data_bmse000879 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID bmse000879 _Entry.Title dGMP _Entry.Version_type update _Entry.Submission_date 2011-11-23 _Entry.Accession_date 2011-11-23 _Entry.Last_release_date 2012-10-17 _Entry.Original_release_date 2011-11-23 _Entry.Origination author _Entry.NMR_STAR_version 3.1.1.21 _Entry.Original_NMR_STAR_version 3.1.1.7 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype solution _Entry.DOI 10.13018/BMSE000879 _Entry.BMRB_internal_directory_name dGMP loop_ _Entry_author.Ordinal _Entry_author.Given_name _Entry_author.Family_name _Entry_author.Middle_initials _Entry_author.Entry_ID 1 Francisca Jofre ? bmse000879 2 Mark Anderson E. bmse000879 3 John Markley L. bmse000879 4 Melanie Ulrich E. bmse000879 stop_ loop_ _Entry_src.ID _Entry_src.Project_name _Entry_src.Organization_full_name _Entry_src.Organization_initials _Entry_src.Entry_ID 1 metabolomics 'National Magnetic Facility at Madison' NMRFAM bmse000879 2 metabolomics 'Biological Magnetic Resonance Bank' BMRB bmse000879 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID assigned_chemical_shifts 1 bmse000879 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID '13C chemical shifts' 12 bmse000879 '1H chemical shifts' 10 bmse000879 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 . . 2011-11-23 2011-11-23 original BMRB 'Original spectra from BMRB' bmse000879 2 . . 2011-12-14 2011-11-23 update BMRB 'Set Assembly.Name to match Chem_comp.name' bmse000879 3 . . 2012-09-13 2011-11-23 update BMRB 'Added PubChem SID 134228446 to database loop' bmse000879 4 . . 2012-09-18 2011-11-23 update BMRB 'Fixed bad reference concentrations in sample loops' bmse000879 5 . . 2012-10-12 2011-11-23 update BMRB 'Set assigned_chemical_shifts with data from bmse000824' bmse000879 6 . . 2012-10-17 2011-11-23 update BMRB 'Set all _Chem_comp_SMILES Types to lower case' bmse000879 7 . . 2017-10-12 2017-10-12 update BMRB 'Remediated Experiment_file loop if present and standardized mol and png file tags.' bmse000879 8 . . 2017-12-19 2017-10-12 update BMRB 'InChI numbering updated according to ALATIS' bmse000879 stop_ save_ ############### # Citations # ############### save_citation_1 _Citation.Sf_category citations _Citation.Sf_framecode citation_1 _Citation.Entry_ID bmse000879 _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. bmse000879 1 2 T. Barrett T. ? bmse000879 1 3 D. Benson D. A. bmse000879 1 4 S. Bryant S. H. bmse000879 1 5 K. Canese K. ? bmse000879 1 6 V. Chetvenin V. ? bmse000879 1 7 D. Church D. M. bmse000879 1 8 M. DiCuccio M. ? bmse000879 1 9 R. Edgar R. ? bmse000879 1 10 S. Federhen S. ? bmse000879 1 11 L. Geer L. Y. bmse000879 1 12 W. Helmberg W. ? bmse000879 1 13 Y. Kapustin Y. ? bmse000879 1 14 D. Kenton D. L. bmse000879 1 15 O. Khovayko O. ? bmse000879 1 16 D. Lipman D. J. bmse000879 1 17 T. Madden T. L. bmse000879 1 18 D. Maglott D. R. bmse000879 1 19 J. Ostell J. ? bmse000879 1 20 K. Pruitt K. D. bmse000879 1 21 G. Schuler G. D. bmse000879 1 22 L. Schriml L. M. bmse000879 1 23 E. Sequeira E. ? bmse000879 1 24 S. Sherry S. T. bmse000879 1 25 K. Sirotkin K. ? bmse000879 1 26 A. Souvorov A. ? bmse000879 1 27 G. Starchenko G. ? bmse000879 1 28 T. Suzek T. O. bmse000879 1 29 R. Tatusov R. ? bmse000879 1 30 T. Tatusova T. A. bmse000879 1 31 L. Bagner L. ? bmse000879 