data_bmse011945 ####################### # Entry information # ####################### save_entry_information_1 _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information_1 _Entry.ID bmse011945 _Entry.Title (5S)-2-methyl-4,5,6,7-tetrahydro-3H-benzimidazol-5-amine _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/bmse011945 loop_ _Entry_experimental_methods.ID _Entry_experimental_methods.Method _Entry_experimental_methods.Subtype _Entry_experimental_methods.Entry_ID 1 NMR solution bmse011945 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. bmse011945 2 Christian Richter C. bmse011945 3 Harald Schwalbe H. bmse011945 4 Hannes Berg . bmse011945 stop_ loop_ _Entry_src.ID _Entry_src.Project_name _Entry_src.Entry_ID 1 EUOS bmse011945 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 bmse011945 stop_ loop_ _Auxiliary_files.ID _Auxiliary_files.Name _Auxiliary_files.Format _Auxiliary_files.URI _Auxiliary_files.Details _Auxiliary_files.Entry_ID 1 bmse011945.mol sdf na 'Structure Definition File' bmse011945 stop_ save_ ############### # Citations # ############### save_citations_1 _Citation.Sf_category citations _Citation.Sf_framecode citations_1 _Citation.Entry_ID bmse011945 _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. bmse011945 1 2 Christian Richter C. bmse011945 1 3 Till Kuehn T. bmse011945 1 4 Kamal Azzaoui K. bmse011945 1 5 'Marcel Jules Jose' Blommers . bmse011945 1 6 Rebecca 'Del Conte' R. bmse011945 1 7 Marco Fragai M. bmse011945 1 8 Nils Trieloff N. bmse011945 1 9 Peter Schmieder P. bmse011945 1 10 Marc Nazare M. bmse011945 1 11 Edgar Specker E. bmse011945 1 12 Vladimir Ivanov V. bmse011945 1 13 Hartmut Oschkinat H. bmse011945 1 14 Lucia Banci L. bmse011945 1 15 Harald Schwalbe H. bmse011945 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly_1 _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly_1 _Assembly.Entry_ID bmse011945 _Assembly.ID 1 _Assembly.Name (5S)-2-methyl-4,5,6,7-tetrahydro-3H-benzimidazol-5-amine _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 bmse011945 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 bmse011945 1 2 1 1 1 1 C2 C bmse011945 1 3 1 1 1 1 C3 C bmse011945 1 4 1 1 1 1 C4 C bmse011945 1 5 1 1 1 1 C5 C bmse011945 1 6 1 1 1 1 C6 C bmse011945 1 7 1 1 1 1 C7 C bmse011945 1 8 1 1 1 1 C8 C bmse011945 1 9 1 1 1 1 N9 N bmse011945 1 10 1 1 1 1 N10 N bmse011945 1 11 1 1 1 1 N11 N bmse011945 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_entity_1 _Entity.Sf_category entity _Entity.Sf_framecode entity_1 _Entity.Entry_ID bmse011945 _Entity.ID 1 _Entity.Name (5S)-2-methyl-4,5,6,7-tetrahydro-3H-benzimidazol-5-amine _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 151.20891999999998 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 bmse011945 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 bmse011945 _Chem_comp.Name (5S)-2-methyl-4,5,6,7-tetrahydro-3H-benzimidazol-5-amine _Chem_comp.Number_atoms_all 11 _Chem_comp.InChI_code InChI=1S/C8H13N3/c1-5-10-7-3-2-6(9)4-8(7)11-5/h6H,2-4,9H2,1H3,(H,10,11)/t6-/m0/s1 _Chem_comp.Formal_charge 0 _Chem_comp.Aromatic yes _Chem_comp.Formula C8H13N3 _Chem_comp.Formula_weight 151.20891999999998 _Chem_comp.Formula_mono_iso_wt_nat 151.110947431 _Chem_comp.Formula_mono_iso_wt_13C 159.13778613500003 _Chem_comp.Formula_mono_iso_wt_15N 154.10205211000002 _Chem_comp.Formula_mono_iso_wt_13C_15N 162.12889081400004 _Chem_comp.Image_file_name bmse011945.png _Chem_comp.Image_file_format png _Chem_comp.Struct_file_name bmse011945.