data_bmse012436 ####################### # Entry information # ####################### save_entry_information_1 _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information_1 _Entry.ID bmse012436 _Entry.Title N-(2-oxo-1,3-dihydrobenzimidazol-5-yl)propanamide _Entry.Type 'metabolite/natural product' _Entry.Version_type original _Entry.Submission_date 2023-04-05 _Entry.Accession_date 2023-04-05 _Entry.Last_release_date 2023-08-11 _Entry.Original_release_date 2023-08-11 _Entry.Origination author _Entry.NMR_STAR_version 3.2.10.4 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype solution _Entry.DOI 10.12018/bmse012436 loop_ _Entry_experimental_methods.ID _Entry_experimental_methods.Method _Entry_experimental_methods.Subtype _Entry_experimental_methods.Entry_ID 1 NMR solution bmse012436 stop_ loop_ _Entry_author.Ordinal _Entry_author.Given_name _Entry_author.Family_name _Entry_author.First_initial _Entry_author.Entry_ID 1 Sridhar Sreeramulu S. bmse012436 2 Christian Richter C. bmse012436 3 Harald Schwalbe H. bmse012436 4 Hannes Berg . bmse012436 stop_ loop_ _Entry_src.ID _Entry_src.Project_name _Entry_src.Entry_ID 1 EUOS bmse012436 stop_ loop_ _Release.Release_number _Release.Format_type _Release.Format_version _Release.Date _Release.Type _Release.Author _Release.Entry_ID 1 NMR-STAR 3.2.1.18 2023-11-09 original author bmse012436 stop_ loop_ _Auxiliary_files.ID _Auxiliary_files.Name _Auxiliary_files.Format _Auxiliary_files.URI _Auxiliary_files.Details _Auxiliary_files.Entry_ID 1 bmse012436.mol sdf na 'Structure Definition File' bmse012436 stop_ save_ ############### # Citations # ############### save_citations_1 _Citation.Sf_category citations _Citation.Sf_framecode citations_1 _Citation.Entry_ID bmse012436 _Citation.ID 1 _Citation.PubMed_ID 32533387 _Citation.DOI 10.1007/s10858-020-00327-9 _Citation.Title 'NMR quality control of fragment libraries for screening.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'J Biomol NMR' _Citation.Journal_name_full 'Journal of biomolecular NMR' _Citation.Journal_volume 74 _Citation.Journal_issue 10-11 _Citation.Journal_ISSN 1573-5001 _Citation.Page_first 555 _Citation.Page_last 563 _Citation.Year 2020 loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Entry_ID _Citation_author.Citation_ID 1 Sridhar Sreeramulu S. bmse012436 1 2 Christian Richter C. bmse012436 1 3 Till Kuehn T. bmse012436 1 4 Kamal Azzaoui K. bmse012436 1 5 'Marcel Jules Jose' Blommers . bmse012436 1 6 Rebecca 'Del Conte' R. bmse012436 1 7 Marco Fragai M. bmse012436 1 8 Nils Trieloff N. bmse012436 1 9 Peter Schmieder P. bmse012436 1 10 Marc Nazare M. bmse012436 1 11 Edgar Specker E. bmse012436 1 12 Vladimir Ivanov V. bmse012436 1 13 Hartmut Oschkinat H. bmse012436 1 14 Lucia Banci L. bmse012436 1 15 Harald Schwalbe H. bmse012436 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly_1 _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly_1 _Assembly.Entry_ID bmse012436 _Assembly.ID 1 _Assembly.Name N-(2-oxo-1,3-dihydrobenzimidazol-5-yl)propanamide _Assembly.Number_of_components 1 _Assembly.Thiol_state 'not present' loop_ _Entity_assembly.ID _Entity_assembly.Entity_assembly_name _Entity_assembly.Entity_ID _Entity_assembly.Experimental_data_reported _Entity_assembly.Physical_state _Entity_assembly.Conformational_isomer _Entity_assembly.Chemical_exchange_state _Entity_assembly.Entry_ID _Entity_assembly.Assembly_ID 1 chem_comp_1 1 yes native no no bmse012436 1 stop_ loop_ _Atom.Assembly_atom_ID _Atom.Entity_assembly_ID _Atom.Entity_ID _Atom.Comp_index_ID _Atom.Seq_ID _Atom.Atom_ID _Atom.Type_symbol _Atom.Entry_ID _Atom.Assembly_ID 1 1 1 1 1 C1 C bmse012436 1 2 1 1 1 1 C2 C bmse012436 1 3 1 1 1 1 C3 C bmse012436 1 4 1 1 1 1 C4 C bmse012436 1 5 1 1 1 1 C5 C bmse012436 1 6 1 1 1 1 C6 C bmse012436 1 7 1 1 1 1 C7 C bmse012436 1 8 1 1 1 1 C8 C bmse012436 1 9 1 1 1 1 C9 C bmse012436 1 10 1 1 1 1 C10 C bmse012436 1 11 1 1 1 1 N11 N bmse012436 1 12 1 1 1 1 N12 N bmse012436 1 13 1 1 1 1 N13 N bmse012436 1 14 1 1 1 1 O14 O bmse012436 1 15 1 1 1 1 O15 O bmse012436 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_entity_1 _Entity.Sf_category entity _Entity.Sf_framecode entity_1 _Entity.Entry_ID bmse012436 _Entity.ID 1 _Entity.Name N-(2-oxo-1,3-dihydrobenzimidazol-5-yl)propanamide _Entity.Type non-polymer _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_linkage no _Entity.Nonpolymer_comp_label chem_comp_1 _Entity.Number_of_monomers 1 _Entity.Number_of_nonpolymer_components 1 _Entity.Thiol_state 'not present' _Entity.Formula_weight 205.21323999999998 loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 1 chem_comp_1 bmse012436 1 stop_ save_ ################################# # Polymer residues and ligands # ################################# save_chem_comp_1 _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_1 _Chem_comp.Entry_ID bmse012436 _Chem_comp.Name N-(2-oxo-1,3-dihydrobenzimidazol-5-yl)propanamide _Chem_comp.Number_atoms_all 15 _Chem_comp.InChI_code InChI=1S/C10H11N3O2/c1-2-9(14)11-6-3-4-7-8(5-6)13-10(15)12-7/h3-5H,2H2,1H3,(H,11,14)(H2,12,13,15) _Chem_comp.Formal_charge 0 _Chem_comp.Aromatic yes _Chem_comp.Formula C10H11N3O2 _Chem_comp.Formula_weight 205.21323999999998 _Chem_comp.Formula_mono_iso_wt_nat 205.085126607 _Chem_comp.Formula_mono_iso_wt_13C 215.11867498700005 _Chem_comp.Formula_mono_iso_wt_15N 208.07623128600002 _Chem_comp.Formula_mono_iso_wt_13C_15N 218.10977966600007 _Chem_comp.Image_file_name bmse012436.png _Chem_comp.Image_file_format png _Chem_comp.Struct_file_name bmse012436.sdf _Chem_comp.Struct_file_format sdf loop_ _Chem_comp_descriptor.Descriptor _Chem_comp_descriptor.Type _Chem_comp_descriptor.Program _Chem_comp_descriptor.Program_version _Chem_comp_descriptor.Entry_ID CCC(=O)Nc1ccc2[nH]c(=O)[nH]c2c1 SMILES_CANONICAL RDKit 2022.03.5 bmse012436 CCC(=O)Nc1ccc2[nH]c(=O)[nH]c2c1 SMILES_ISOMERIC RDKit 2022.03.5 bmse012436 CCC(=O)Nc1ccc2[nH]c(=O)[nH]c2c1 SMILES RDKit 2022.03.5 bmse012436 CCC(=O)Nc1ccc2c(c1)[nH]c(=O)[nH]2 SMILES_CANONICAL OpenBabel 3.1.0 bmse012436 CCC(=O)Nc1ccc2c(c1)[nH]c(=O)[nH]2 SMILES OpenBabel 3.1.0 bmse012436 InChI=1S/C10H11N3O2/c1-2-9(14)11-6-3-4-7-8(5-6)13-10(15)12-7/h3-5H,2H2,1H3,(H,11,14)(H2,12,13,15) InChI OpenBabel 3.1.0 bmse012436 VBJWIRGHLZMDOV-UHFFFAOYSA-N InChI_KEY OpenBabel 3.1.0 bmse012436 InChI=1S/C10H11N3O2/c1-2-9(14)11-6-3-4-7-8(5-6)13-10(15)12-7/h3-5H,2H2,1H3,(H,11,14)(H2,12,13,15) InChI ALATIS na bmse012436 stop_ loop_ _Chem_comp_atom.Atom_ID _Chem_comp_atom.Type_symbol _Chem_comp_atom.Stereo_config _Chem_comp_atom.Charge _Chem_comp_atom.Aromatic_flag _Chem_comp_atom.PDBX_ordinal _Chem_comp_atom.Entry_ID C1 C N 0 no 1 bmse012436 C2 C N 0 no 2 bmse012436 C3 C N 0 yes 3 bmse012436 C4 C N 0 yes 4 bmse012436 C5 C N 0 yes 5 bmse012436 C6 C N 0 yes 6 bmse012436 C7 C N 0 yes 7 bmse012436 C8 C N 0 yes 8 bmse012436 C9 C N 0 no 9 bmse012436 C10 C N 0 yes 10 bmse012436 N11 N N 0 no 11 bmse012436 N12 N N 0 yes 12 bmse012436 N13 N N 0 yes 13 bmse012436 O14 O N 0 no 14 bmse012436 O15 O N 0 no 15 bmse012436 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID C15 C1 ALATIS bmse012436 C14 C2 ALATIS bmse012436 C13 C3 ALATIS bmse012436 C12 C4 ALATIS bmse012436 C6 C5 ALATIS bmse012436 C9 C6 ALATIS bmse012436 C5 C7 ALATIS bmse012436 C4 C8 ALATIS bmse012436 C7 C9 ALATIS bmse012436 C1 C10 ALATIS bmse012436 N8 N11 ALATIS bmse012436 N3 N12 ALATIS bmse012436 N2 N13 ALATIS bmse012436 O11 O14 ALATIS bmse012436 O10 O15 ALATIS bmse012436 stop_ loop_ _Chem_comp_bond.ID _Chem_comp_bond.Type _Chem_comp_bond.Value_order _Chem_comp_bond.Atom_ID_1 _Chem_comp_bond.Atom_ID_2 _Chem_comp_bond.Aromatic_flag _Chem_comp_bond.Stereo_config _Chem_comp_bond.Ordinal _Chem_comp_bond.Entry_ID 1 covalent SING C2 C1 no N 1 bmse012436 2 covalent AROM C4 C3 yes N 2 bmse012436 3 covalent AROM C5 C6 yes N 3 bmse012436 4 covalent AROM C6 C3 yes N 4 bmse012436 5 covalent AROM C7 C4 yes N 5 bmse012436 6 covalent AROM C8 C5 yes N 6 bmse012436 7 covalent AROM C8 C7 yes N 7 bmse012436 8 covalent SING C9 C2 no N 8 bmse012436 9 amide SING C9 N11 no N 9 bmse012436 10 carbonyl DOUB C9 O14 no N 10 bmse012436 11 amide AROM C10 N12 yes N 11 bmse012436 12 amide AROM C10 N13 yes N 12 bmse012436 13 carbonyl DOUB C10 O15 no N 13 bmse012436 14 covalent SING N11 C6 no N 14 bmse012436 15 covalent AROM N12 C7 yes N 15 bmse012436 16 covalent AROM N13 C8 yes N 16 bmse012436 stop_ loop_ _Chem_comp_db_link.Database_code _Chem_comp_db_link.Accession_code _Chem_comp_db_link.Accession_code_type _Chem_comp_db_link.Entry_ID EU-OPENSCREEN EOS103193 'compound ID' bmse012436 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID bmse012436 _Sample.ID 1 _Sample.Name 'sample 1' _Sample.Type solution _Sample.Aggregate_sample_number 1 loop_ _Sample_component.ID _Sample_component.Mol_common_name _Sample_component.Isotopic_labeling _Sample_component.Assembly_ID _Sample_component.Assembly_label _Sample_component.Entity_ID _Sample_component.Entity_label _Sample_component.Type _Sample_component.Concentration_val _Sample_component.Concentration_val_units _Sample_component.Entry_ID _Sample_component.Sample_ID 1 N-(2-oxo-1,3-dihydrobenzimidazol-5-yl)propanamide 'natural abundance' 1 $assembly_1 1 $entity_1 solute 2 mM bmse012436 1 2 'Sodium phosphate' 'natural abundance' . . . . buffer 25 mM bmse012436 1 3 'Sodium chloride' 'natural abundance' . . . . salt 150 mM bmse012436 1 4 DSS 'natural abundance' . . . . reference 10 uM bmse012436 1 5 H2O 'natural abundance' . . . . solvent 95 % bmse012436 1 6 DMSO '[2H U-100%]' . . . . solvent 5 % bmse012436 1 stop_ save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Sample_condition_list.Sf_category sample_conditions _Sample_condition_list.Sf_framecode sample_conditions_1 _Sample_condition_list.Entry_ID bmse012436 _Sample_condition_list.ID 1 _Sample_condition_list.Name 'sample conditions 1' loop_ _Sample_condition_variable.Type _Sample_condition_variable.Val _Sample_condition_variable.Val_err _Sample_condition_variable.Val_units _Sample_condition_variable.Entry_ID _Sample_condition_variable.Sample_condition_list_ID pH 7.5 . pH bmse012436 1 pressure 1 . atm bmse012436 1 temperature 298 0.1 K bmse012436 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmse012436 _Software.ID 1 _Software.Name TopSpin _Software.Version 4.0.3 loop_ _Vendor.Name _Vendor.Electronic_address _Vendor.Entry_ID _Vendor.Software_ID 'Bruker Biospin' http://www.bruker.com/products/mr/nmr/nmr-software/software/topspin/ bmse012436 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'data analysis' bmse012436 1 'peak picking' bmse012436 1 processing bmse012436 1 stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _NMR_spectrometer.Sf_category NMR_spectrometer _NMR_spectrometer.Sf_framecode NMR_spectrometer_1 _NMR_spectrometer.Entry_ID bmse012436 _NMR_spectrometer.ID 1 _NMR_spectrometer.Name 'spectrometer Bruker' _NMR_spectrometer.Manufacturer Bruker _NMR_spectrometer.Model Avance _NMR_spectrometer.Field_strength 600 save_ ############################# # NMR applied experiments # ############################# save_experiment_list_1 _Experiment_list.Sf_category experiment_list _Experiment_list.Sf_framecode experiment_list_1 _Experiment_list.Entry_ID bmse012436 _Experiment_list.ID 1 loop_ _Experiment.ID _Experiment.Name _Experiment.Raw_data_flag _Experiment.Sample_ID _Experiment.Sample_label _Experiment.Sample_state _Experiment.Sample_condition_list_ID _Experiment.Sample_condition_list_label _Experiment.NMR_spectrometer_ID _Experiment.NMR_spectrometer_label _Experiment.Entry_ID _Experiment.Experiment_list_ID 1 '1D 1H' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $NMR_spectrometer_1 bmse012436 1 stop_ loop_ _Experiment_file.Experiment_ID _Experiment_file.Name _Experiment_file.Type _Experiment_file.Content _Experiment_file.Directory_path _Experiment_file.Entry_ID _Experiment_file.Experiment_list_ID 1 1 text/directory 'NMR experiment directory' nmr/set01/ bmse012436 1 1 cmcproject.xml text/xml 'spectrum analysis' nmr/set01/1/pdata/1/ bmse012436 1 1 multiplet.txt text 'Peak list' nmr/set01/1/pdata/1/ bmse012436 1 1 spectrum_overview.pdf pdf 'Spectrum image' nmr/set01/1/pdata/1/ bmse012436 1 1 spectrum_overview.png image/png 'Spectral image' nmr/set01/1/pdata/1/ bmse012436 1 stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Chem_shift_reference.Sf_category chem_shift_reference _Chem_shift_reference.Sf_framecode chem_shift_reference_1 _Chem_shift_reference.Entry_ID bmse012436 _Chem_shift_reference.ID 1 _Chem_shift_reference.Name 'chem shift ref set' loop_ _Chem_shift_ref.Atom_type _Chem_shift_ref.Atom_isotope_number _Chem_shift_ref.Mol_common_name _Chem_shift_ref.Atom_group _Chem_shift_ref.Chem_shift_units _Chem_shift_ref.Chem_shift_val _Chem_shift_ref.Ref_method _Chem_shift_ref.Ref_type _Chem_shift_ref.Indirect_shift_ratio _Chem_shift_ref.Entry_ID _Chem_shift_ref.Chem_shift_reference_ID H 1 DSS 'methyl protons' ppm 0.0 internal direct 1.0 bmse012436 1 stop_ save_ ######################### # Spectral peak lists # ######################### save_spectral_peak_list_1 _Spectral_peak_list.Sf_category spectral_peak_list _Spectral_peak_list.Sf_framecode spectral_peak_list_1 _Spectral_peak_list.Entry_ID bmse012436 _Spectral_peak_list.ID 1 _Spectral_peak_list.Name 'spectral peaks 1D 1H' _Spectral_peak_list.Sample_ID 1 _Spectral_peak_list.Sample_label $sample_1 _Spectral_peak_list.Sample_condition_list_ID 1 _Spectral_peak_list.Sample_condition_list_label $sample_conditions_1 _Spectral_peak_list.Chem_shift_reference_ID 1 _Spectral_peak_list.Experiment_ID 1 _Spectral_peak_list.Experiment_name '1D 1H' _Spectral_peak_list.Number_of_spectral_dimensions 1 _Spectral_peak_list.Assigned_chem_shift_list_ID 1 _Spectral_peak_list.Details 'F1: 1H' loop_ _Spectral_dim.ID _Spectral_dim.Spectrometer_frequency _Spectral_dim.Atom_type _Spectral_dim.Atom_isotope_number _Spectral_dim.Spectral_region _Spectral_dim.Sweep_width _Spectral_dim.Sweep_width_units _Spectral_dim.Entry_ID _Spectral_dim.Spectral_peak_list_ID 1 600.1728185 H 1 'Full H' 12.0157698570257 ppm bmse012436 1 stop_ loop_ _Spectral_peak_software.Software_ID _Spectral_peak_software.Software_label _Spectral_peak_software.Entry_ID _Spectral_peak_software.Spectral_peak_list_ID 1 $software_1 bmse012436 1 stop_ loop_ _Peak.ID _Peak.Entry_ID _Peak.Spectral_peak_list_ID 1 bmse012436 1 2 bmse012436 1 3 bmse012436 1 4 bmse012436 1 5 bmse012436 1 6 bmse012436 1 7 bmse012436 1 8 bmse012436 1 stop_ loop_ _Peak_char.Peak_ID _Peak_char.Spectral_dim_ID _Peak_char.Chem_shift_val _Peak_char.Details _Peak_char.Entry_ID _Peak_char.Spectral_peak_list_ID 1 1 6.9514 10_dd_Q3 bmse012436 1 2 1 0.0352 TMS bmse012436 1 3 1 7.0732 8,11_m bmse012436 1 4 1 2.3133 14_ddd_Q2 bmse012436 1 5 1 1.0818 15_t_Q1 bmse012436 1 6 1 7.1892 7_d bmse012436 1 7 1 4.6542 SUP bmse012436 1 8 1 2.5698 DMSO bmse012436 1 stop_ loop_ _Spectral_transition.ID _Spectral_transition.Entry_ID _Spectral_transition.Spectral_peak_list_ID 1 bmse012436 1 2 bmse012436 1 3 bmse012436 1 4 bmse012436 1 5 bmse012436 1 6 bmse012436 1 7 bmse012436 1 8 bmse012436 1 9 bmse012436 1 10 bmse012436 1 11 bmse012436 1 12 bmse012436 1 13 bmse012436 1 14 bmse012436 1 15 bmse012436 1 16 bmse012436 1 17 bmse012436 1 18 bmse012436 1 19 bmse012436 1 20 bmse012436 1 21 bmse012436 1 22 bmse012436 1 stop_ loop_ _Spectral_transition_char.Spectral_transition_ID _Spectral_transition_char.Spectral_dim_ID _Spectral_transition_char.Chem_shift_val _Spectral_transition_char.Entry_ID _Spectral_transition_char.Spectral_peak_list_ID 1 1 6.9601 bmse012436 1 2 1 6.9569 bmse012436 1 3 1 6.9459 bmse012436 1 4 1 6.9427 bmse012436 1 5 1 0.0352 bmse012436 1 6 1 7.1184 bmse012436 1 7 1 7.0280 bmse012436 1 8 1 2.3330 bmse012436 1 9 1 2.3198 bmse012436 1 10 1 2.3198 bmse012436 1 11 1 2.3066 bmse012436 1 12 1 2.3198 bmse012436 1 13 1 2.3066 bmse012436 1 14 1 2.3066 bmse012436 1 15 1 2.2936 bmse012436 1 16 1 1.0950 bmse012436 1 17 1 1.0818 bmse012436 1 18 1 1.0686 bmse012436 1 19 1 7.1907 bmse012436 1 20 1 7.1878 bmse012436 1 21 1 4.6542 bmse012436 1 22 1 2.5698 bmse012436 1 stop_ loop_ _Peak_coupling.ID _Peak_coupling.Peak_ID _Peak_coupling.Spectral_dim_ID _Peak_coupling.Coupling_val _Peak_coupling.Entry_ID _Peak_coupling.Spectral_peak_list_ID 1 1 1 8.5097 bmse012436 1 2 2 1 0.0000 bmse012436 1 3 3 1 54.2574 bmse012436 1 4 4 1 7.8862 bmse012436 1 5 5 1 0.0000 bmse012436 1 6 6 1 0.0000 bmse012436 1 7 7 1 0.0000 bmse012436 1 8 8 1 0.0000 bmse012436 1 stop_ save_