data_18633 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; solution structure of small molecule-influenza RNA complex, Seattle Structural Genomics Center for Infectious Disease (SSGCID) ; _BMRB_accession_number 18633 _BMRB_flat_file_name bmr18633.str _Entry_type original _Submission_date 2012-08-01 _Accession_date 2012-08-01 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lee M. K. . 2 Varani G. . . 3 Choi B. S. . 4 Pellecchia M. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 186 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-02-19 update BMRB 'update entry citation' 2013-02-14 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'A novel small-molecule binds to the influenza A virus RNA promoter and inhibits viral replication.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24247110 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lee Mi-Kyung . . 2 Bottini Angel . . 3 Kim Meehyein . . 4 Bardaro Michael F. Jr. 5 Zhang Ziming . . 6 Pellecchia Maurizio . . 7 Choi Byong-Seok . . 8 Varani Gabriele . . stop_ _Journal_abbreviation 'Chem. Commun. (Camb.)' _Journal_name_full 'Chemical communications (Cambridge, England)' _Journal_volume 50 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 368 _Page_last 370 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'small molecule-influenza RNA complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'influenza A virus RNA promoter' $influenza_A_virus_RNA_promoter 6,7-dimethoxy-2-(piperazin-1-yl)quinazolin-4-amine $entity_0EC stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_influenza_A_virus_RNA_promoter _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common influenza_A_virus_RNA_promoter _Molecular_mass 10258.172 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 32 _Mol_residue_sequence ; GAGUAGAAACAAGGCUUCGG CCUGCUUUUGCU ; loop_ _Residue_seq_code _Residue_label 1 G 2 A 3 G 4 U 5 A 6 G 7 A 8 A 9 A 10 C 11 A 12 A 13 G 14 G 15 C 16 U 17 U 18 C 19 G 20 G 21 C 22 C 23 U 24 G 25 C 26 U 27 U 28 U 29 U 30 G 31 C 32 U stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_0EC _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 6,7-dimethoxy-2-(piperazin-1-yl)quinazolin-4-amine _BMRB_code 0EC _PDB_code 0EC _Molecular_mass 289.333 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? N2 N2 N . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? N5 N5 N . 0 . ? N6 N6 N . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? O8 O8 O . 0 . ? C9 C9 C . 0 . ? O9 O9 O . 0 . ? C10 C10 C . 0 . ? N11 N11 N . 0 . ? C12 C12 C . 0 . ? C13 C13 C . 0 . ? N14 N14 N . 0 . ? C15 C15 C . 0 . ? C16 C16 C . 0 . ? C8A C8A C . 0 . ? C9A C9A C . 0 . ? H7 H7 H . 0 . ? H10 H10 H . 0 . ? HN14 HN14 H . 0 . ? H12 H12 H . 