data_bmse000886 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID bmse000886 _Entry.Title adonitol _Entry.Version_type update _Entry.Submission_date 2011-12-23 _Entry.Accession_date 2011-12-23 _Entry.Last_release_date 2012-10-17 _Entry.Original_release_date 2011-12-23 _Entry.Origination author _Entry.NMR_STAR_version 3.1.1.21 _Entry.Original_NMR_STAR_version 3.1 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype solution _Entry.DOI 10.13018/BMSE000886 _Entry.BMRB_internal_directory_name adonitol loop_ _Entry_author.Ordinal _Entry_author.Given_name _Entry_author.Family_name _Entry_author.First_initial _Entry_author.Entry_ID 1 Dan Bearden D. bmse000886 stop_ loop_ _Entry_src.ID _Entry_src.Organization_full_name _Entry_src.Organization_initials _Entry_src.Entry_ID 1 'National Institute of Standards and Technology, Hollings Marine Laboratory' NIST bmse000886 stop_ loop_ _Release.Release_number _Release.Date _Release.Submission_date _Release.Type _Release.Author _Release.Detail _Release.Entry_ID 1 2012-01-05 2011-12-23 original BMRB 'Original spectra from Birmingham' bmse000886 2 2012-09-13 2011-12-23 update BMRB 'Added PubChem SID 134228453 to database loop' bmse000886 3 2012-09-18 2011-12-23 update BMRB 'Fixed bad reference concentrations in sample loops' bmse000886 4 2012-10-17 2011-12-23 update BMRB 'Set all _Chem_comp_SMILES Types to lower case' bmse000886 5 2017-10-12 2017-10-12 update BMRB 'Remediated Experiment_file loop if present and standardized mol and png file tags.' bmse000886 6 2017-12-19 2017-10-12 update BMRB 'InChI numbering updated according to ALATIS' bmse000886 stop_ save_ ############### # Citations # ############### save_citation_1 _Citation.Sf_category citations _Citation.Sf_framecode citation_1 _Citation.Entry_ID bmse000886 _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. bmse000886 1 2 T. Barrett T. ? bmse000886 1 3 D. Benson D. A. bmse000886 1 4 S. Bryant S. H. bmse000886 1 5 K. Canese K. ? bmse000886 1 6 V. Chetvenin V. ? bmse000886 1 7 D. Church D. M. bmse000886 1 8 M. DiCuccio M. ? bmse000886 1 9 R. Edgar R. ? bmse000886 1 10 S. Federhen S. ? bmse000886 1 11 L. Geer L. Y. bmse000886 1 12 W. Helmberg W. ? bmse000886 1 13 Y. Kapustin Y. ? bmse000886 1 14 D. Kenton D. L. bmse000886 1 15 O. Khovayko O. ? bmse000886 1 16 D. Lipman D. J. bmse000886 1 17 T. Madden T. L. bmse000886 1 18 D. Maglott D. R. bmse000886 1 19 J. Ostell J. ? bmse000886 1 20 K. Pruitt K. D. bmse000886 1 21 G. Schuler G. D. bmse000886 1 22 L. Schriml L. M. bmse000886 1 23 E. Sequeira E. ? bmse000886 1 24 S. Sherry S. T. bmse000886 1 25 K. Sirotkin K. ? bmse000886 1 26 A. Souvorov A. ? bmse000886 1 27 G. Starchenko G. ? bmse000886 1 28 T. Suzek T. O. bmse000886 1 29 R. Tatusov R. ? bmse000886 1 30 T. Tatusova T. A. bmse000886 1 31 L. Bagner L. ? bmse000886 1 32 E. Yaschenko E. ? bmse000886 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID bmse000886 _Assembly.ID 1 _Assembly.Name Adonitol _Assembly.Number_of_components 1 _Assembly.Organic_ligands 0 _Assembly.Non_standard_bonds no _Assembly.Paramagnetic no _Assembly.Thiol_state 'not reported' loop_ _Entity_assembly.ID _Entity_assembly.Entity_assembly_name _Entity_assembly.Entity_ID _Entity_assembly.Entity_label _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 adonitol 1 $adonitol yes native no no bmse000886 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_adonitol _Entity.Sf_category entity _Entity.Sf_framecode adonitol _Entity.Entry_ID