1 32 E. Yaschenko E. ? bmse000879 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID bmse000879 _Assembly.ID 1 _Assembly.Name "2'-Deoxyguanosine 5'-monophosphate" _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 "2'-Deoxyguanosine 5'-monophosphate" 1 $2-Deoxyguanosine-5-monophosphate yes native no no bmse000879 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_2-Deoxyguanosine-5-monophosphate _Entity.Sf_category entity _Entity.Sf_framecode 2-Deoxyguanosine-5-monophosphate _Entity.Entry_ID bmse000879 _Entity.ID 1 _Entity.Name "2'-Deoxyguanosine 5'-monophosphate" _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 bmse000879 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 bmse000879 _Entity_natural_src_list.ID 1 loop_ _Entity_natural_src.ID _Entity_natural_src.Entity_ID _Entity_natural_src.Entity_label _Entity_natural_src.Organism_name_scientific _Entity_natural_src.Entry_ID _Entity_natural_src.Entity_natural_src_list_ID 1 1 $2-Deoxyguanosine-5-monophosphate 'not applicable' bmse000879 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 bmse000879 _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 $2-Deoxyguanosine-5-monophosphate 'chemical synthesis' bmse000879 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 bmse000879 _Chem_comp.ID 1 _Chem_comp.Name "2'-Deoxyguanosine 5'-monophosphate" _Chem_comp.Type non-polymer _Chem_comp.BMRB_code bmse000824 _Chem_comp.InChI_code InChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1 _Chem_comp.Paramagnetic no _Chem_comp.Aromatic yes _Chem_comp.Formula 'C10 H14 N5 O7 P' _Chem_comp.Formula_weight 347.221221 _Chem_comp.Formula_mono_iso_wt_nat 347.0630843401 _Chem_comp.Formula_mono_iso_wt_13C 357.0966327181 _Chem_comp.Formula_mono_iso_wt_15N 352.0482588061 _Chem_comp.Formula_mono_iso_wt_13C_15N 362.0818071841 _Chem_comp.Image_file_name bmse000879.png _Chem_comp.Image_file_format png _Chem_comp.Struct_file_name bmse000879.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 dGMP synonym bmse000879 1 GMP synonym bmse000879 1 "2'-Deoxyguanylic acid" synonym bmse000879 1 2'-dGMP synonym bmse000879 1 'Deoxyguanosine monophosphate' synonym bmse000879 1 deoxyguanosine-phosphate synonym bmse000879 1 2'-Deoxy-5'-GMP synonym bmse000879 1 "2'-Deoxyguanosine 5'-monophosphate" synonym bmse000879 1 "2'-Deoxyguanosine 5'-phosphate" synonym bmse000879 1 'guanine riboside' synonym bmse000879 1 "Guanosine, 2'-deoxy-, 5'-(dihydrogen phosphate)" synonym bmse000879 1 Deoxy-GMP synonym bmse000879 1 "Guanosine, 2'-deoxy-, 5'-phosphoric acid" synonym bmse000879 1 "2'-Deoxy-5'-guanylic acid" synonym bmse000879 1 vernine synonym bmse000879 1 "Guanosine, 2'-deoxy-, 5'-(dihydrogen phosphate) (8CI)" synonym bmse000879 1 "5'-Guanylic acid, 2'-deoxy-" synonym bmse000879 1 "Deoxyguanosine 5'-monophosphate" synonym bmse000879 1 "Deoxyguanosine 5'-phosphate" synonym bmse000879 1 "5'-Guanylic acid, 2'-deoxy- (9CI)" synonym bmse000879 1 5'-DGMP synonym bmse000879 1 "2'-Deoxyguanosine 5'MP" synonym bmse000879 1 Deoxyguanylate synonym bmse000879 1 'Deoxyguanylic acid' synonym bmse000879 1 "Guanosine, 2'-deoxy-, 5'-phosphate (6CI)" synonym bmse000879 1 '6H-purin-6-one, 2-amino-9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,9-dihydro-' synonym bmse000879 1 'Deoxy GMP' synonym bmse000879 1 2'-dG-5'-MP synonym bmse000879 