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 Cc1nc2c([nH]1)C[C@@H](N)CC2 SMILES_CANONICAL RDKit 2022.03.5 bmse011945 Cc1nc2c([nH]1)C[C@@H](N)CC2 SMILES_ISOMERIC RDKit 2022.03.5 bmse011945 Cc1nc2c([nH]1)C[C@@H](N)CC2 SMILES RDKit 2022.03.5 bmse011945 N[C@H]1CCc2c(C1)[nH]c(n2)C SMILES_CANONICAL OpenBabel 3.1.0 bmse011945 N[C@H]1CCc2c(C1)[nH]c(n2)C SMILES OpenBabel 3.1.0 bmse011945 InChI=1S/C8H13N3/c1-5-10-7-3-2-6(9)4-8(7)11-5/h6H,2-4,9H2,1H3,(H,10,11)/t6-/m0/s1 InChI OpenBabel 3.1.0 bmse011945 JGCNHPQMPGHGHT-LURJTMIESA-N InChI_KEY OpenBabel 3.1.0 bmse011945 InChI=1S/C8H13N3/c1-5-10-7-3-2-6(9)4-8(7)11-5/h6H,2-4,9H2,1H3,(H,10,11)/t6-/m0/s1 InChI ALATIS na bmse011945 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 bmse011945 C2 C N 0 no 2 bmse011945 C3 C N 0 no 3 bmse011945 C4 C N 0 no 4 bmse011945 C5 C N 0 yes 5 bmse011945 C6 C S 0 no 6 bmse011945 C7 C N 0 yes 7 bmse011945 C8 C N 0 yes 8 bmse011945 N9 N N 0 no 9 bmse011945 N10 N N 0 yes 10 bmse011945 N11 N N 0 yes 11 bmse011945 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID C5 C1 ALATIS bmse011945 C8 C2 ALATIS bmse011945 C7 C3 ALATIS bmse011945 C11 C4 ALATIS bmse011945 C3 C5 ALATIS bmse011945 C9 C6 ALATIS bmse011945 C6 C7 ALATIS bmse011945 C1 C8 ALATIS bmse011945 N10 N9 ALATIS bmse011945 N4 N10 ALATIS bmse011945 N2 N11 ALATIS bmse011945 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 C6 no N 1 bmse011945 2 covalent SING C3 C2 no N 2 bmse011945 3 covalent SING C5 C1 no N 3 bmse011945 4 covalent AROM C5 N10 yes N 4 bmse011945 5 covalent SING C6 C4 no N 5 bmse011945 6 covalent SING C6 N9 no N 6 bmse011945 7 covalent SING C7 C3 no N 7 bmse011945 8 covalent SING C8 C4 no N 8 bmse011945 9 covalent AROM C8 C7 yes N 9 bmse011945 10 covalent AROM C8 N11 yes N 10 bmse011945 11 covalent AROM N10 C7 yes N 11 bmse011945 12 covalent AROM N11 C5 yes N 12 bmse011945 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 EOS102656 'compound ID' bmse011945 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID bmse011945 _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 (5S)-2-methyl-4,5,6,7-tetrahydro-3H-benzimidazol-5-amine 'natural abundance' 1 $assembly_1 1 $entity_1 solute 2 mM bmse011945 1 2 'Sodium phosphate' 'natural abundance' . . . . buffer 25 mM bmse011945 1 3 'Sodium chloride' 'natural abundance' . . . . salt 150 mM bmse011945 1 4 DSS 'natural abundance' . . . . reference 10 uM bmse011945 1 5 H2O 'natural abundance' . . . . solvent 95 % bmse011945 1 6 DMSO '[2H U-100%]' . . . . solvent 5 % bmse011945 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 bmse011945 _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 bmse011945 1 pressure 1 . atm bmse011945 1 temperature 298 0.1 K bmse011945 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmse011945 _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/ bmse011945 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'data analysis' bmse011945 1 'peak picking' bmse011945 1 processing bmse011945 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 bmse011945 _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 