data_bmse000386 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID bmse000386 _Entry.Title Malonic _Entry.Version_type original _Entry.Submission_date 2008-01-29 _Entry.Accession_date 2008-01-29 _Entry.Last_release_date 2008-01-29 _Entry.Original_release_date 2008-01-29 _Entry.Origination author _Entry.NMR_STAR_version 'NMR STAR v3.1' _Entry.Original_NMR_STAR_version 'NMR STAR v3.1' _Entry.Experimental_method NMR _Entry.Experimental_method_subtype solution _Entry.DOI 10.13018/BMSE000386 _Entry.BMRB_internal_directory_name Malonic_acid loop_ _Entry_author.Ordinal _Entry_author.Given_name _Entry_author.Family_name _Entry_author.Middle_initials _Entry_author.Entry_ID 1 Qiu Cui ? bmse000386 2 Ian Lewis ? bmse000386 3 Mark Anderson E. bmse000386 4 John Markley L. bmse000386 stop_ loop_ _Entry_src.ID _Entry_src.Project_name _Entry_src.Organization_full_name _Entry_src.Organization_initials _Entry_src.Entry_ID 1 metabolomics 'Madison Metabolomics Consortium' MMC bmse000386 stop_ loop_ _Data_set.Entry_ID bmse000386 stop_ loop_ _Datum.Entry_ID bmse000386 stop_ loop_ _Release.Release_number _Release.Format_type _Release.Format_version _Release.Date _Release.Submission_date _Release.Type _Release.Author _Release.Detail _Release.Entry_ID 1 . . 2008-01-29 2008-01-29 original BMRB 'Original spectra from MMC' bmse000386 2 . . 2008-02-28 2008-02-28 update BMRB 'Fixed mismatch between software ids and framecodes' bmse000386 3 . . 2008-07-09 2008-07-09 update BMRB 'fixed misplaced 2D coordinates' bmse000386 4 . . 2017-10-12 2017-10-12 update BMRB 'Remediated Experiment_file loop if present and standardized mol and png file tags.' bmse000386 5 . . 2017-12-19 2017-10-12 update BMRB 'InChI numbering updated according to ALATIS' bmse000386 stop_ save_ ############### # Citations # ############### save_citations _Citation.Sf_category citations _Citation.Sf_framecode citations _Citation.Entry_ID bmse000386 _Citation.ID 1 _Citation.Class 'reference citation' _Citation.PubMed_ID 17170002 _Citation.Title ; Database resources of the National Center for Biotechnology Information. ; _Citation.Status published _Citation.Type internet _Citation.WWW_URL http://pubchem.ncbi.nlm.nih.gov/ _Citation.Year 2006 loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Entry_ID _Citation_author.Citation_ID 1 D. Wheeler D. L. bmse000386 1 2 T. Barrett T. ? bmse000386 1 3 D. Benson D. A. bmse000386 1 4 S. Bryant S. H. bmse000386 1 5 K. Canese K. ? bmse000386 1 6 V. Chetvenin V. ? bmse000386 1 7 D. Church D. M. bmse000386 1 8 M. DiCuccio M. ? bmse000386 1 9 R. Edgar R. ? bmse000386 1 10 S. Federhen S. ? bmse000386 1 11 L. Geer L. Y. bmse000386 1 12 W. Helmberg W. ? bmse000386 1 13 Y. Kapustin Y. ? bmse000386 1 14 D. Kenton D. L. bmse000386 1 15 O. Khovayko O. ? bmse000386 1 16 D. Lipman D. J. bmse000386 1 17 T. Madden T. L. bmse000386 1 18 D. Maglott D. R. bmse000386 1 19 J. Ostell J. ? bmse000386 1 20 K. Pruitt K. D. bmse000386 1 21 G. Schuler G. D. bmse000386 1 22 L. Schriml L. M. bmse000386 1 23 E. Sequeira E. ? bmse000386 1 24 S. Sherry S. T. bmse000386 1 25 K. Sirotkin K. ? bmse000386 1 26 A. Souvorov A. ? bmse000386 1 27 G. Starchenko G. ? bmse000386 1 28 T. Suzek T. O. bmse000386 1 29 R. Tatusov R. ? bmse000386 1 30 T. Tatusova T. A. bmse000386 1 31 L. Bagner L. ? bmse000386 1 32 E. Yaschenko E. ? bmse000386 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_entity _Entity.Sf_category entity _Entity.Sf_framecode entity _Entity.Entry_ID bmse000386 _Entity.ID 1 _Entity.Name 'Malonic acid' _Entity.Type non-polymer _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_monomer no _Entity.Nstd_chirality no _Entity.Nstd_linkage no _Entity.Paramagnetic no _Entity.Thiol_state 'not reported' loop_ _Entity_comp_index.ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 1 $chem_comp_1 bmse000386 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 bmse000386 _Chem_comp.ID 1 _Chem_comp.Name 'Malonic acid' _Chem_comp.Type non-polymer _Chem_comp.BMRB_code bmse000386 _Chem_comp.InChI_code InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7) _Chem_comp.Formula 'C3 H4 O4' _Chem_comp.Formula_weight 104.06146 _Chem_comp.Formula_mono_iso_wt_nat 104.0109586168 _Chem_comp.Formula_mono_iso_wt_13C 107.0210231302 _Chem_comp.Formula_mono_iso_wt_15N 104.0109586168 _Chem_comp.Formula_mono_iso_wt_13C_15N 107.0210231302 _Chem_comp.Image_file_name bmse000386.png _Chem_comp.Image_file_format png _Chem_comp.Struct_file_name bmse000386.mol _Chem_comp.Struct_file_format mol loop_ _Chem_comp_common_name.Name _Chem_comp_common_name.Type _Chem_comp_common_name.Entry_ID _Chem_comp_common_name.Comp_ID 'Malonic acid' synonym bmse000386 1 HOOC-CH2-COOH synonym bmse000386 1 MALONATE synonym bmse000386 1 Malonate synonym bmse000386 1 H2malo synonym bmse000386 1 'Propanedioic acid' synonym bmse000386 1 'alpha,omega-Dicarboxylic acid' synonym bmse000386 1 'malonic acid' synonym bmse000386 1 'propanedioic acid' synonym bmse000386 1 MLI synonym bmse000386 1 'Dicarboxylic acid' synonym bmse000386 1 'Propanedioic acid Malonic Acid' synonym bmse000386 1 Dicarboxylate synonym bmse000386 1 'PROPANEDIOIC ACID MALONIC ACID' synonym bmse000386 1 'Malonate standard for IC' synonym bmse000386 1 stop_ loop_ _Chem_comp_descriptor.Descriptor _Chem_comp_descriptor.Type _Chem_comp_descriptor.Program _Chem_comp_descriptor.Program_version _Chem_comp_descriptor.Entry_ID _Chem_comp_descriptor.Comp_ID ; InChI=1/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)/f/h4,6H ; INCHI na na bmse000386 1 InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7) INCHI ALATIS 3.003 bmse000386 1 stop_ loop_ _Chem_comp_systematic_name.Name _Chem_comp_systematic_name.Naming_system _Chem_comp_systematic_name.Entry_ID _Chem_comp_systematic_name.Comp_ID 'Malonic acid' PUBCHEM_IUPAC_NAME bmse000386 1 'Malonic acid' PUBCHEM_IUPAC_TRADITIONAL_NAME bmse000386 1 'Malonic acid' PUBCHEM_IUPAC_OPENEYE_NAME bmse000386 1 'Malonic acid' PUBCHEM_IUPAC_CAS_NAME bmse000386 1 'Malonic acid' PUBCHEM_IUPAC_SYSTEMATIC_NAME bmse000386 1 stop_ loop_ _Chem_comp_SMILES.Type _Chem_comp_SMILES.String _Chem_comp_SMILES.Entry_ID _Chem_comp_SMILES.Comp_ID Canonical C(C(=O)O)C(=O)O bmse000386 1 Isomeric C(C(=O)O)C(=O)O bmse000386 1 stop_ loop_ _Chem_comp_atom.Atom_ID _Chem_comp_atom.Type_symbol _Chem_comp_atom.Drawing_2D_coord_x _Chem_comp_atom.Drawing_2D_coord_y _Chem_comp_atom.PDBX_ordinal _Chem_comp_atom.Entry_ID _Chem_comp_atom.Comp_ID O4 O 2.5369 0.7500 1 bmse000386 1 O6 O 6.0010 0.7500 2 bmse000386 1 O5 O 3.4030 -0.7500 3 bmse000386 1 O7 O 5.1350 -0.7500 4 bmse000386 1 C1 C 4.2690 0.7500 5 bmse000386 1 C2 C 3.4030 0.2500 6 bmse000386 1 C3 C 5.1350 0.2500 7 bmse000386 1 H8 H 4.6675 1.2250 8 bmse000386 1 H9 H 3.8705 1.2250 9 bmse000386 1 H10 H 2.0000 0.4400 10 bmse000386 1 H11 H 6.5380 0.4400 11 bmse000386 1 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID _Atom_nomenclature.Comp_ID O4 O1 BMRB bmse000386 1 O6 O2 BMRB bmse000386 1 O5 O3 BMRB bmse000386 1 O7 O4 BMRB bmse000386 1 C1 C5 BMRB bmse000386 1 C2 C6 BMRB bmse000386 1 C3 C7 BMRB bmse000386 1 H8 H8 BMRB bmse000386 1 H9 H9 BMRB bmse000386 1 H10 H10 BMRB bmse000386 1 H11 H11 BMRB bmse000386 1 O4 O4 ALATIS bmse000386 1 O6 O6 ALATIS bmse000386 1 O5 O5 ALATIS bmse000386 1 O7 O7 ALATIS bmse000386 1 C1 C1 ALATIS bmse000386 1 C2 C2 ALATIS bmse000386 1 C3 C3 ALATIS bmse000386 1 H8 H8 ALATIS bmse000386 1 H9 H9 ALATIS bmse000386 1 H10 H10 ALATIS bmse000386 1 H11 H11 ALATIS bmse000386 1 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.Entry_ID _Chem_comp_bond.Comp_ID 1 covalent SING O4 C2 bmse000386 1 2 covalent SING O4 H10 bmse000386 1 3 covalent SING O6 C3 bmse000386 1 4 covalent SING O6 H11 bmse000386 1 5 covalent DOUB O5 C2 bmse000386 1 6 covalent DOUB O7 C3 bmse000386 1 7 covalent SING C1 C2 bmse000386 1 8 covalent SING C1 C3 bmse000386 1 9 covalent SING C1 H8 bmse000386 1 10 covalent SING C1 H9 bmse000386 1 stop_ loop_ _Chem_comp_db_link.Author_supplied _Chem_comp_db_link.Database_code _Chem_comp_db_link.Accession_code _Chem_comp_db_link.Accession_code_type _Chem_comp_db_link.Entry_mol_name _Chem_comp_db_link.Entry_relation_type _Chem_comp_db_link.Entry_ID _Chem_comp_db_link.Comp_ID no PubChem 867 cid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 8145222 sid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 6731 sid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 2922 sid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 24872812 sid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 7991353 sid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 5582010 sid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 29196142 sid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 5122 sid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 3673 sid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 10507833 sid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 587339 sid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 7853147 sid 'Malonic acid' 'matching entry' bmse000386 1 no PubChem 38285850 sid 'Malonic acid' 'matching entry' bmse000386 1 no 'CAS Registry' 141-82-2 'registry number' 'Malonic acid' 'matching entry' bmse000386 1 no Sigma-Aldrich 49323_FLUKA ? 'Malonic acid' 'matching entry' bmse000386 1 no ChEBI CHEBI:30794 ? 'Malonic acid' 'matching entry' bmse000386 1 no 'CambridgeSoft Corporation' 5990 ? 'Malonic acid' 'matching entry' bmse000386 1 no 'EPA DSSTox' 1659 ? 'Malonic acid' 'matching entry' bmse000386 1 no BioCyc MALONATE ? 'Malonic acid' 'matching entry' bmse000386 1 no ChemSpider 11220390 ? 'Malonic acid' 'matching entry' bmse000386 1 no MMDB 60607.3 ? 'Malonic acid' 'matching entry' bmse000386 1 no NMRShiftDB 10005915 ? 'Malonic acid' 'matching entry' bmse000386 1 no KEGG C04025 'compound ID' 'Malonic acid' 'matching entry' bmse000386 1 no ChemDB 3969355 ? 'Malonic acid' 'matching entry' bmse000386 1 no 'NIST Chemistry WebBook' 888291099 ? 'Malonic acid' 'matching entry' bmse000386 1 stop_ loop_ _Chem_comp_citation.Citation_ID _Chem_comp_citation.Citation_label _Chem_comp_citation.Entry_ID _Chem_comp_citation.Comp_ID 1 $citations bmse000386 1 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID bmse000386 _Sample.ID 1 _Sample.Type solution loop_ _Sample_component.ID _Sample_component.Mol_common_name _Sample_component.Isotopic_labeling _Sample_component.Entity_ID _Sample_component.Entity_label _Sample_component.Type _Sample_component.Concentration_val _Sample_component.Concentration_val_units _Sample_component.Vendor _Sample_component.Vendor_product_name _Sample_component.Entry_ID _Sample_component.Sample_ID 1 'Malonic acid' 'natural abundance' 1 $entity Solute 100 mM sigma 'Malonic acid' bmse000386 1 2 D2O ? 1 ? Solvent 100 % ? ? bmse000386 1 3 'sodium phosphate' ? 1 ? Buffer 50 mM ? ? bmse000386 1 4 'sodium azide' ? 1 ? Cytocide 500 uM ? ? bmse000386 1 5 DSS ? 