bmse000886 _Entity.ID 1 _Entity.Name adonitol _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 bmse000886 1 stop_ save_ #################### # Natural source # #################### save_natural_source _Entity_natural_src_list.Sf_category natural_source _Entity_natural_src_list.Sf_framecode natural_source _Entity_natural_src_list.Entry_ID bmse000886 _Entity_natural_src_list.ID 1 loop_ _Entity_natural_src.ID _Entity_natural_src.Entity_ID _Entity_natural_src.Entity_label _Entity_natural_src.NCBI_taxonomy_ID _Entity_natural_src.Type _Entity_natural_src.Common _Entity_natural_src.Organism_name_scientific _Entity_natural_src.Organism_name_common _Entity_natural_src.Superkingdom _Entity_natural_src.Kingdom _Entity_natural_src.Genus _Entity_natural_src.Species _Entity_natural_src.Entry_ID _Entity_natural_src.Entity_natural_src_list_ID 1 1 $adonitol n/a 'multiple natural sources' yes 'not applicable' n/a n/a n/a n/a n/a bmse000886 1 stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Entity_experimental_src_list.Sf_category experimental_source _Entity_experimental_src_list.Sf_framecode experimental_source _Entity_experimental_src_list.Entry_ID bmse000886 _Entity_experimental_src_list.ID 1 loop_ _Entity_experimental_src.ID _Entity_experimental_src.Entity_ID _Entity_experimental_src.Entity_label _Entity_experimental_src.Production_method _Entity_experimental_src.Entry_ID _Entity_experimental_src.Entity_experimental_src_list_ID 1 1 $adonitol 'chemical synthesis' bmse000886 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 bmse000886 _Chem_comp.ID 1 _Chem_comp.Provenance PubChem _Chem_comp.Name Adonitol _Chem_comp.Type non-polymer _Chem_comp.InChI_code InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5+ _Chem_comp.Paramagnetic no _Chem_comp.Aromatic no _Chem_comp.Formula 'C5 H12 O5' _Chem_comp.Formula_weight 152.1457800000 _Chem_comp.Formula_mono_iso_wt_nat 152.068473496 _Chem_comp.Formula_mono_iso_wt_13C 157.085247685 _Chem_comp.Formula_mono_iso_wt_15N 152.068473496 _Chem_comp.Formula_mono_iso_wt_13C_15N 157.085247685 _Chem_comp.Image_file_name bmse000886.png _Chem_comp.Image_file_format png _Chem_comp.Struct_file_name bmse000886.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 Adonit synonym bmse000886 1 Adonite synonym bmse000886 1 Adonitol synonym bmse000886 1 1,2,3,4,5-Pentanepentol synonym bmse000886 1 Ribitol synonym bmse000886 1 Pentitol synonym bmse000886 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=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5? INCHI na na bmse000886 1 InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5+ INCHI ALATIS 3.003 bmse000886 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 pentane-1,2,3,4,5-pentol IUPAC bmse000886 1 pentane-1,2,3,4,5-pentol IUPAC_TRADITIONAL bmse000886 1 pentane-1,2,3,4,5-pentol IUPAC_CAS bmse000886 1 pentane-1,2,3,4,5-pentol IUPAC_OPENEYE bmse000886 1 pentane-1,2,3,4,5-pentol IUPAC_SYSTEMATIC bmse000886 1 stop_ loop_ _Chem_comp_SMILES.Type _Chem_comp_SMILES.String _Chem_comp_SMILES.Entry_ID _Chem_comp_SMILES.Comp_ID isomeric C(C(C(C(CO)O)O)O)O bmse000886 1 canonical C(C(C(C(CO)O)O)O)O bmse000886 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 O10 O 5.1350 -1.2500 1 bmse000886 1 O9 O 6.0010 1.2500 2 bmse000886 1 O8 O 4.2690 1.2500 3 bmse000886 1 O7 O 7.7331 0.2500 4 bmse000886 1 O6 O 2.5369 0.2500 5 bmse000886 1 C5 C 5.1350 -0.2500 6 bmse000886 1 C4 C 6.0010 0.2500 7 bmse000886 1 C3 C 4.2690 0.2500 8 