1 "5'-Deoxyguanylic acid" synonym bmse000879 1 "2'-Deoxyguanosine 5'-phosphoric acid" synonym bmse000879 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/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1 ; INCHI na na bmse000879 1 InChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1 INCHI ALATIS 3.003 bmse000879 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 '[(2R,3S,5R)-5-(2-amino-6-oxo-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl dihydrogen phosphate' PUBCHEM_IUPAC_NAME bmse000879 1 ; [(2R,3S,5R)-5-(2-amino-6-keto-3H-purin-9-yl)-3-hydroxy-tetrahydrofuran-2-yl]methyl dihydrogen phosphate ; PUBCHEM_IUPAC_TRADITIONAL_NAME bmse000879 1 ; [(2R,3S,5R)-5-(2-amino-6-oxo-3H-purin-9-yl)-3-hydroxy-tetrahydrofuran-2-yl]methyl dihydrogen phosphate ; PUBCHEM_IUPAC_OPENEYE_NAME bmse000879 1 '[(2R,3S,5R)-5-(2-amino-6-oxo-3H-purin-9-yl)-3-hydroxy-2-oxolanyl]methyl dihydrogen phosphate' PUBCHEM_IUPAC_CAS_NAME bmse000879 1 ; [(2R,3S,5R)-5-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate ; PUBCHEM_IUPAC_SYSTEMATIC_NAME bmse000879 1 stop_ loop_ _Chem_comp_SMILES.Type _Chem_comp_SMILES.String _Chem_comp_SMILES.Entry_ID _Chem_comp_SMILES.Comp_ID canonical C1C(C(OC1N2C=NC3=C2NC(=NC3=O)N)COP(=O)(O)O)O bmse000879 1 isomeric C1[C@@H]([C@H](O[C@H]1N2C=NC3=C2NC(=NC3=O)N)COP(=O)(O)O)O bmse000879 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 P23 P 9.8781 2.4346 1 bmse000879 1 O22 O 7.3435 0.6702 2 bmse000879 1 O16 O 6.0873 2.9324 3 bmse000879 1 O21 O 9.0681 1.8482 4 bmse000879 1 O18 O 10.6882 3.0210 5 bmse000879 1 O19 O 10.4645 1.6246 6 bmse000879 1 O17 O 4.2690 -3.3924 7 bmse000879 1 O20 O 9.2917 3.2446 8 bmse000879 1 N15 N 6.0812 -0.5877 9 bmse000879 1 N13 N 4.2690 -0.3925 10 bmse000879 1 N12 N 6.0812 -2.1972 11 bmse000879 1 N14 N 3.4030 -1.8924 12 bmse000879 1 N11 N 2.5369 -0.3925 13 bmse000879 1 C6 C 6.3919 0.3628 14 bmse000879 1 C4 C 6.3947 1.9808 15 bmse000879 1 C1 C 5.8055 1.1728 16 bmse000879 1 C5 C 7.3452 1.6702 17 bmse000879 1 C2 C 8.1552 2.2566 18 bmse000879 1 C8 C 5.1350 -0.8925 19 bmse000879 1 C3 C 6.6648 -1.3924 20 bmse000879 1 C7 C 5.1350 -1.8924 21 bmse000879 1 C9 C 4.2690 -2.3925 22 bmse000879 1 C10 C 3.4030 -0.8925 23 bmse000879 1 H31 H 5.7794 0.2669 24 bmse000879 1 H29 H 5.7825 2.0789 25 bmse000879 1 H24 H 5.3455 1.5885 26 bmse000879 1 H25 H 5.3440 0.7588 27 bmse000879 1 H30 H 7.8972 1.3877 28 bmse000879 1 H26 H 8.5028 2.7700 29 bmse000879 1 H27 H 7.7100 2.6880 30 bmse000879 1 H35 H 6.5030 3.3924 31 bmse000879 1 H28 H 7.2848 -1.3924 32 bmse000879 1 H34 H 4.2690 0.2275 33 bmse000879 1 H32 H 2.0000 -0.7025 34 bmse000879 1 H33 H 2.5369 0.2275 35 bmse000879 1 H37 H 10.2113 1.0586 36 bmse000879 1 H36 H 11.2541 2.7678 37 bmse000879 1 stop_ loop_ _Atom_nomenclature.Atom_ID _Atom_nomenclature.Atom_name _Atom_nomenclature.Naming_system _Atom_nomenclature.Entry_ID _Atom_nomenclature.Comp_ID P23 P1 BMRB bmse000879 1 O22 O2 BMRB bmse000879 1 O16 O3 BMRB bmse000879 1 O21 O4 BMRB bmse000879 1 O18 O5 BMRB bmse000879 1 O19 O6 BMRB bmse000879 1 O17 O7 BMRB bmse000879 1 O20 O8 BMRB bmse000879 1 N15 N9 BMRB bmse000879 1 N13 N10 BMRB bmse000879 1 N12 N11 BMRB bmse000879 1 N14 N12 BMRB bmse000879 1 N11 N13 BMRB bmse000879 1 C6 C14 BMRB bmse000879 1 C4 C15 BMRB bmse000879 1 C1 C16 BMRB bmse000879 1 C5 C17 BMRB bmse000879 1 C2 C18 BMRB bmse000879 1 