ? HN12 AR1 12 A 1 HETATM 40 H HN13 AR1 . . . C 2 15.303 0.771 8.659 1 1.04 ? HN13 AR1 12 A 1 HETATM 41 H H51 AR1 . . . C 2 12.277 2.802 8.229 1 0.27 ? H51 AR1 12 A 1 HETATM 42 H HN2 AR1 . . . C 2 12.953 -0.255 12.728 1 0.25 ? HN2 AR1 12 A 1 HETATM 43 H HN21 AR1 . . . C 2 17.54 -3.826 14.92 1 1 ? HN21 AR1 12 A 1 HETATM 44 H HN22 AR1 . . . C 2 17.722 -2.403 15.98 1 1.12 ? HN22 AR1 12 A 1 HETATM 45 H HN23 AR1 . . . C 2 18.289 -2.339 14.291 1 0.97 ? HN23 AR1 12 A 1 HETATM 46 H H52 AR1 . . . C 2 16.724 -0.884 12.925 1 0.24 ? H52 AR1 12 A 1 HETATM 47 H HN3 AR1 . . . C 2 12.79 -3.756 15.748 1 0.22 ? HN3 AR1 12 A 1 HETATM 48 H HN31 AR1 . . . C 2 12.624 -5.893 21.53 1 1.09 ? HN31 AR1 12 A 1 HETATM 49 H HN32 AR1 . . . C 2 14.35 -5.866 21.098 1 1.05 ? HN32 AR1 12 A 1 HETATM 50 H HN33 AR1 . . . C 2 13.399 -7.354 20.87 1 1.01 ? HN33 AR1 12 A 1 HETATM 51 H H53 AR1 . . . C 2 14.793 -4.758 18.872 1 0.23 ? H53 AR1 12 A 1 HETATM 52 H HT AR1 . . . C 2 9.723 -6.82 17.513 1 0.22 ? HT AR1 12 A 1 HETATM 53 H H1T1 AR1 . . . C 2 9.283 -9.027 19.322 1 0.27 ? H1T1 AR1 12 A 1 HETATM 54 H H1T2 AR1 . . . C 2 8.363 -8.627 17.802 1 0.37 ? H1T2 AR1 12 A 1 HETATM 55 H H2T1 AR1 . . . C 2 6.659 -8.034 19.466 1 0.4 ? H2T1 AR1 12 A 1 HETATM 56 H H2T2 AR1 . . . C 2 7.73 -6.542 19.604 1 0.34 ? H2T2 AR1 12 A 1 HETATM 57 H HNT AR1 . . . C 2 9.025 -7.988 21.183 1 0.28 ? HNT AR1 12 A 1 HETATM 58 H HNT1 AR1 . . . C 2 7.961 -6.018 21.897 1 1.18 ? HNT1 AR1 12 A 1 HETATM 59 H HNT2 AR1 . . . C 2 8.126 -7.277 23.123 1 1.05 ? HNT2 AR1 12 A 1 HETATM 60 H HNT3 AR1 . . . C 2 6.559 -7.019 22.34 1 0.97 ? HNT3 AR1 12 A 1 HETATM 61 H HMT1 AR1 . . . C 2 6.613 -9.595 21.309 1 1.06 ? HMT1 AR1 12 A 1 HETATM 62 H HMT2 AR1 . . . C 2 7.792 -9.509 22.631 1 1.1 ? HMT2 AR1 12 A 1 HETATM 63 H HMT3 AR1 . . . C 2 8.292 -10.107 21.048 1 1.14 ? HMT3 AR1 12 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 63 #