data_bmse012328 ####################### # Entry information # ####################### save_entry_information_1 _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information_1 _Entry.ID bmse012328 _Entry.Title 5-chloro-1H-pyrimidin-2-one _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/bmse012328 loop_ _Entry_experimental_methods.ID _Entry_experimental_methods.Method _Entry_experimental_methods.Subtype _Entry_experimental_methods.Entry_ID 1 NMR solution bmse012328 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. bmse012328 2 Christian Richter C. bmse012328 3 Harald Schwalbe H. bmse012328 4 Hannes Berg . bmse012328 stop_ loop_ _Entry_src.ID _Entry_src.Project_name _Entry_src.Entry_ID 1 EUOS bmse012328 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 bmse012328 stop_ loop_ _Auxiliary_files.ID _Auxiliary_files.Name _Auxiliary_files.Format _Auxiliary_files.URI _Auxiliary_files.Details _Auxiliary_files.Entry_ID 1 bmse012328.mol sdf na 'Structure Definition File' bmse012328 stop_ save_ ############### # Citations # ############### save_citations_1 _Citation.Sf_category citations _Citation.Sf_framecode citations_1 _Citation.Entry_ID bmse012328 _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. bmse012328 1 2 Christian Richter C. bmse012328 1 3 Till Kuehn T. bmse012328 1 4 Kamal Azzaoui K. bmse012328 1 5 'Marcel Jules Jose' Blommers . bmse012328 1 6 Rebecca 'Del Conte' R. bmse012328 1 7 Marco Fragai M. bmse012328 1 8 Nils Trieloff N. bmse012328 1 9 Peter Schmieder P. bmse012328 1 10 Marc Nazare M. bmse012328 1 11 Edgar Specker E. bmse012328 1 12 Vladimir Ivanov V. bmse012328 1 13 Hartmut Oschkinat H. bmse012328 1 14 Lucia Banci L. bmse012328 1 15 Harald Schwalbe H. bmse012328 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly_1 _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly_1 _Assembly.Entry_ID bmse012328 _Assembly.ID 1 _Assembly.Name 5-chloro-1H-pyrimidin-2-one _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 bmse012328 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 bmse012328 1 2 1 1 1 1 C2 C bmse012328 1 3 1 1 1 1 C3 C bmse012328 1 4 1 1 1 1 C4 C bmse012328 1 5 1 1 1 1 Cl5 Cl bmse012328 1 6 1 1 1 1 N6 N bmse012328 1 7 1 1 1 1 N7 N bmse012328 1 8 1 1 1 1 O8 O bmse012328 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_entity_1 _Entity.Sf_category entity _Entity.Sf_framecode entity_1 _Entity.Entry_ID bmse012328 _Entity.ID 1 _Entity.Name 5-chloro-1H-pyrimidin-2-one _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 130.53241999999997 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 bmse012328 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 bmse012328 _Chem_comp.Name 5-chloro-1H-pyrimidin-2-one _Chem_comp.Number_atoms_all 8 _Chem_comp.InChI_code InChI=1S/C4H3ClN2O/c5-3-1-6-4(8)7-2-3/h1-2H,(H,6,7,8) _Chem_comp.Formal_charge 0 _Chem_comp.Aromatic yes _Chem_comp.Formula C4H3ClN2O _Chem_comp.Formula_weight 130.53241999999997 _Chem_comp.Formula_mono_iso_wt_nat 129.993390406 _Chem_comp.Formula_mono_iso_wt_13C 134.006809758 _Chem_comp.Formula_mono_iso_wt_15N 131.98746019200001 _Chem_comp.Formula_mono_iso_wt_13C_15N 136.00087954400001 _Chem_comp.Image_file_name bmse012328.png _Chem_comp.Image_file_format png _Chem_comp.Struct_file_name bmse012328.