data_bmse012646 ####################### # Entry information # ####################### save_entry_information_1 _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information_1 _Entry.ID bmse012646 _Entry.Title 1,4,5,6-tetrahydropyrimidin-2-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/bmse012646 loop_ _Entry_experimental_methods.ID _Entry_experimental_methods.Method _Entry_experimental_methods.Subtype _Entry_experimental_methods.Entry_ID 1 NMR solution bmse012646 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. bmse012646 2 Christian Richter C. bmse012646 3 Harald Schwalbe H. bmse012646 4 Hannes Berg . bmse012646 stop_ loop_ _Entry_src.ID _Entry_src.Project_name _Entry_src.Entry_ID 1 EUOS bmse012646 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 bmse012646 stop_ loop_ _Auxiliary_files.ID _Auxiliary_files.Name _Auxiliary_files.Format _Auxiliary_files.URI _Auxiliary_files.Details _Auxiliary_files.Entry_ID 1 bmse012646.mol sdf na 'Structure Definition File' bmse012646 stop_ save_ ############### # Citations # ############### save_citations_1 _Citation.Sf_category citations _Citation.Sf_framecode citations_1 _Citation.Entry_ID bmse012646 _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. bmse012646 1 2 Christian Richter C. bmse012646 1 3 Till Kuehn T. bmse012646 1 4 Kamal Azzaoui K. bmse012646 1 5 'Marcel Jules Jose' Blommers . bmse012646 1 6 Rebecca 'Del Conte' R. bmse012646 1 7 Marco Fragai M. bmse012646 1 8 Nils Trieloff N. bmse012646 1 9 Peter Schmieder P. bmse012646 1 10 Marc Nazare M. bmse012646 1 11 Edgar Specker E. bmse012646 1 12 Vladimir Ivanov V. bmse012646 1 13 Hartmut Oschkinat H. bmse012646 1 14 Lucia Banci L. bmse012646 1 15 Harald Schwalbe H. bmse012646 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly_1 _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly_1 _Assembly.Entry_ID bmse012646 _Assembly.ID 1 _Assembly.Name 1,4,5,6-tetrahydropyrimidin-2-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 bmse012646 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 bmse012646 1 2 1 1 1 1 C2 C bmse012646 1 3 1 1 1 1 C3 C bmse012646 1 4 1 1 1 1 C4 C bmse012646 1 5 1 1 1 1 N5 N bmse012646 1 6 1 1 1 1 N6 N bmse012646 1 7 1 1 1 1 N7 N bmse012646 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_entity_1 _Entity.Sf_category entity _Entity.Sf_framecode entity_1 _Entity.Entry_ID bmse012646 _Entity.ID 1 _Entity.Name 1,4,5,6-tetrahydropyrimidin-2-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 99.13435999999999 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 bmse012646 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 bmse012646 _Chem_comp.Name 1,4,5,6-tetrahydropyrimidin-2-amine _Chem_comp.Number_atoms_all 7 _Chem_comp.InChI_code InChI=1S/C4H9N3/c5-4-6-2-1-3-7-4/h1-3H2,(H3,5,6,7) _Chem_comp.Formal_charge 0 _Chem_comp.Aromatic no _Chem_comp.Formula C4H9N3 _Chem_comp.Formula_weight 99.13435999999999 _Chem_comp.Formula_mono_iso_wt_nat 99.079647303 _Chem_comp.Formula_mono_iso_wt_13C 103.093066655 _Chem_comp.Formula_mono_iso_wt_15N 102.07075198200002 _Chem_comp.Formula_mono_iso_wt_13C_15N 106.08417133400002 _Chem_comp.Image_file_name bmse012646.png _Chem_comp.Image_file_format png _Chem_comp.Struct_file_name bmse012646.