bmse011945 _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 bmse011945 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/ bmse011945 1 1 cmcproject.xml text/xml 'spectrum analysis' nmr/set01/1/pdata/1/ bmse011945 1 1 multiplet.txt text 'Peak list' nmr/set01/1/pdata/1/ bmse011945 1 1 spectrum_overview.pdf pdf 'Spectrum image' nmr/set01/1/pdata/1/ bmse011945 1 1 spectrum_overview.png image/png 'Spectral image' nmr/set01/1/pdata/1/ bmse011945 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 bmse011945 _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 bmse011945 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 bmse011945 _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 bmse011945 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 bmse011945 1 stop_ loop_ _Peak.ID _Peak.Entry_ID _Peak.Spectral_peak_list_ID 1 bmse011945 1 2 bmse011945 1 3 bmse011945 1 4 bmse011945 1 5 bmse011945 1 6 bmse011945 1 7 bmse011945 1 8 bmse011945 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 2.9472 7_m bmse011945 1 2 1 0.0354 TMS bmse011945 1 3 1 2.0958 11_m bmse011945 1 4 1 2.3332 9_s_Q2 bmse011945 1 5 1 3.6215 7_m_Q3 bmse011945 1 6 1 1.8849 11_m_Q1 bmse011945 1 7 1 4.6544 SUP bmse011945 1 8 1 2.5840 DMSO bmse011945 1 stop_ loop_ _Spectral_transition.ID _Spectral_transition.Entry_ID _Spectral_transition.Spectral_peak_list_ID 1 bmse011945 1 2 bmse011945 1 3 bmse011945 1 4 bmse011945 1 5 bmse011945 1 6 bmse011945 1 7 bmse011945 1 8 bmse011945 1 9 bmse011945 1 10 bmse011945 1 11 bmse011945 1 12 bmse011945 1 13 bmse011945 1 14 bmse011945 1 15 bmse011945 1 16 bmse011945 1 17 bmse011945 1 18 bmse011945 1 19 bmse011945 1 20 bmse011945 1 21 bmse011945 1 22 bmse011945 1 23 bmse011945 1 24 bmse011945 1 25 bmse011945 1 26 bmse011945 1 27 bmse011945 1 28 bmse011945 1 29 bmse011945 1 30 bmse011945 1 31 bmse011945 1 32 bmse011945 1 33 bmse011945 1 34 bmse011945 1 35 bmse011945 1 36 bmse011945 1 37 bmse011945 1 38 bmse011945 1 39 bmse011945 1 40 bmse011945 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 2.9659 bmse011945 1 2 1 2.9561 bmse011945 1 3 1 2.9375 bmse011945 1 4 1 2.9285 bmse011945 1 5 1 0.0354 bmse011945 1 6 1 2.1192 bmse011945 1 7 1 2.1092 bmse011945 1 8 1 2.1058 bmse011945 1 9 1 2.0969 bmse011945 1 10 1 2.0877 bmse011945 1 11 1 2.0818 bmse011945 1 12 1 2.0725 bmse011945 1 13 1 2.3332 bmse011945 1 14 1 3.6436 bmse011945 1 15 1 3.6387 bmse011945 1 16 1 3.6336 bmse011945 1 17 1 3.6299 bmse011945 1 18 1 3.6258 bmse011945 1 19 1 3.6216 bmse011945 1 20 1 3.6128 bmse011945 1 21 1 3.6089 bmse011945 1 22 1 3.6040 bmse011945 1 23 1 3.5994 bmse011945 1 24 1 1.9172 bmse011945 1 25 1 1.9054 bmse011945 1 26 1 1.9001 bmse011945 1 27 1 1.8927 bmse011945 1 28 1 1.8888 bmse011945 1 29 1 1.8832 bmse011945 1 30 1 1.8754 bmse011945 1 31 1 1.8697 bmse011945 1 32 1 1.8693 bmse011945 1 33 1 1.8666 bmse011945 1 34 1 1.8661 bmse011945 1 35 1 1.8526 bmse011945 1 36 1 4.6544 bmse011945 1 37 1 2.6005 bmse011945 1 38 1 2.5731 bmse011945 1 39 1 2.5702 bmse011945 1 40 1 2.5675 bmse011945 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 7.4827 bmse011945 1 2 2 1 0.0000 bmse011945 1 3 3 1 4.6706 bmse011945 1 4 4 1 0.0000 bmse011945 1 5 5 1 2.9507 bmse011945 1 6 6 1 3.5213 bmse011945 1 7 7 1 0.0000 bmse011945 1 8 8 1 6.6024 bmse011945 1 stop_ save_