0 . ? H12A H12A H . 0 . ? H13 H13 H . 0 . ? H13A H13A H . 0 . ? HN5 HN5 H . 0 . ? H15 H15 H . 0 . ? HN5A HN5A H . 0 . ? H15A H15A H . 0 . ? H16 H16 H . 0 . ? H16A H16A H . 0 . ? H8A H8A H . 0 . ? H8AA H8AA H . 0 . ? H8AB H8AB H . 0 . ? H9A H9A H . 0 . ? H9AA H9AA H . 0 . ? H9AB H9AB H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB N6 C1 ? ? SING C1 N11 ? ? SING C1 N2 ? ? DOUB C3 N2 ? ? SING C4 C3 ? ? SING C3 C7 ? ? DOUB C5 C4 ? ? SING C10 C4 ? ? SING N5 C5 ? ? SING C5 N6 ? ? SING HN5A N5 ? ? SING N5 HN5 ? ? DOUB C8 C7 ? ? SING C7 H7 ? ? SING C9 C8 ? ? SING C8 O8 ? ? SING C8A O8 ? ? DOUB C10 C9 ? ? SING O9 C9 ? ? SING C9A O9 ? ? SING H10 C10 ? ? SING C16 N11 ? ? SING N11 C12 ? ? SING C13 C12 ? ? SING C12 H12 ? ? SING C12 H12A ? ? SING N14 C13 ? ? SING H13 C13 ? ? SING C13 H13A ? ? SING C15 N14 ? ? SING N14 HN14 ? ? SING H15A C15 ? ? SING H15 C15 ? ? SING C15 C16 ? ? SING H16 C16 ? ? SING C16 H16A ? ? SING H8A C8A ? ? SING H8AB C8A ? ? SING C8A H8AA ? ? SING H9AB C9A ? ? SING H9AA C9A ? ? SING C9A H9A ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain $influenza_A_virus_RNA_promoter 'influenza A virus' 11320 . Viruses . . 'influenza A virus' stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $influenza_A_virus_RNA_promoter 'enzymatic semisynthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '20mM phosphate buffer' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $influenza_A_virus_RNA_promoter 1 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' 'phosphate buffer' 20 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '20mM phosphate buffer' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $influenza_A_virus_RNA_promoter 1 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' 'phosphate buffer' 20 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address Brunger . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_H2O_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'H2O NOESY' _Sample_label $sample_1 save_ save_D2O_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'D2O NOESY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 50 . mM pH 6.0 . pH pressure 1 . atm temperature 283 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio water H 1 protons ppm 4.7 internal indirect . . . 1.0 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label 'H2O NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'influenza A virus RNA promoter' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 G H1' H 5.293 0.001 1 2 1 1 G H2' H 4.552 0.000 2 3 1 1 G H3' H 4.479 0.001 1 4 1 1 G H8 H 7.687 0.000 1 5 2 2 A H1' H 5.766 0.001 1 6 2 2 A H2' H 4.722 0.000 2 7 2 2 A H3' H 4.569 0.000 1 8 2 2 A H4' H 4.424 0.000 1 9 2 2 A H8 H 8.116 0.000 1 10 3 