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 NC1=NCCCN1 SMILES_CANONICAL RDKit 2022.03.5 bmse012646 NC1=NCCCN1 SMILES_ISOMERIC RDKit 2022.03.5 bmse012646 NC1=NCCCN1 SMILES RDKit 2022.03.5 bmse012646 NC1=NCCCN1 SMILES_CANONICAL OpenBabel 3.1.0 bmse012646 NC1=NCCCN1 SMILES OpenBabel 3.1.0 bmse012646 InChI=1S/C4H9N3/c5-4-6-2-1-3-7-4/h1-3H2,(H3,5,6,7) InChI OpenBabel 3.1.0 bmse012646 PEHDFSFYZKSKGH-UHFFFAOYSA-N InChI_KEY OpenBabel 3.1.0 bmse012646 InChI=1S/C4H9N3/c5-4-6-2-1-3-7-4/h1-3H2,(H3,5,6,7) InChI ALATIS na bmse012646 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 bmse012646 C2 C N 0 no 2 bmse012646 C3 C N 0 no 3 bmse012646 C4 C N 0 no 4 bmse012646 N5 N N 0 no 5 bmse012646 N6 N N 0 no 6 bmse012646 N7 N N 0 no 7 bmse012646 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID C5 C1 ALATIS bmse012646 C4 C2 ALATIS bmse012646 C6 C3 ALATIS bmse012646 C1 C4 ALATIS bmse012646 N2 N5 ALATIS bmse012646 N3 N6 ALATIS bmse012646 N7 N7 ALATIS bmse012646 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 C1 C3 no N 1 bmse012646 2 covalent SING C2 C1 no N 2 bmse012646 3 covalent SING C3 N7 no N 3 bmse012646 4 covalent SING C4 N5 no N 4 bmse012646 5 covalent DOUB C4 N6 no N 5 bmse012646 6 covalent SING C4 N7 no N 6 bmse012646 7 covalent SING N6 C2 no N 7 bmse012646 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 EOS103477 'compound ID' bmse012646 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID bmse012646 _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 1,4,5,6-tetrahydropyrimidin-2-amine 'natural abundance' 1 $assembly_1 1 $entity_1 solute 2 mM bmse012646 1 2 'Sodium phosphate' 'natural abundance' . . . . buffer 25 mM bmse012646 1 3 'Sodium chloride' 'natural abundance' . . . . salt 150 mM bmse012646 1 4 DSS 'natural abundance' . . . . reference 10 uM bmse012646 1 5 H2O 'natural abundance' . . . . solvent 95 % bmse012646 1 6 DMSO '[2H U-100%]' . . . . solvent 5 % bmse012646 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 bmse012646 _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 bmse012646 1 pressure 1 . atm bmse012646 1 temperature 298 0.1 K bmse012646 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmse012646 _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/ bmse012646 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'data analysis' bmse012646 1 'peak picking' bmse012646 1 processing bmse012646 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 bmse012646 _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 bmse012646 _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 bmse012646 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/ bmse012646 1 1 cmcproject.xml text/xml 'spectrum analysis' nmr/set01/1/pdata/1/ bmse012646 1 1 multiplet.txt text 'Peak list' nmr/set01/1/pdata/1/ bmse012646 1 1 spectrum_overview.pdf pdf 'Spectrum image' nmr/set01/1/pdata/1/ bmse012646 1 1 spectrum_overview.png image/png 'Spectral image' nmr/set01/1/pdata/1/ bmse012646 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 bmse012646 _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 bmse012646 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 bmse012646 _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 bmse012646 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 bmse012646 1 stop_ loop_ _Peak.ID _Peak.Entry_ID _Peak.Spectral_peak_list_ID 1 bmse012646 1 2 bmse012646 1 3 bmse012646 1 4 bmse012646 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 -0.0001 TMS bmse012646 1 2 1 3.3198 4,8_m_Q2 bmse012646 1 3 1 1.9078 7_quint_Q1 bmse012646 1 4 1 4.7693 SUP bmse012646 1 stop_ loop_ _Spectral_transition.ID _Spectral_transition.Entry_ID _Spectral_transition.Spectral_peak_list_ID 1 bmse012646 1 2 bmse012646 1 3 bmse012646 1 4 bmse012646 1 5 bmse012646 1 6 bmse012646 1 7 bmse012646 1 8 bmse012646 1 9 bmse012646 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 -0.0001 bmse012646 1 2 1 3.3571 bmse012646 1 3 1 3.2825 bmse012646 1 4 1 1.8882 bmse012646 1 5 1 1.8980 bmse012646 1 6 1 1.9078 bmse012646 1 7 1 1.9176 bmse012646 1 8 1 1.9274 bmse012646 1 9 1 4.7693 bmse012646 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 0.0000 bmse012646 1 2 2 1 44.7839 bmse012646 1 3 3 1 5.8784 bmse012646 1 4 4 1 0.0000 bmse012646 1 stop_ save_