data_bmse011906 ####################### # Entry information # ####################### save_entry_information_1 _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information_1 _Entry.ID bmse011906 _Entry.Title [(2S)-1-(2,3-dihydroindol-1-yl)-1-oxopropan-2-yl]urea _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/bmse011906 loop_ _Entry_experimental_methods.ID _Entry_experimental_methods.Method _Entry_experimental_methods.Subtype _Entry_experimental_methods.Entry_ID 1 NMR solution bmse011906 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. bmse011906 2 Christian Richter C. bmse011906 3 Harald Schwalbe H. bmse011906 4 Hannes Berg . bmse011906 stop_ loop_ _Entry_src.ID _Entry_src.Project_name _Entry_src.Entry_ID 1 EUOS bmse011906 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 bmse011906 stop_ loop_ _Auxiliary_files.ID _Auxiliary_files.Name _Auxiliary_files.Format _Auxiliary_files.URI _Auxiliary_files.Details _Auxiliary_files.Entry_ID 1 bmse011906.mol sdf na 'Structure Definition File' bmse011906 stop_ save_ ############### # Citations # ############### save_citations_1 _Citation.Sf_category citations _Citation.Sf_framecode citations_1 _Citation.Entry_ID bmse011906 _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. bmse011906 1 2 Christian Richter C. bmse011906 1 3 Till Kuehn T. bmse011906 1 4 Kamal Azzaoui K. bmse011906 1 5 'Marcel Jules Jose' Blommers . bmse011906 1 6 Rebecca 'Del Conte' R. bmse011906 1 7 Marco Fragai M. bmse011906 1 8 Nils Trieloff N. bmse011906 1 9 Peter Schmieder P. bmse011906 1 10 Marc Nazare M. bmse011906 1 11 Edgar Specker E. bmse011906 1 12 Vladimir Ivanov V. bmse011906 1 13 Hartmut Oschkinat H. bmse011906 1 14 Lucia Banci L. bmse011906 1 15 Harald Schwalbe H. bmse011906 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly_1 _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly_1 _Assembly.Entry_ID bmse011906 _Assembly.ID 1 _Assembly.Name [(2S)-1-(2,3-dihydroindol-1-yl)-1-oxopropan-2-yl]urea _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 bmse011906 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 bmse011906 1 2 1 1 1 1 C2 C bmse011906 1 3 1 1 1 1 C3 C bmse011906 1 4 1 1 1 1 C4 C bmse011906 1 5 1 1 1 1 C5 C bmse011906 1 6 1 1 1 1 C6 C bmse011906 1 7 1 1 1 1 C7 C bmse011906 1 8 1 1 1 1 C8 C bmse011906 1 9 1 1 1 1 C9 C bmse011906 1 10 1 1 1 1 C10 C bmse011906 1 11 1 1 1 1 C11 C bmse011906 1 12 1 1 1 1 C12 C bmse011906 1 13 1 1 1 1 N13 N bmse011906 1 14 1 1 1 1 N14 N bmse011906 1 15 1 1 1 1 N15 N bmse011906 1 16 1 1 1 1 O16 O bmse011906 1 17 1 1 1 1 O17 O bmse011906 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_entity_1 _Entity.Sf_category entity _Entity.Sf_framecode entity_1 _Entity.Entry_ID bmse011906 _Entity.ID 1 _Entity.Name [(2S)-1-(2,3-dihydroindol-1-yl)-1-oxopropan-2-yl]urea _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 233.2664 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 bmse011906 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 bmse011906 _Chem_comp.Name [(2S)-1-(2,3-dihydroindol-1-yl)-1-oxopropan-2-yl]urea _Chem_comp.Number_atoms_all 17 _Chem_comp.InChI_code InChI=1S/C12H15N3O2/c1-8(14-12(13)17)11(16)15-7-6-9-4-2-3-5-10(9)15/h2-5,8H,6-7H2,1H3,(H3,13,14,17)/t8-/m0/s1 _Chem_comp.Formal_charge 0 _Chem_comp.Aromatic yes _Chem_comp.Formula C12H15N3O2 _Chem_comp.Formula_weight 233.2664 _Chem_comp.Formula_mono_iso_wt_nat 233.116426735 _Chem_comp.Formula_mono_iso_wt_13C 245.15668479100006 _Chem_comp.Formula_mono_iso_wt_15N 236.10753141400002 _Chem_comp.Formula_mono_iso_wt_13C_15N 248.14778947000008 _Chem_comp.Image_file_name bmse011906.png _Chem_comp.Image_file_format png _Chem_comp.Struct_file_name bmse011906.