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 Oc1ncc(Cl)cn1 SMILES_CANONICAL RDKit 2022.03.5 bmse012328 Oc1ncc(Cl)cn1 SMILES_ISOMERIC RDKit 2022.03.5 bmse012328 Oc1ncc(Cl)cn1 SMILES RDKit 2022.03.5 bmse012328 Clc1cnc(nc1)O SMILES_CANONICAL OpenBabel 3.1.0 bmse012328 Clc1cnc(nc1)O SMILES OpenBabel 3.1.0 bmse012328 InChI=1S/C4H3ClN2O/c5-3-1-6-4(8)7-2-3/h1-2H,(H,6,7,8) InChI OpenBabel 3.1.0 bmse012328 OCSYCDVQABSEPJ-UHFFFAOYSA-N InChI_KEY OpenBabel 3.1.0 bmse012328 InChI=1S/C4H3ClN2O/c5-3-1-6-4(8)7-2-3/h1-2H,(H,6,7,8) InChI ALATIS na bmse012328 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 yes 1 bmse012328 C2 C N 0 yes 2 bmse012328 C3 C N 0 yes 3 bmse012328 C4 C N 0 yes 4 bmse012328 Cl5 Cl N 0 no 5 bmse012328 N6 N N 0 yes 6 bmse012328 N7 N N 0 yes 7 bmse012328 O8 O N 0 no 8 bmse012328 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID C4 C1 ALATIS bmse012328 C6 C2 ALATIS bmse012328 C5 C3 ALATIS bmse012328 C1 C4 ALATIS bmse012328 Cl8 Cl5 ALATIS bmse012328 N3 N6 ALATIS bmse012328 N7 N7 ALATIS bmse012328 O2 O8 ALATIS bmse012328 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 AROM C1 C3 yes N 1 bmse012328 2 covalent AROM C2 N7 yes N 2 bmse012328 3 covalent AROM C3 C2 yes N 3 bmse012328 4 covalent SING C3 Cl5 no N 4 bmse012328 5 covalent AROM C4 N6 yes N 5 bmse012328 6 covalent AROM C4 N7 yes N 6 bmse012328 7 covalent SING C4 O8 no N 7 bmse012328 8 covalent AROM N6 C1 yes N 8 bmse012328 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 EOS103073 'compound ID' bmse012328 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID bmse012328 _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 5-chloro-1H-pyrimidin-2-one 'natural abundance' 1 $assembly_1 1 $entity_1 solute 2 mM bmse012328 1 2 'Sodium phosphate' 'natural abundance' . . . . buffer 25 mM bmse012328 1 3 'Sodium chloride' 'natural abundance' . . . . salt 150 mM bmse012328 1 4 DSS 'natural abundance' . . . . reference 10 uM bmse012328 1 5 H2O 'natural abundance' . . . . solvent 95 % bmse012328 1 6 DMSO '[2H U-100%]' . . . . solvent 5 % bmse012328 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 bmse012328 _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 bmse012328 1 pressure 1 . atm bmse012328 1 temperature 298 0.1 K bmse012328 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmse012328 _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/ bmse012328 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'data analysis' bmse012328 1 'peak picking' bmse012328 1 processing bmse012328 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 bmse012328 _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 bmse012328 _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 bmse012328 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/ bmse012328 1 1 cmcproject.xml text/xml 'spectrum analysis' nmr/set01/1/pdata/1/ bmse012328 1 1 multiplet.txt text 'Peak list' nmr/set01/1/pdata/1/ bmse012328 1 1 spectrum_overview.pdf pdf 'Spectrum image' nmr/set01/1/pdata/1/ bmse012328 1 1 spectrum_overview.png image/png 'Spectral image' nmr/set01/1/pdata/1/ bmse012328 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 bmse012328 _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 bmse012328 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 bmse012328 _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 bmse012328 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 bmse012328 1 stop_ loop_ _Peak.ID _Peak.Entry_ID _Peak.Spectral_peak_list_ID 1 bmse012328 1 2 bmse012328 1 3 bmse012328 1 4 bmse012328 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 4.6544 SUP bmse012328 1 2 1 2.5702 DMSO bmse012328 1 3 1 0.0357 TMS bmse012328 1 4 1 8.1765 3,4_s_Q1 bmse012328 1 stop_ loop_ _Spectral_transition.ID _Spectral_transition.Entry_ID _Spectral_transition.Spectral_peak_list_ID 1 bmse012328 1 2 bmse012328 1 3 bmse012328 1 4 bmse012328 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 4.6544 bmse012328 1 2 1 2.5702 bmse012328 1 3 1 0.0357 bmse012328 1 4 1 8.1765 bmse012328 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 bmse012328 1 2 2 1 0.0000 bmse012328 1 3 3 1 0.0000 bmse012328 1 4 4 1 0.0000 bmse012328 1 stop_ save_