3 G H1' H 5.518 0.001 1 11 3 3 G H2' H 4.449 0.000 2 12 3 3 G H3' H 4.077 0.001 1 13 3 3 G H4' H 4.072 0.000 1 14 3 3 G H5' H 4.175 0.000 2 15 3 3 G H8 H 7.292 0.001 1 16 4 4 U H1' H 5.291 0.001 1 17 4 4 U H2' H 4.454 0.000 1 18 4 4 U H3' H 4.027 0.000 1 19 4 4 U H5 H 5.181 0.000 1 20 4 4 U H6 H 7.540 0.001 1 21 5 5 A H1' H 5.855 0.001 1 22 5 5 A H2 H 6.632 0.000 1 23 5 5 A H2' H 4.563 0.001 2 24 5 5 A H3' H 4.293 0.000 1 25 5 5 A H4' H 4.026 0.000 1 26 5 5 A H8 H 8.142 0.001 1 27 6 6 G H1' H 5.303 0.000 1 28 6 6 G H2' H 4.483 0.000 2 29 6 6 G H3' H 4.011 0.000 1 30 6 6 G H4' H 4.086 0.000 1 31 6 6 G H5' H 3.890 0.000 2 32 6 6 G H8 H 6.778 0.000 1 33 7 7 A H1' H 5.690 0.000 1 34 7 7 A H2 H 7.098 0.000 1 35 7 7 A H2' H 4.488 0.001 2 36 7 7 A H3' H 4.334 0.000 1 37 7 7 A H8 H 7.448 0.000 1 38 8 8 A H1' H 5.614 0.001 1 39 8 8 A H2 H 6.853 0.000 1 40 8 8 A H2' H 4.371 0.000 2 41 8 8 A H3' H 4.348 0.001 1 42 8 8 A H4' H 4.498 0.000 1 43 8 8 A H5' H 3.920 0.000 2 44 8 8 A H8 H 7.362 0.001 1 45 9 9 A H1' H 5.833 0.001 1 46 9 9 A H2 H 7.939 0.000 1 47 9 9 A H2' H 4.348 0.002 2 48 9 9 A H3' H 4.327 0.000 1 49 9 9 A H8 H 7.616 0.001 1 50 10 10 C H1' H 5.247 0.001 1 51 10 10 C H2' H 3.928 0.001 2 52 10 10 C H3' H 4.277 0.001 1 53 10 10 C H4' H 4.172 0.001 1 54 10 10 C H5 H 5.126 0.001 1 55 10 10 C H5' H 3.883 0.001 2 56 10 10 C H6 H 7.272 0.001 1 57 11 11 A H1' H 5.699 0.002 1 58 11 11 A H2 H 6.911 0.000 1 59 11 11 A H2' H 4.227 0.001 2 60 11 11 A H3' H 4.469 0.000 1 61 11 11 A H4' H 4.281 0.001 1 62 11 11 A H5' H 4.012 0.000 2 63 11 11 A H8 H 7.814 0.000 1 64 12 12 A H1' H 5.723 0.001 1 65 12 12 A H2 H 7.505 0.001 1 66 12 12 A H2' H 4.511 0.001 2 67 12 12 A H3' H 4.349 0.001 1 68 12 12 A H4' H 4.200 0.000 1 69 12 12 A H5' H 4.017 0.000 2 70 12 12 A H8 H 7.905 0.001 1 71 13 13 G H1' H 5.521 0.000 1 72 13 13 G H2' H 4.448 0.000 2 73 13 13 G H3' H 4.260 0.000 1 74 13 13 G H4' H 4.182 0.000 1 75 13 13 G H5' H 4.012 0.000 2 76 13 13 G H8 H 7.217 0.001 1 77 14 14 G H1' H 5.648 0.001 1 78 14 14 G H2' H 4.375 0.000 2 79 14 14 G H3' H 4.310 0.000 1 80 14 14 G H4' H 4.256 0.000 1 81 14 14 G H5' H 3.938 0.000 2 82 14 14 G H8 H 7.203 0.001 1 83 15 15 C H1' H 5.352 0.000 1 84 15 15 C H2' H 4.353 0.002 2 85 15 15 C H3' H 4.056 0.000 1 86 15 15 C H4' H 4.059 0.000 1 87 15 15 C H5 H 5.026 0.000 1 88 15 15 C H5' H 3.859 0.000 2 89 15 15 C H6 H 7.241 0.001 1 90 16 16 U H1' H 5.510 0.001 1 91 16 16 U H2' H 3.631 0.001 1 92 16 16 U H3' H 4.349 0.000 1 93 16 16 U H4' H 4.204 0.001 1 94 16 16 U H5 H 5.542 0.000 1 95 16 16 U H6 H 7.599 0.001 1 96 17 17 U H1' H 5.933 0.001 1 97 17 17 U H2' H 4.516 0.001 1 98 17 17 U H3' H 4.066 0.001 1 99 17 17 U H4' H 4.310 0.000 1 100 17 17 U H5 H 5.688 0.001 1 101 17 17 U