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 C[C@H](NC(N)=O)C(=O)N1CCc2ccccc21 SMILES_CANONICAL RDKit 2022.03.5 bmse011906 C[C@H](NC(N)=O)C(=O)N1CCc2ccccc21 SMILES_ISOMERIC RDKit 2022.03.5 bmse011906 C[C@H](NC(N)=O)C(=O)N1CCc2ccccc21 SMILES RDKit 2022.03.5 bmse011906 NC(=O)N[C@H](C(=O)N1CCc2c1cccc2)C SMILES_CANONICAL OpenBabel 3.1.0 bmse011906 NC(=O)N[C@H](C(=O)N1CCc2c1cccc2)C SMILES OpenBabel 3.1.0 bmse011906 InChI=1S/C12H15N3O2/c1-8(14-12(13)17)11(16)15-7-6-9-4-2-3-5-10(9)15/h2-5,8H,6-7H2,1H3,(H3,13,14,17)/t8-/m0/s1 InChI OpenBabel 3.1.0 bmse011906 ZIRVFIXBVPVFGN-QMMMGPOBSA-N InChI_KEY OpenBabel 3.1.0 bmse011906 InChI=1S/C12H15N3O2/c1-8(14-12(13)17)11(16)15-7-6-9-4-2-3-5-10(9)15/h2-5,8H,6-7H2,1H3,(H3,13,14,17)/t8-/m0/s1 InChI ALATIS na bmse011906 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 bmse011906 C2 C N 0 yes 2 bmse011906 C3 C N 0 yes 3 bmse011906 C4 C N 0 yes 4 bmse011906 C5 C N 0 yes 5 bmse011906 C6 C N 0 no 6 bmse011906 C7 C N 0 no 7 bmse011906 C8 C S 0 no 8 bmse011906 C9 C N 0 yes 9 bmse011906 C10 C N 0 yes 10 bmse011906 C11 C N 0 no 11 bmse011906 C12 C N 0 no 12 bmse011906 N13 N N 0 no 13 bmse011906 N14 N N 0 no 14 bmse011906 N15 N N 0 no 15 bmse011906 O16 O N 0 no 16 bmse011906 O17 O N 0 no 17 bmse011906 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID C14 C1 ALATIS bmse011906 C17 C2 ALATIS bmse011906 C16 C3 ALATIS bmse011906 C15 C4 ALATIS bmse011906 C13 C5 ALATIS bmse011906 C11 C6 ALATIS bmse011906 C6 C7 ALATIS bmse011906 C7 C8 ALATIS bmse011906 C9 C9 ALATIS bmse011906 C3 C10 ALATIS bmse011906 C2 C11 ALATIS bmse011906 C4 C12 ALATIS bmse011906 N12 N13 ALATIS bmse011906 N5 N14 ALATIS bmse011906 N1 N15 ALATIS bmse011906 O8 O16 ALATIS bmse011906 O10 O17 ALATIS bmse011906 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 C3 C2 yes N 1 bmse011906 2 covalent AROM C4 C2 yes N 2 bmse011906 3 covalent AROM C5 C3 yes N 3 bmse011906 4 covalent SING C7 C6 no N 4 bmse011906 5 covalent SING C8 C1 no N 5 bmse011906 6 covalent AROM C9 C4 yes N 6 bmse011906 7 covalent SING C9 C6 no N 7 bmse011906 8 covalent AROM C10 C5 yes N 8 bmse011906 9 covalent AROM C10 C9 yes N 9 bmse011906 10 covalent SING C11 C8 no N 10 bmse011906 11 carbonyl DOUB C11 O16 no N 11 bmse011906 12 amide SING C12 N13 no N 12 bmse011906 13 amide SING C12 N14 no N 13 bmse011906 14 carbonyl DOUB C12 O17 no N 14 bmse011906 15 covalent SING N14 C8 no N 15 bmse011906 16 covalent SING N15 C7 no N 16 bmse011906 17 covalent SING N15 C10 no N 17 bmse011906 18 amide SING N15 C11 no N 18 bmse011906 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 EOS102613 'compound ID' bmse011906 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID bmse011906 _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 [(2S)-1-(2,3-dihydroindol-1-yl)-1-oxopropan-2-yl]urea 'natural abundance' 1 $assembly_1 1 $entity_1 solute 2 mM bmse011906 1 2 'Sodium phosphate' 'natural abundance' . . . . buffer 25 mM bmse011906 1 3 'Sodium chloride' 'natural abundance' . . . . salt 150 mM bmse011906 1 4 DSS 'natural abundance' . . . . reference 10 uM bmse011906 1 5 H2O 'natural abundance' . . . . solvent 95 % bmse011906 1 6 DMSO '[2H U-100%]' . . . . solvent 