C8 C19 BMRB bmse000879 1 C3 C20 BMRB bmse000879 1 C7 C21 BMRB bmse000879 1 C9 C22 BMRB bmse000879 1 C10 C23 BMRB bmse000879 1 H31 H24 BMRB bmse000879 1 H29 H25 BMRB bmse000879 1 H24 H26 BMRB bmse000879 1 H25 H27 BMRB bmse000879 1 H30 H28 BMRB bmse000879 1 H26 H29 BMRB bmse000879 1 H27 H30 BMRB bmse000879 1 H35 H31 BMRB bmse000879 1 H28 H32 BMRB bmse000879 1 H34 H33 BMRB bmse000879 1 H32 H34 BMRB bmse000879 1 H33 H35 BMRB bmse000879 1 H37 H36 BMRB bmse000879 1 H36 H37 BMRB bmse000879 1 P23 P23 ALATIS bmse000879 1 O22 O22 ALATIS bmse000879 1 O16 O16 ALATIS bmse000879 1 O21 O21 ALATIS bmse000879 1 O18 O18 ALATIS bmse000879 1 O19 O19 ALATIS bmse000879 1 O17 O17 ALATIS bmse000879 1 O20 O20 ALATIS bmse000879 1 N15 N15 ALATIS bmse000879 1 N13 N13 ALATIS bmse000879 1 N12 N12 ALATIS bmse000879 1 N14 N14 ALATIS bmse000879 1 N11 N11 ALATIS bmse000879 1 C6 C6 ALATIS bmse000879 1 C4 C4 ALATIS bmse000879 1 C1 C1 ALATIS bmse000879 1 C5 C5 ALATIS bmse000879 1 C2 C2 ALATIS bmse000879 1 C8 C8 ALATIS bmse000879 1 C3 C3 ALATIS bmse000879 1 C7 C7 ALATIS bmse000879 1 C9 C9 ALATIS bmse000879 1 C10 C10 ALATIS bmse000879 1 H31 H31 ALATIS bmse000879 1 H29 H29 ALATIS bmse000879 1 H24 H24 ALATIS bmse000879 1 H25 H25 ALATIS bmse000879 1 H30 H30 ALATIS bmse000879 1 H26 H26 ALATIS bmse000879 1 H27 H27 ALATIS bmse000879 1 H35 H35 ALATIS bmse000879 1 H28 H28 ALATIS bmse000879 1 H34 H34 ALATIS bmse000879 1 H32 H32 ALATIS bmse000879 1 H33 H33 ALATIS bmse000879 1 H37 H37 ALATIS bmse000879 1 H36 H36 ALATIS bmse000879 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 P23 O21 bmse000879 1 2 covalent SING P23 O18 bmse000879 1 3 covalent SING P23 O19 bmse000879 1 4 covalent DOUB P23 O20 bmse000879 1 5 covalent SING O22 C6 bmse000879 1 6 covalent SING O22 C5 bmse000879 1 7 covalent SING C4 O16 bmse000879 1 8 covalent SING O16 H35 bmse000879 1 9 covalent SING O21 C2 bmse000879 1 10 covalent SING O18 H36 bmse000879 1 11 covalent SING O19 H37 bmse000879 1 12 covalent DOUB O17 C9 bmse000879 1 13 covalent SING C6 N15 bmse000879 1 14 covalent SING N15 C8 bmse000879 1 15 covalent SING N15 C3 bmse000879 1 16 covalent SING N13 C8 bmse000879 1 17 covalent SING N13 C10 bmse000879 1 18 covalent SING N13 H34 bmse000879 1 19 covalent DOUB N12 C3 bmse000879 1 20 covalent SING N12 C7 bmse000879 1 21 covalent SING N14 C9 bmse000879 1 22 covalent DOUB N14 C10 bmse000879 1 23 covalent SING N11 C10 bmse000879 1 24 covalent SING N11 H32 bmse000879 1 25 covalent SING N11 H33 bmse000879 1 26 covalent SING C6 C1 bmse000879 1 27 covalent SING C6 H31 bmse000879 1 28 covalent SING C4 C1 bmse000879 1 29 covalent SING C4 C5 bmse000879 1 30 covalent SING C4 H29 bmse000879 1 31 covalent SING C1 H24 bmse000879 1 32 covalent SING C1 H25 bmse000879 1 33 covalent SING C5 C2 bmse000879 1 34 covalent SING C5 H30 bmse000879 1 35 covalent SING C2 H26 bmse000879 1 36 covalent SING C2 H27 bmse000879 1 37 covalent DOUB C8 C7 bmse000879 1 38 covalent SING C3 H28 bmse000879 1 39 covalent SING C7 C9 bmse000879 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 134228446 sid "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 yes PubChem 65059 cid "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 yes PubChem 24894297 sid "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 yes 'MDL number' MFCD00150780 ? "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 