bmse000886 1 C2 C 6.8671 -0.2500 9 bmse000886 1 C1 C 3.4030 -0.2500 10 bmse000886 1 H22 H 4.5981 -1.5600 11 bmse000886 1 H20 H 3.7321 1.5600 12 bmse000886 1 H21 H 6.5380 1.5600 13 bmse000886 1 H18 H 2.0000 -0.0600 14 bmse000886 1 H19 H 8.2700 -0.0600 15 bmse000886 1 H17 H 5.6719 -0.5600 16 bmse000886 1 H16 H 4.8059 0.5600 17 bmse000886 1 H15 H 6.5380 0.5600 18 bmse000886 1 H11 H 3.0044 -0.7249 19 bmse000886 1 H12 H 3.8015 -0.7249 20 bmse000886 1 H13 H 7.2656 -0.7249 21 bmse000886 1 H14 H 6.4685 -0.7249 22 bmse000886 1 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID _Atom_nomenclature.Comp_ID O10 O1 BMRB bmse000886 1 O9 O2 BMRB bmse000886 1 O8 O3 BMRB bmse000886 1 O7 O4 BMRB bmse000886 1 O6 O5 BMRB bmse000886 1 C5 C6 BMRB bmse000886 1 C4 C7 BMRB bmse000886 1 C3 C8 BMRB bmse000886 1 C2 C9 BMRB bmse000886 1 C1 C10 BMRB bmse000886 1 H22 H11 BMRB bmse000886 1 H20 H12 BMRB bmse000886 1 H21 H13 BMRB bmse000886 1 H18 H14 BMRB bmse000886 1 H19 H15 BMRB bmse000886 1 H17 H16 BMRB bmse000886 1 H16 H17 BMRB bmse000886 1 H15 H18 BMRB bmse000886 1 H11 H19 BMRB bmse000886 1 H12 H20 BMRB bmse000886 1 H13 H21 BMRB bmse000886 1 H14 H22 BMRB bmse000886 1 O10 O10 ALATIS bmse000886 1 O9 O9 ALATIS bmse000886 1 O8 O8 ALATIS bmse000886 1 O7 O7 ALATIS bmse000886 1 O6 O6 ALATIS bmse000886 1 C5 C5 ALATIS bmse000886 1 C4 C4 ALATIS bmse000886 1 C3 C3 ALATIS bmse000886 1 C2 C2 ALATIS bmse000886 1 C1 C1 ALATIS bmse000886 1 H22 H22 ALATIS bmse000886 1 H20 H20 ALATIS bmse000886 1 H21 H21 ALATIS bmse000886 1 H18 H18 ALATIS bmse000886 1 H19 H19 ALATIS bmse000886 1 H17 H17 ALATIS bmse000886 1 H16 H16 ALATIS bmse000886 1 H15 H15 ALATIS bmse000886 1 H11 H11 ALATIS bmse000886 1 H12 H12 ALATIS bmse000886 1 H13 H13 ALATIS bmse000886 1 H14 H14 ALATIS bmse000886 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 O10 C5 bmse000886 1 2 covalent SING O10 H22 bmse000886 1 3 covalent SING C4 O9 bmse000886 1 4 covalent SING O9 H21 bmse000886 1 5 covalent SING C3 O8 bmse000886 1 6 covalent SING O8 H20 bmse000886 1 7 covalent SING O7 C2 bmse000886 1 8 covalent SING O7 H19 bmse000886 1 9 covalent SING O6 C1 bmse000886 1 10 covalent SING O6 H18 bmse000886 1 11 covalent SING C5 C4 bmse000886 1 12 covalent SING C5 C3 bmse000886 1 13 covalent SING C5 H17 bmse000886 1 14 covalent SING C4 C2 bmse000886 1 15 covalent SING C4 H16 bmse000886 1 16 covalent SING C3 C1 bmse000886 1 17 covalent SING C3 H15 bmse000886 1 18 covalent SING C2 H13 bmse000886 1 19 covalent SING C2 H14 bmse000886 1 20 covalent SING C1 H11 bmse000886 1 21 covalent SING C1 H12 bmse000886 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 134228453 sid Adonitol 'matching entry' bmse000886 1 no PubChem 841607 sid Adonitol 'matching entry' bmse000886 1 no PubChem 153529 sid Adonitol 'matching entry' bmse000886 1 no PubChem 827 cid Adonitol 'matching entry' bmse000886 1 no PubChem 3757 sid Adonitol 'matching entry' bmse000886 1 no KEGG C00474 'compound ID' Adonitol 'matching entry' bmse000886 1 no 'CAS Registry' 28296-13-1 'registry number' Adonitol 'matching entry' bmse000886 1 no 'CAS Registry' 488-81-3 'registry number' Adonitol 'matching entry' bmse000886 1 no 'CAS Registry' 84709-28-4 'registry number' Adonitol 'matching entry' bmse000886 1 no CHEBI 15963 ? Adonitol 'matching entry' bmse000886 1 no EINECS 207-685-7 ? Adonitol 'matching entry' bmse000886 1 no 'Beilstein Handbook Reference' 4-01-00-02832 ? Adonitol 'matching entry' bmse000886 1 no NSC 16868 ? Adonitol 'matching entry' bmse000886 