H5'' H 3.848 0.002 2 102 17 17 U H6 H 7.859 0.001 1 103 18 18 C H1' H 5.784 0.001 1 104 18 18 C H2' H 3.923 0.001 2 105 18 18 C H3' H 4.300 0.001 1 106 18 18 C H4' H 3.615 0.001 1 107 18 18 C H5 H 5.960 0.001 1 108 18 18 C H5'' H 3.425 0.001 2 109 18 18 C H6 H 7.518 0.001 1 110 19 19 G H1' H 5.781 0.001 1 111 19 19 G H2' H 4.668 0.001 2 112 19 19 G H3' H 5.446 0.001 1 113 19 19 G H4' H 3.998 0.001 1 114 19 19 G H5' H 4.218 0.001 2 115 19 19 G H5'' H 4.006 0.000 2 116 19 19 G H8 H 7.679 0.000 1 117 20 20 G H2' H 4.257 0.000 2 118 20 20 G H3' H 4.070 0.000 1 119 20 20 G H4' H 4.276 0.000 1 120 20 20 G H5'' H 4.216 0.000 2 121 20 20 G H8 H 8.103 0.000 1 122 21 21 C H1' H 5.352 0.000 1 123 21 21 C H2' H 4.294 0.001 2 124 21 21 C H3' H 4.249 0.000 1 125 21 21 C H5 H 5.083 0.001 1 126 21 21 C H6 H 7.499 0.001 1 127 22 22 C H1' H 5.389 0.000 1 128 22 22 C H2' H 4.249 0.000 2 129 22 22 C H3' H 4.435 0.001 1 130 22 22 C H5 H 5.382 0.000 1 131 22 22 C H6 H 7.556 0.000 1 132 23 23 U H1' H 5.496 0.001 1 133 23 23 U H2' H 4.306 0.001 1 134 23 23 U H3' H 4.250 0.000 1 135 23 23 U H4' H 4.425 0.000 1 136 23 23 U H5 H 5.342 0.000 1 137 23 23 U H5' H 3.938 0.000 2 138 23 23 U H6 H 7.633 0.000 1 139 24 24 G H1' H 5.388 0.001 1 140 24 24 G H2' H 4.445 0.001 2 141 24 24 G H3' H 4.294 0.001 1 142 24 24 G H5'' H 3.964 0.000 2 143 24 24 G H8 H 7.604 0.000 1 144 25 25 C H1' H 5.225 0.001 1 145 25 25 C H2' H 3.988 0.000 2 146 25 25 C H3' H 4.305 0.001 1 147 25 25 C H4' H 4.168 0.000 1 148 25 25 C H5 H 5.320 0.001 1 149 25 25 C H5'' H 4.046 0.000 2 150 25 25 C H6 H 7.664 0.001 1 151 26 26 U H1' H 5.484 0.000 1 152 26 26 U H2' H 4.307 0.000 1 153 26 26 U H3' H 4.257 0.000 1 154 26 26 U H5 H 5.303 0.000 1 155 26 26 U H6 H 7.611 0.000 1 156 27 27 U H1' H 5.332 0.001 1 157 27 27 U H2' H 4.449 0.000 1 158 27 27 U H3' H 4.083 0.000 1 159 27 27 U H5 H 5.307 0.000 1 160 27 27 U H6 H 7.672 0.001 1 161 28 28 U H1' H 5.258 0.001 1 162 28 28 U H2' H 3.926 0.001 1 163 28 28 U H3' H 4.400 0.000 1 164 28 28 U H4' H 4.259 0.000 1 165 28 28 U H5 H 5.543 0.001 1 166 28 28 U H6 H 7.778 0.002 1 167 29 29 U H1' H 5.390 0.000 1 168 29 29 U H2' H 4.385 0.001 1 169 29 29 U H3' H 4.445 0.000 1 170 29 29 U H5 H 5.418 0.001 1 171 29 29 U H6 H 7.823 0.002 1 172 30 30 G H1' H 5.597 0.001 1 173 30 30 G H2' H 4.471 0.001 2 174 30 30 G H3' H 4.137 0.000 1 175 30 30 G H4' H 4.327 0.000 1 176 30 30 G H8 H 7.570 0.000 1 177 31 31 C H1' H 5.273 0.001 1 178 31 31 C H2' H 3.977 0.000 2 179 31 31 C H3' H 4.183 0.000 1 180 31 31 C H5 H 5.134 0.005 1 181 31 31 C H6 H 7.468 0.001 1 182 32 32 U H1' H 5.673 0.000 1 183 32 32 U H2' H 3.957 0.000 1 184 32 32 U H3' H 4.056 0.001 1 185 32 32 U H5 H 5.301 0.000 1 186 32 32 U H6 H 7.574 0.002 1 stop_ save_