yes PDB DGP 'Chemical Component' "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 yes MMCD cq_00261 ? "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 yes 'EC Number' 251-517-5 ? "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 no PubChem 841411 sid "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 no PubChem 43121900 sid "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 no PubChem 3653 sid "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 no PubChem 207013 sid "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 no 'CAS Registry' 902-04-5 'registry number' "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 no ChemSpider 58570 ? "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 no BIND 656 ? "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 no EINECS 212-988-2 ? "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 no KEGG C00362 'compound ID' "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 1 no ChemIDplus 000902045 ? "2'-Deoxyguanosine 5'-monophosphate" 'matching entry' bmse000879 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 bmse000879 1 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID bmse000879 _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 "2'-Deoxyguanosine 5'-monophosphate" 'natural abundance' 1 $2-Deoxyguanosine-5-monophosphate Solute Saturated n/a sigma '2-Deoxyguanosine 5-monophosphate disodium salt hydrate' bmse000879 1 2 D2O ? ? ? Solvent 100 % ? ? bmse000879 1 3 'sodium phosphate' ? ? ? Buffer 50 mM ? ? bmse000879 1 4 'sodium azide' ? ? ? Cytocide 500 uM ? ? bmse000879 1 5 DSS ? ? ? Reference 0.1 % ? ? bmse000879 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 bmse000879 _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 bmse000879 1 temperature 298 K bmse000879 1 stop_ save_ save_sample_conditions_4 _Sample_condition_list.Sf_category sample_conditions _Sample_condition_list.Sf_framecode sample_conditions_4 _Sample_condition_list.Entry_ID bmse000879 _Sample_condition_list.ID 4 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 7.40 pH bmse000879 4 temperature 298 K bmse000879 4 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID bmse000879 _Software.ID 1 _Software.Name TopSpin _Software.Version 2.1 loop_ _Vendor.Name _Vendor.Entry_ID _Vendor.Software_ID 'Bruker Biospin' bmse000879 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID Collection bmse000879 1 Processing bmse000879 1 'Data analysis' bmse000879 1 'Peak picking' bmse000879 1 stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Bruker_DMX_600 _NMR_spectrometer.Sf_category NMR_spectrometer _NMR_spectrometer.Sf_framecode Bruker_DMX_600 _NMR_spectrometer.Entry_ID bmse000879 _NMR_spectrometer.ID 1 _NMR_spectrometer.Manufacturer Bruker _NMR_spectrometer.Model DMX _NMR_spectrometer.Field_strength 600 save_ ############################# # NMR applied experiments # ############################# save_experiment_list _Experiment_list.Sf_category experiment_list _Experiment_list.Sf_framecode experiment_list _Experiment_list.Entry_ID bmse000879 _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_600 bmse000879 1 2 '2D [1H,1H]-TOCSY' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_600 bmse000879 1 3 '1D DEPT90' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_600 bmse000879 