1 ? Reference 500 uM ? ? bmse000386 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 bmse000386 _Sample_condition_list.ID 1 loop_ _Sample_condition_variable.Type _Sample_condition_variable.Val _Sample_condition_variable.Val_units _Sample_condition_variable.Entry_ID _Sample_condition_variable.Sample_condition_list_ID pH 7.4 pH bmse000386 1 temperature 298 K bmse000386 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmse000386 _Software.ID 1 _Software.Name NMRPipe loop_ _Vendor.Name _Vendor.Entry_ID _Vendor.Software_ID 'F Delaglio, S Grzesiek, GW Vuister, G Zhu, J Pfeifer and A Bax' bmse000386 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID Processing bmse000386 1 stop_ save_ save_software_2 _Software.Sf_category software _Software.Sf_framecode software_2 _Software.Entry_ID bmse000386 _Software.ID 2 _Software.Name XWIN-NMR _Software.Version 3.5 loop_ _Vendor.Name _Vendor.Entry_ID _Vendor.Software_ID 'Bruker Biospin' bmse000386 2 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID Collection bmse000386 2 Processing bmse000386 2 'Data analysis' bmse000386 2 'Peak picking' bmse000386 2 stop_ save_ save_software_3 _Software.Sf_category software _Software.Sf_framecode software_3 _Software.Entry_ID bmse000386 _Software.ID 3 _Software.Name NMRDraw _Software.Version 2.3 loop_ _Vendor.Name _Vendor.Entry_ID _Vendor.Software_ID 'F Delaglio, S Grzesiek, GW Vuister, G Zhu, J Pfeifer and A Bax' bmse000386 3 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'Data analysis' bmse000386 3 'Peak picking' bmse000386 3 stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Bruker_DMX_500 _NMR_spectrometer.Sf_category NMR_spectrometer _NMR_spectrometer.Sf_framecode Bruker_DMX_500 _NMR_spectrometer.Entry_ID bmse000386 _NMR_spectrometer.ID 1 _NMR_spectrometer.Manufacturer Bruker _NMR_spectrometer.Model DMX _NMR_spectrometer.Field_strength 500 save_ ############################# # NMR applied experiments # ############################# save_experiment_list _Experiment_list.Sf_category experiment_list _Experiment_list.Sf_framecode experiment_list _Experiment_list.Entry_ID bmse000386 _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 $Bruker_DMX_500 bmse000386 1 2 '2D [1H,1H]-TOCSY' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000386 1 3 '1D 13C' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000386 1 4 '1D DEPT90' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000386 1 5 '1D DEPT135' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000386 1 6 '2D [1H,13C]-HSQC' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000386 1 7 '2D [1H,13C]-HMBC' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_500 bmse000386 1 stop_ loop_ _Experiment_file.Experiment_ID _Experiment_file.Name _Experiment_file.Type _Experiment_file.Directory_path _Experiment_file.Details _Experiment_file.Entry_ID _Experiment_file.Experiment_list_ID 1 1 text/directory nmr/set01 'NMR experiment directory' bmse000386 1 1 1H.png image/png nmr/set01/spectra 'Spectral image' bmse000386 1 2 2 text/directory nmr/set01 'NMR experiment directory' bmse000386 1 2 HH_TOCSY.png image/png nmr/set01/spectra 'Spectral image' bmse000386 1 3 3 text/directory nmr/set01 'NMR experiment directory' bmse000386 1 3 13C.png image/png nmr/set01/spectra 'Spectral image' bmse000386 1 4 4 text/directory nmr/set01 'NMR experiment directory' bmse000386 1 5 5 text/directory nmr/set01 'NMR experiment directory' bmse000386 1 6 6 text/directory nmr/set01 'NMR experiment directory' bmse000386 1 6 1H_13C_HSQC.png image/png nmr/set01/spectra 'Spectral image' bmse000386 1 7 7 text/directory nmr/set01 'NMR experiment directory' bmse000386 1 7 1H_13C_HMBC.png image/png nmr/set01/spectra 'Spectral image' bmse000386 1 stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference _Chem_shift_reference.Sf_category chem_shift_reference _Chem_shift_reference.Sf_framecode chem_shift_reference _Chem_shift_reference.Entry_ID bmse000386 _Chem_shift_reference.ID 1 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 0.00 internal direct 1.000000000 bmse000386 1 C 13 DSS 'methyl protons' ppm 0.00 ? indirect 0.251449530 bmse000386 1 stop_ save_