data_20070 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Design, Synthesis, Biological Evaluation, and Structural Characterization of Potent Histone Deacetylase Inhibitors Based on Cyclic alpha/beta-tetrapeptide architectures ; _BMRB_accession_number 20070 _BMRB_flat_file_name bmr20070.str _Entry_type original _Submission_date 2009-01-13 _Accession_date 2009-01-13 _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 Beierle John M. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 41 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-02-22 update BMRB 'PDBj annotated the coordinate file' 2009-02-26 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 20064 'cyclo[Ala-Aod-BTrp-Leu] alpha/beta-tetrapeptide' 20065 'cyclo[Trp-Leu-BAla-Aod] alpha/beta-tetrapeptide' 20066 'cyclo[Trp-BLeu-Ala-Aod] alpha/beta-tetrapeptide' 20067 'cyclo[NMeTrp-BLeu-Ala-Aod] alpha/beta-tetrapeptide' 20068 'cyclo[Trp-BLeu-Pro-Aod] alpha/beta-tetrapeptide' 20069 'cyclo[Trp-BLeu-BAla-Aod] alpha/beta-tetrapeptide' stop_ save_ ############################# # Citation for this entry # ############################# save_Citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Design, Synthesis, Biological Evaluation, and Structural Characterization of Potent Histone Deacetylase Inhibitors Based on Cyclic alpha/beta-Tetrapeptide Architectures ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19239270 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Montero Ana . . 2 Beierle John M. . 3 Olsen Christian A. . 4 Ghadiri 'M. Reza' . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 131 _Journal_issue 8 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3033 _Page_last 3041 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Cyclic Tetrapeptide 1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'cyclo[BTrp-BLeu-Ala-Aod] Cyclic Tetrapeptide' $cyclo_BTrp-BLeu-Ala-Aod 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_cyclo_BTrp-BLeu-Ala-Aod _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common cyclo[BTrp-BLeu-Ala-Aod] _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 4 _Mol_residue_sequence XXAX loop_ _Residue_seq_code _Residue_label 1 UVR 2 B3L 3 ALA 4 UVR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_UVR _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common 'UNVALIDATED POLYMER RESIDUE FOR SMS' _BMRB_code . _PDB_code UVR _Standard_residue_derivative . _Molecular_mass . _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Feb 15 14:20:13 2011 ; save_ save_chem_comp_B3L _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common '(3S)-3-amino-5-methylhexanoic acid' _BMRB_code . _PDB_code B3L _Standard_residue_derivative . _Molecular_mass 145.200 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Feb 15 14:28:04 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O O O . 0 . ? C C C . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? N N N . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? CE2 CE2 C . 0 . ? CE1 CE1 C . 0 . ? HA HA H . 0 . ? HAA HAA H . 0 . ? HB HB H . 0 . ? HN HN H . 0 . ? HG HG H . 0 . ? HGA HGA H . 0 . ? HD HD H . 0 . ? H3E2 H3E2 H . 0 . ? H2E2 H2E2 H . 0 . ? H1E2 H1E2 H . 0 . ? H3E1 H3E1 H . 0 . ? H2E1 H2E1 H . 0 . ? H1E1 H1E1 H . 0 . ? OXT OXT O . 0 . ? HNA HNA H . 0 . ? HXT HXT 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 C O ? ? SING C OXT ? ? SING CA C ? ? SING CB CA ? ? SING CB HB ? ? SING N CB ? ? SING N HNA ? ? SING CG CB ? ? SING CG HG ? ? SING CD CG ? ? SING CD CE1 ? ? SING CE2 CD ? ? SING CE2 H1E2 ? ? SING CE1 H1E1 ? ? SING CE1 H3E1 ? ? SING HA CA ? ? SING HAA CA ? ? SING HN N ? ? SING HGA CG ? ? SING HD CD ? ? SING H3E2 CE2 ? ? SING H2E2 CE2 ? ? SING H2E1 CE1 ? ? SING OXT HXT ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $cyclo_BTrp-BLeu-Ala-Aod . . . . . . 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 $cyclo_BTrp-BLeu-Ala-Aod 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $cyclo_BTrp-BLeu-Ala-Aod 1-10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_ROESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 . pH temperature 298 . 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 DMSO-d6 H 1 'methyl protons' ppm 2.495 internal direct . . . 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 '2D 1H-1H TOCSY' '2D 1H-1H ROESY' 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 'cyclo[BTrp-BLeu-Ala-Aod] Cyclic Tetrapeptide' _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 UVR H H 7.528 0 1 2 1 1 UVR HA H 3.959 0.003 1 3 1 1 UVR HB2 H 2.872 0.103 2 4 1 1 UVR HB3 H 2.872 0.103 2 5 1 1 UVR HD1 H 7.059 0.003 1 6 1 1 UVR HE1 H 10.869 0 1 7 1 1 UVR HE3 H 7.574 0 1 8 1 1 UVR HZ2 H 7.311 0 1 9 1 1 UVR BT H 2.125 0.003 1 10 2 2 B3L H H 6.867 0.003 1 11 2 2 B3L HA H 4.223 0.012 1 12 2 2 B3L HB2 H 1.171 0.068 2 13 2 2 B3L HB3 H 1.171 0.068 2 14 2 2 B3L HD11 H 0.805 0.002 2 15 2 2 B3L HD12 H 0.805 0.002 2 16 2 2 B3L HD13 H 0.805 0.002 2 17 2 2 B3L HD21 H 0.805 0.002 2 18 2 2 B3L HD22 H 0.805 0.002 2 19 2 2 B3L HD23 H 0.805 0.002 2 20 2 2 B3L HG H 1.413 0.002 1 21 2 2 B3L BT H 2.152 0.009 1 22 3 3 ALA H H 7.908 0.001 1 23 3 3 ALA HA H 3.889 0.003 1 24 3 3 ALA HB H 1.192 0 1 25 4 4 UVR HA H 4.094 0.005 1 26 4 4 UVR HN H 7.475 0.002 1 27 4 4 UVR HB2 H 1.571 0.096 2 28 4 4 UVR HB3 H 1.571 0.096 2 29 4 4 UVR HG2 H 1.189 0.005 2 30 4 4 UVR HG3 H 1.189 0.005 2 31 4 4 UVR HD2 H 1.202 0 2 32 4 4 UVR HD3 H 1.202 0 2 33 4 4 UVR HE2 H 1.412 0 2 34 4 4 UVR HE3 H 1.412 0 2 35 4 4 UVR HF2 H 2.359 0 2 36 4 4 UVR HF3 H 2.359 0 2 37 4 4 UVR HY2 H 2.39 0 2 38 4 4 UVR HY3 H 2.39 0 2 39 4 4 UVR HZ1 H 0.895 0 2 40 4 4 UVR HZ2 H 0.895 0 2 41 4 4 UVR HZ3 H 0.895 0 2 stop_ save_