data_2N09 # _entry.id 2N09 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_code _database_2.database_id RCSB104258 RCSB 2N09 PDB 26536 BMRB D_1000104258 WWPDB # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 26536 BMRB unspecified . 2N08 PDB unspecified . 2N0I PDB unspecified . 2N0N PDB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2N09 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2015-03-04 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hoang, H.N.' 1 'Song, K.' 2 'Hill, T.A.' 3 'Derksen, D.R.' 4 'Edmonds, D.J.' 5 'Kok, W.M.' 6 'Limberakis, C.' 7 'Liras, S.' 8 'Loria, P.M.' 9 'Mascitti, V.' 10 'Mathiowetz, A.M.' 11 'Mitchell, J.M.' 12 'Piotrowski, D.W.' 13 'Price, D.A.' 14 'Stanton, R.V.' 15 'Suen, J.Y.' 16 'Withka, J.M.' 17 'Griffith, D.A.' 18 'Fairlie, D.P.' 19 # _citation.id primary _citation.title 'Short Hydrophobic Peptides with Cyclic Constraints Are Potent Glucagon-like Peptide-1 Receptor (GLP-1R) Agonists.' _citation.journal_abbrev J.Med.Chem. _citation.journal_volume 58 _citation.page_first 4080 _citation.page_last 4085 _citation.year 2015 _citation.journal_id_ASTM JMCMAR _citation.country US _citation.journal_id_ISSN 0022-2623 _citation.journal_id_CSD 0151 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25839426 _citation.pdbx_database_id_DOI 10.1021/acs.jmedchem.5b00166 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Hoang, H.N.' 1 primary 'Song, K.' 2 primary 'Hill, T.A.' 3 primary 'Derksen, D.R.' 4 primary 'Edmonds, D.J.' 5 primary 'Kok, W.M.' 6 primary 'Limberakis, C.' 7 primary 'Liras, S.' 8 primary 'Loria, P.M.' 9 primary 'Mascitti, V.' 10 primary 'Mathiowetz, A.M.' 11 primary 'Mitchell, J.M.' 12 primary 'Piotrowski, D.W.' 13 primary 'Price, D.A.' 14 primary 'Stanton, R.V.' 15 primary 'Suen, J.Y.' 16 primary 'Withka, J.M.' 17 primary 'Griffith, D.A.' 18 primary 'Fairlie, D.P.' 19 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'Short hydrophobic peptide with cyclic constraints' _entity.formula_weight 1271.335 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'H(AIB)EGTFTSDFF(NH2)' _entity_poly.pdbx_seq_one_letter_code_can HAEGTFTSDFFX _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 HIS n 1 2 AIB n 1 3 GLU n 1 4 GLY n 1 5 THR n 1 6 PHE n 1 7 THR n 1 8 SER n 1 9 ASP n 1 10 PHE n 1 11 PHE n 1 12 NH2 n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2N09 _struct_ref.pdbx_db_accession 2N09 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2N09 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2N09 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 12 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 12 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight AIB 'L-peptide linking' n 'ALPHA-AMINOISOBUTYRIC ACID' ? 'C4 H9 N O2' 103.120 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 NH2 non-polymer . 'AMINO GROUP' ? 'H2 N' 16.023 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 # _pdbx_nmr_exptl.conditions_id 1 _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.solution_id 1 _pdbx_nmr_exptl.type NOESY # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0.01 _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents '1 mM peptide, 25% DMSO-d6, 75% H2O' _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '25% DMSO-d6/75% H2O' # _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model Avance _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2N09 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 50 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2N09 _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation 0.2 _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation 0.2 _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2N09 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Brunger, A.T. et al.' 'structure solution' xplor ? 1 'Brunger, A.T. et al.' refinement xplor ? 