data_20040 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Cyclic Pseudotetrapeptide D-Phe-D-Trp-D-Lys-L-Thr ; _BMRB_accession_number 20040 _BMRB_flat_file_name bmr20040.str _Entry_type new _Submission_date 2008-08-21 _Accession_date 2008-08-21 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'This is an unnatural cyclic tetrapeptide derivative with a 1,4-disubstituted 1,2,3-triazole as a trans amide bond surrogate.' 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" 28 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-03-15 update BMRB 'PDBj annotated the coordinate file' 2009-06-10 update BMRB 'complete entry citation' 2009-03-06 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 20036 'Cyclic Pseudotetrapeptide (7a)' 20037 'Cyclic Pseudotetrapeptide (7b)' 20038 'Cyclic Pseudotetrapeptide (7c)' 20039 'Cyclic Pseudotetrapeptide (7d)' 20041 'Cyclic Pseudotetrapeptide (7f)' 20042 'Cyclic Pseudotetrapeptide (7g)' 20043 'Cyclic Pseudotetrapeptide (7h)' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Conformationally Homogeneous Heterocyclic Pseudotetrapeptides as Three-Dimensional Scaffolds for Rational Drug Design: Receptor-Selective Somatostatin Analogues ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19266506 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Beierle John M. . 2 Horne 'W. Seth' . . 3 'van Maarseveen' Jan H. . 4 Waser Beatrice . . 5 Reubi 'Jean Claude' . . 6 Ghadiri 'M. Reza' . . stop_ _Journal_abbreviation 'Angew. Chem., Int. Ed.' _Journal_volume 48 _Journal_issue 26 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4725 _Page_last 4729 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Cyclic Pseudotetrapeptide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Cyclic pseudotetrapeptide' $14dFdWdKT stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details ; The D-PHE and THR residues are linked via a 1,2,3-triazole, where the D-PHE amine is N1 and the THR carbonyl is C4 and C5. The triazole is an amide bond surrogate. It is a 1,4-disubstituted triazole where N1 is the D-Phe amine and C4 is the Thr carbonyl carbon. ; save_ ######################## # Monomeric polymers # ######################## save_14dFdWdKT _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 14dFdWdKT _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function 'Somatostatin Mimic' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 4 _Mol_residue_sequence XXXT loop_ _Residue_seq_code _Residue_label 1 DPN 2 DTR 3 DLY 4 THR stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DPN _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common D-PHENYLALANINE _BMRB_code . _PDB_code DPN _Standard_residue_derivative DPN _Molecular_mass 165.189 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Feb 15 18:42:00 2008 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N N 0 . ? CA CA C R 0 . ? C C C N 0 . ? O O O N 0 . ? OXT OXT O N 0 . ? CB CB C N 0 . ? CG CG C N 0 . ? CD1 CD1 C N 0 . ? CD2 CD2 C N 0 . ? CE1 CE1 C N 0 . ? CE2 CE2 C N 0 . ? CZ CZ C N 0 . ? H H H N 0 . ? H2 H2 H N 0 . ? HA HA H N 0 . ? HXT HXT H N 0 . ? HB2 HB2 H N 0 . ? HB3 HB3 H N 0 . ? HD1 HD1 H N 0 . ? HD2 HD2 H N 0 . ? HE1 HE1 H N 0 . ? HE2 HE2 H N 0 . ? HZ HZ H N 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 SING N CA ? ? SING N H ? ? SING N H2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 CE1 ? ? SING CD1 HD1 ? ? DOUB CD2 CE2 ? ? SING CD2 HD2 ? ? DOUB CE1 CZ ? ? SING CE1 HE1 ? ? SING CE2 CZ ? ? SING CE2 HE2 ? ? SING CZ HZ ? ? stop_ save_ save_DTR _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common D-TRYPTOPHAN _Abbreviation_common DTR _BMRB_code DTR _PDB_code DTR _Standard_residue_derivative TRP loop_ _Mol_label _Residue_seq_code $14dFdWdKT 2 stop_ _Molecular_mass . _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N . N . 