5 % bmse011906 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 bmse011906 _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 bmse011906 1 pressure 1 . atm bmse011906 1 temperature 298 0.1 K bmse011906 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmse011906 _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/ bmse011906 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'data analysis' bmse011906 1 'peak picking' bmse011906 1 processing bmse011906 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 bmse011906 _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 bmse011906 _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 bmse011906 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/ bmse011906 1 1 cmcproject.xml text/xml 'spectrum analysis' nmr/set01/1/pdata/1/ bmse011906 1 1 multiplet.txt text 'Peak list' nmr/set01/1/pdata/1/ bmse011906 1 1 spectrum_overview.pdf pdf 'Spectrum image' nmr/set01/1/pdata/1/ bmse011906 1 1 spectrum_overview.png image/png 'Spectral image' nmr/set01/1/pdata/1/ bmse011906 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 bmse011906 _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 bmse011906 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 bmse011906 _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 bmse011906 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 bmse011906 1 stop_ loop_ _Peak.ID _Peak.Entry_ID _Peak.Spectral_peak_list_ID 1 bmse011906 1 2 bmse011906 1 3 bmse011906 1 4 bmse011906 1 5 bmse011906 1 6 bmse011906 1 7 bmse011906 1 8 bmse011906 1 9 bmse011906 1 10 bmse011906 1 11 bmse011906 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 3.1469 14_m bmse011906 1 2 1 7.0592 16_dd_Q1 bmse011906 1 3 1 4.6544 SUP bmse011906 1 4 1 7.1623 17_dd_Q2 bmse011906 1 5 1 2.5704 DMSO bmse011906 1 6 1 5.5932 4_m bmse011906 1 7 1 7.9340 15_d bmse011906 1 8 1 6.6372 3_d bmse011906 1 9 1 7.2502 13_d_Q3 bmse011906 1 10 1 0.0350 TMS bmse011906 1 11 1 1.2715 7_d bmse011906 1 stop_ loop_ _Spectral_transition.ID _Spectral_transition.Entry_ID _Spectral_transition.Spectral_peak_list_ID 1 bmse011906 1 2 bmse011906 1 3 bmse011906 1 4 bmse011906 1 5 bmse011906 1 6 bmse011906 1 7 bmse011906 1 8 bmse011906 1 9 bmse011906 1 10 bmse011906 1 11 bmse011906 1 12 bmse011906 1 13 bmse011906 1 14 bmse011906 1 15 bmse011906 1 16 bmse011906 1 17 bmse011906 1 18 bmse011906 1 19 bmse011906 1 20 bmse011906 1 21 bmse011906 1 22 bmse011906 1 23 bmse011906 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 3.1618 bmse011906 1 2 1 3.1471 bmse011906 1 3 1 3.1320 bmse011906 1 4 1 7.0718 bmse011906 1 5 1 7.0591 bmse011906 1 6 1 7.0591 bmse011906 1 7 1 7.0466 bmse011906 1 8 1 4.6544 bmse011906 1 9 1 7.1760 bmse011906 1 10 1 7.1623 bmse011906 1 11 1 7.1623 bmse011906 1 12 1 7.1486 bmse011906 1 13 1 2.5704 bmse011906 1 14 1 5.5932 bmse011906 1 15 1 7.9413 bmse011906 1 16 1 7.9268 bmse011906 1 17 1 6.6411 bmse011906 1 18 1 6.6333 bmse011906 1 19 1 7.2567 bmse011906 1 20 1 7.2437 bmse011906 1 21 1 0.0350 bmse011906 1 22 1 1.2774 bmse011906 1 23 1 1.2656 bmse011906 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 8.9499 bmse011906 1 2 2 1 7.5560 bmse011906 1 3 3 1 0.0000 bmse011906 1 4 4 1 8.2163 bmse011906 1 5 5 1 0.0000 bmse011906 1 6 6 1 0.0000 bmse011906 1 7 7 1 0.0000 bmse011906 1 8 8 1 0.0000 bmse011906 1 9 9 1 0.0000 bmse011906 1 10 10 1 0.0000 bmse011906 1 11 11 1 0.0000 bmse011906 1 stop_ save_