2 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.entry_id 2N09 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2N09 _struct.title 'NMR structure of a short hydrophobic 11mer peptide in DMSO-d6/H2O (1:3) solution' _struct.pdbx_descriptor 'Short hydrophobic peptide with cyclic constraints' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2N09 _struct_keywords.pdbx_keywords 'DE NOVO PROTEIN' _struct_keywords.text 'hydrophobic peptide, GLP-1R agonist, DE NOVO PROTEIN' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 _struct_biol.details ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id GLY _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 4 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id PHE _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 10 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id GLY _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 4 _struct_conf.end_auth_comp_id PHE _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 10 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 7 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_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_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale1 covale ? ? A PHE 11 C ? ? ? 1_555 A NH2 12 N ? ? A PHE 11 A NH2 12 1_555 ? ? ? ? ? ? ? 1.328 ? covale2 covale ? ? A HIS 1 C ? ? ? 1_555 A AIB 2 N ? ? A HIS 1 A AIB 2 1_555 ? ? ? ? ? ? ? 1.330 ? covale3 covale ? ? A AIB 2 C ? ? ? 1_555 A GLU 3 N ? ? A AIB 2 A GLU 3 1_555 ? ? ? ? ? ? ? 1.332 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 2N09 _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 HIS 1 1 1 HIS HIS A . n A 1 2 AIB 2 2 2 AIB ALA A . n A 1 3 GLU 3 3 3 GLU GLU A . n A 1 4 GLY 4 4 4 GLY GLY A . n A 1 5 THR 5 5 5 THR THR A . n A 1 6 PHE 6 6 6 PHE PHE A . n A 1 7 THR 7 7 7 THR THR A . n A 1 8 SER 8 8 8 SER SER A . n A 1 9 ASP 9 9 9 ASP ASP A . n A 1 10 PHE 10 10 10 PHE PHE A . n A 1 11 PHE 11 11 11 PHE PHE A . n A 1 12 NH2 12 12 11 NH2 PHE A . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id AIB _pdbx_struct_mod_residue.label_seq_id 2 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id AIB _pdbx_struct_mod_residue.auth_seq_id 2 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id ALA _pdbx_struct_mod_residue.details 'ALPHA-AMINOISOBUTYRIC ACID' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _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] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2015-04-15 2 'Structure model' 1 1 2015-05-27 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # _pdbx_nmr_exptl_sample.component peptide-1 _pdbx_nmr_exptl_sample.concentration 1 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mM _pdbx_nmr_exptl_sample.isotopic_labeling ? _pdbx_nmr_exptl_sample.solution_id 1 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2N09 _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_other-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count ? _pdbx_nmr_constraints.NOE_constraints_total 96 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count 30 _pdbx_nmr_constraints.NOE_long_range_total_count ? _pdbx_nmr_constraints.NOE_medium_range_total_count 60 _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count ? _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 AIB A 2 ? ? 57.69 -86.55 2 1 THR A 5 ? ? 51.83 -174.81 3 1 PHE A 10 ? ? -49.08 173.64 4 2 AIB A 2 ? ? 56.30 -89.88 5 2 THR A 5 ? ? 47.98 -170.67 6 3 THR A 5 ? ? 44.55 -170.74 7 4 AIB A 2 ? ? 60.07 -83.25 8 4 THR A 5 ? ? 67.12 170.80 9 5 THR A 5 ? ? 52.81 -178.68 10 5 PHE A 10 ? ? 63.67 -79.73 11 6 THR A 5 ? ? 55.75 -173.39 12 6 PHE A 10 ? ? 63.47 -79.15 13 7 AIB A 2 ? ? 57.72 -87.44 14 7 THR A 5 ? ? 54.96 -169.61 15 7 THR A 7 ? ? -53.50 -76.01 16 7 PHE A 10 ? ? 65.99 -76.74 17 8 THR A 5 ? ? 46.08 -169.77 18 9 AIB A 2 ? ? 61.16 -84.09 19 9 THR A 5 ? ? 55.62 176.52 20 9 ASP A 9 ? ? -57.55 -78.48 21 9 PHE A 10 ? ? 62.08 148.07 22 10 THR A 5 ? ? 52.44 -172.83 23 10 ASP A 9 ? ? -58.33 -72.86 24 10 PHE A 10 ? ? 66.20 -71.44 #