1 4 '1D DEPT135' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_600 bmse000879 1 5 '2D [1H,13C]-HSQC' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_600 bmse000879 1 6 '2D [1H,13C]-HMBC' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_600 bmse000879 1 7 '2D [1H,1H]-COSY' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_600 bmse000879 1 8 '2D [1H,13C]-HMQC' yes 1 $sample_1 isotropic 1 $sample_conditions_1 1 $Bruker_DMX_600 bmse000879 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 text/directory nmr/set01/ 'NMR experiment directory' bmse000879 1 1 00.png image/png nmr/set01/spectra/1H 'Spectral image' bmse000879 1 1 01.png image/png nmr/set01/spectra/1H 'Spectral image' bmse000879 1 1 02.png image/png nmr/set01/spectra/1H 'Spectral image' bmse000879 1 2 HH_TOCSY text/directory nmr/set01/ 'NMR experiment directory' bmse000879 1 2 00.png image/png nmr/set01/spectra/HH_TOCSY 'Spectral image' bmse000879 1 2 01.png image/png nmr/set01/spectra/HH_TOCSY 'Spectral image' bmse000879 1 3 DEPT_90 text/directory nmr/set01/ 'NMR experiment directory' bmse000879 1 3 00.png image/png nmr/set01/spectra/DEPT_90 'Spectral image' bmse000879 1 3 01.png image/png nmr/set01/spectra/DEPT_90 'Spectral image' bmse000879 1 4 DEPT_135 text/directory nmr/set01/ 'NMR experiment directory' bmse000879 1 4 00.png image/png nmr/set01/spectra/DEPT_135 'Spectral image' bmse000879 1 4 01.png image/png nmr/set01/spectra/DEPT_135 'Spectral image' bmse000879 1 5 1H_13C_HSQC text/directory nmr/set01/ 'NMR experiment directory' bmse000879 1 5 00.png image/png nmr/set01/spectra/1H_13C_HSQC 'Spectral image' bmse000879 1 5 01.png image/png nmr/set01/spectra/1H_13C_HSQC 'Spectral image' bmse000879 1 6 1H_13C_HMBC text/directory nmr/set01/ 'NMR experiment directory' bmse000879 1 6 00.png image/png nmr/set01/spectra/1H_13C_HMBC 'Spectral image' bmse000879 1 6 01.png image/png nmr/set01/spectra/1H_13C_HMBC 'Spectral image' bmse000879 1 7 HH_COSY text/directory nmr/set01/ 'NMR experiment directory' bmse000879 1 7 00.png image/png nmr/set01/spectra/HH_COSY 'Spectral image' bmse000879 1 7 01.png image/png nmr/set01/spectra/HH_COSY 'Spectral image' bmse000879 1 8 1H_13C_HMQC text/directory nmr/set01/ 'NMR experiment directory' bmse000879 1 8 00.png image/png nmr/set01/spectra/1H_13C_HMQC 'Spectral image' bmse000879 1 8 01.png image/png nmr/set01/spectra/1H_13C_HMQC 'Spectral image' bmse000879 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 bmse000879 _Chem_shift_reference.ID 1 loop_ _Chem_shift_ref.Atom_type _Chem_shift_ref.Atom_isotope_number _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 'methyl protons' ppm 0.00 internal direct 1.000000000 bmse000879 1 C 13 'methyl carbons' ppm 0.00 internal direct 1.000000000 bmse000879 1 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chemical_shifts _Assigned_chem_shift_list.Sf_category assigned_chemical_shifts _Assigned_chem_shift_list.Sf_framecode assigned_chemical_shifts _Assigned_chem_shift_list.Entry_ID bmse000879 _Assigned_chem_shift_list.ID 1 _Assigned_chem_shift_list.Sample_condition_list_ID 1 _Assigned_chem_shift_list.Sample_condition_list_label $sample_conditions_1 _Assigned_chem_shift_list.Chem_shift_reference_ID 1 _Assigned_chem_shift_list.Chem_shift_reference_label $chem_shift_reference _Assigned_chem_shift_list.Details 