1 stop_ loop_ _Chem_comp_citation.Citation_ID _Chem_comp_citation.Citation_label _Chem_comp_citation.Entry_ID _Chem_comp_citation.Comp_ID 1 $citation_1 bmse000886 1 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID bmse000886 _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 adonitol 'natural abundance' 1 $adonitol Solute 20 mM sigma adonitol bmse000886 1 2 D2O ? ? ? Solvent 100 % ? ? bmse000886 1 3 'sodium phosphate' ? ? ? Buffer 200 mM ? ? bmse000886 1 4 'sodium azide' ? ? ? Cytocide 500 uM ? ? bmse000886 1 5 DSS ? ? ? Reference 500 uM ? ? bmse000886 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 bmse000886 _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 bmse000886 1 temperature 298 K bmse000886 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmse000886 _Software.ID 1 _Software.Name TopSpin _Software.Version 2.1 loop_ _Vendor.Name _Vendor.Entry_ID _Vendor.Software_ID 'Bruker Biospin' bmse000886 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID Collection bmse000886 1 Processing bmse000886 1 'Data analysis' bmse000886 1 'Peak picking' bmse000886 1 stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Bruker_700 _NMR_spectrometer.Sf_category NMR_spectrometer _NMR_spectrometer.Sf_framecode Bruker_700 _NMR_spectrometer.Entry_ID bmse000886 _NMR_spectrometer.ID 1 _NMR_spectrometer.Manufacturer Bruker _NMR_spectrometer.Model 'Avance II' _NMR_spectrometer.Field_strength 700 save_ save_TCI_cryoprobe _NMR_spectrometer_probe.Sf_category NMR_spectrometer_probe _NMR_spectrometer_probe.Sf_framecode TCI_cryoprobe _NMR_spectrometer_probe.Entry_ID bmse000886 _NMR_spectrometer_probe.ID 1 _NMR_spectrometer_probe.Details 'single z-axis gradient' _NMR_spectrometer_probe.Manufacturer Bruker _NMR_spectrometer_probe.Model 'TCI CryoProbe' _NMR_spectrometer_probe.Diameter 5 loop_ _NMR_probe.Type _NMR_probe.Entry_ID _NMR_probe.NMR_spectrometer_probe_ID Cryoprobe bmse000886 1 stop_ save_ ############################# # NMR applied experiments # ############################# save_experiment_list _Experiment_list.Sf_category experiment_list _Experiment_list.Sf_framecode experiment_list _Experiment_list.Entry_ID bmse000886 _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 '2D J-resolved 1H' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_700 bmse000886 1 2 '2D [1H,13C]-HSQC' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_700 bmse000886 1 3 '1D 1H, NOESY' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_700 bmse000886 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 1H_1H_JRES text/directory nmr/set01/ 'NMR experiment directory' bmse000886 1 1 00.png image/png nmr/set01/spectra/1H_1H_JRES 'Spectral image' bmse000886 1 1 01.png image/png nmr/set01/spectra/1H_1H_JRES 'Spectral image' bmse000886 1 2 1H_13C_HSQC text/directory nmr/set01/ 'NMR experiment directory' bmse000886 1 2 00.png image/png nmr/set01/spectra/1H_13C_HSQC 'Spectral image' bmse000886 1 2 01.png image/png nmr/set01/spectra/1H_13C_HSQC 'Spectral image' bmse000886 1 3 1H_NOESY text/directory nmr/set01/ 'NMR experiment directory' bmse000886 1 3 00.png image/png nmr/set01/spectra/1H_NOESY 'Spectral image' bmse000886 1 3 01.png image/png nmr/set01/spectra/1H_NOESY 'Spectral image' bmse000886 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 bmse000886 _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 bmse000886 1 C 13 DSS 'methyl carbons' ppm 0.00 internal direct 1.000000000 bmse000886 1 stop_ save_