0 . ? CA . C . 0 . ? CB . C . 0 . ? CG . C . 0 . ? CD1 . C . 0 . ? NE1 . N . 0 . ? CE2 . C . 0 . ? CZ2 . C . 0 . ? CH2 . C . 0 . ? CZ3 . C . 0 . ? CE3 . C . 0 . ? CD2 . C . 0 . ? C . C . 0 . ? O . O . 0 . ? OXT . O . 0 . ? H . H . 0 . ? HN2 . H . 0 . ? HA . H . 0 . ? HB2 . H . 0 . ? HB3 . H . 0 . ? HD1 . H . 0 . ? HE1 . H . 0 . ? HZ2 . H . 0 . ? HH2 . H . 0 . ? HZ3 . H . 0 . ? HE3 . H . 0 . ? 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 SING N CA ? ? SING N H ? ? SING N HN2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 NE1 ? ? SING CD1 HD1 ? ? SING NE1 CE2 ? ? SING NE1 HE1 ? ? DOUB CE2 CZ2 ? ? SING CE2 CD2 ? ? SING CZ2 CH2 ? ? SING CZ2 HZ2 ? ? DOUB CH2 CZ3 ? ? SING CH2 HH2 ? ? SING CZ3 CE3 ? ? SING CZ3 HZ3 ? ? DOUB CE3 CD2 ? ? SING CE3 HE3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DLY _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-LYSINE _BMRB_code . _PDB_code DLY _Standard_residue_derivative DLY _Molecular_mass 146.188 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Feb 15 18:39:03 2008 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N N 0 . ? CA CA C R 0 . ? C C C N 0 . ? O O O N 0 . ? CB CB C N 0 . ? CG CG C N 0 . ? CD CD C N 0 . ? CE CE C N 0 . ? NZ NZ N N 0 . ? OXT OXT O N 0 . ? H H H N 0 . ? H2 H2 H N 0 . ? HA HA H N 0 . ? HB2 HB2 H N 0 . ? HB3 HB3 H N 0 . ? HG2 HG2 H N 0 . ? HG3 HG3 H N 0 . ? HD2 HD2 H N 0 . ? HD3 HD3 H N 0 . ? HE2 HE2 H N 0 . ? HE3 HE3 H N 0 . ? HZ1 HZ1 H N 0 . ? HZ2 HZ2 H N 0 . ? HXT HXT H N 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 SING N CA ? ? SING N H ? ? SING N H2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD CE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING CE NZ ? ? SING CE HE2 ? ? SING CE HE3 ? ? SING NZ HZ1 ? ? SING NZ HZ2 ? ? 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 _Details $14dFdWdKT . . . . . . 'not a natural peptide' 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 $14dFdWdKT '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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $14dFdWdKT . mM 7 12 '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 'structure solution' 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_ROESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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 temperature 295 . K pH . . pH 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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 'The proton located at C5 on the triazole ring has the value of 7.648 ppm.' loop_ _Experiment_label '2D 1H-1H ROESY' '2D 1H-1H TOCSY' 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 'Cyclic pseudotetrapeptide' _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 DPN HA H 5.014 . 1 2 1 1 DPN HB2 H 3.511 . 2 3 1 1 DPN HB3 H 3.511 . 2 4 1 1 DPN HD1 H 6.778 . 3 5 1 1 DPN HD2 H 6.778 . 3 6 2 2 DTR H H 8.082 . 1 7 2 2 DTR HA H 4.564 . 1 8 2 2 DTR HB2 H 3.046 . 2 9 2 2 DTR HB3 H 3.046 . 2 10 2 2 DTR HD1 H 7.123 . 1 11 2 2 DTR HE1 H 10.918 . 1 12 3 3 DLY H H 7.222 . 1 13 3 3 DLY HA H 4.218 . 1 14 3 3 DLY HB2 H 1.523 . 2 15 3 3 DLY HB3 H 1.523 . 2 16 3 3 DLY HD2 H 1.513 . 2 17 3 3 DLY HD3 H 1.513 . 2 18 3 3 DLY HE2 H 2.746 . 2 19 3 3 DLY HE3 H 2.746 . 2 20 3 3 DLY HG2 H 1.166 . 2 21 3 3 DLY HG3 H 1.166 . 2 22 3 3 DLY HZ1 H 7.686 . 1 23 3 3 DLY HZ2 H 7.686 . 1 24 3 3 DLY HZ3 H 7.686 . 1 25 4 4 THR H H 8.243 . 1 26 4 4 THR HA H 4.812 . 1 27 4 4 THR HB H 3.949 . 1 28 4 4 THR HG2 H 1.122 . 1 stop_ save_