'The chemical shift assignments have been taken from BMRB entry bmse000824' loop_ _Atom_chem_shift.ID _Atom_chem_shift.Entity_ID _Atom_chem_shift.Comp_index_ID _Atom_chem_shift.Comp_ID _Atom_chem_shift.Atom_ID _Atom_chem_shift.Atom_type _Atom_chem_shift.Atom_isotope_number _Atom_chem_shift.Val _Atom_chem_shift.Ambiguity_code _Atom_chem_shift.Auth_atom_ID _Atom_chem_shift.Entry_ID _Atom_chem_shift.Assigned_chem_shift_list_ID 1 1 1 1 C6 C 13 86.051 1 C14 bmse000879 1 2 1 1 1 C4 C 13 74.254 1 C15 bmse000879 1 3 1 1 1 C1 C 13 41.648 1 C16 bmse000879 1 4 1 1 1 C5 C 13 89.025 1 C17 bmse000879 1 5 1 1 1 C5 C 13 88.958 1 C17 bmse000879 1 6 1 1 1 C2 C 13 66.738 1 C18 bmse000879 1 7 1 1 1 C2 C 13 66.702 1 C18 bmse000879 1 8 1 1 1 C8 C 13 153.868 1 C19 bmse000879 1 9 1 1 1 C3 C 13 140.187 1 C20 bmse000879 1 10 1 1 1 C7 C 13 118.638 1 C21 bmse000879 1 11 1 1 1 C9 C 13 161.455 1 C22 bmse000879 1 12 1 1 1 C10 C 13 156.526 1 C23 bmse000879 1 13 1 1 1 H31 H 1 6.243 1 H24 bmse000879 1 14 1 1 1 H29 H 1 4.705 1 H25 bmse000879 1 15 1 1 1 H24 H 1 2.762 2 H26 bmse000879 1 16 1 1 1 H24 H 1 2.533 2 H26 bmse000879 1 17 1 1 1 H25 H 1 2.762 2 H27 bmse000879 1 18 1 1 1 H25 H 1 2.533 2 H27 bmse000879 1 19 1 1 1 H30 H 1 4.229 1 H28 bmse000879 1 20 1 1 1 H26 H 1 3.972 1 H29 bmse000879 1 21 1 1 1 H27 H 1 3.972 1 H30 bmse000879 1 22 1 1 1 H28 H 1 8.121 1 H32 bmse000879 1 stop_ loop_ _Ambiguous_atom_chem_shift.Ambiguous_shift_set_ID _Ambiguous_atom_chem_shift.Atom_chem_shift_ID _Ambiguous_atom_chem_shift.Entry_ID _Ambiguous_atom_chem_shift.Assigned_chem_shift_list_ID 1 15 bmse000879 1 1 17 bmse000879 1 2 16 bmse000879 1 2 18 bmse000879 1 stop_ save_ ######################### # Spectral peak lists # ######################### save_spectral_peak_1H _Spectral_peak_list.Sf_category spectral_peak_list _Spectral_peak_list.Sf_framecode spectral_peak_1H _Spectral_peak_list.Entry_ID bmse000879 _Spectral_peak_list.ID 1 _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.Experiment_ID 1 _Spectral_peak_list.Experiment_name '1D 1H' _Spectral_peak_list.Number_of_spectral_dimensions 1 loop_ _Spectral_dim.ID _Spectral_dim.Atom_type _Spectral_dim.Atom_isotope_number _Spectral_dim.Spectral_region _Spectral_dim.Sweep_width _Spectral_dim.Entry_ID _Spectral_dim.Spectral_peak_list_ID 1 H 1 'Full H' 9615.38461538462 bmse000879 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 bmse000879 1 stop_ loop_ _Spectral_transition.ID _Spectral_transition.Entry_ID _Spectral_transition.Spectral_peak_list_ID 1 bmse000879 1 2 bmse000879 1 3 bmse000879 1 4 bmse000879 1 5 bmse000879 1 6 bmse000879 1 7 bmse000879 1 8 bmse000879 1 9 bmse000879 1 10 bmse000879 1 11 bmse000879 1 12 bmse000879 1 13 bmse000879 1 14 bmse000879 1 15 bmse000879 1 16 bmse000879 1 17 bmse000879 1 18 bmse000879 1 19 bmse000879 1 20 bmse000879 1 21 bmse000879 1 22 bmse000879 1 23 bmse000879 1 24 bmse000879 1 25 bmse000879 1 26 bmse000879 1 27 bmse000879 1 stop_ loop_ _Spectral_transition_general_char.Spectral_transition_ID _Spectral_transition_general_char.Intensity_val _Spectral_transition_general_char.Measurement_method _Spectral_transition_general_char.Entry_ID _Spectral_transition_general_char.Spectral_peak_list_ID 1 13.36 Height bmse000879 1 2 3.94 Height bmse000879 1 3 7.27 Height bmse000879 1 4 4.04 Height bmse000879 1 5 1.97 Height bmse000879 1 6 3.89 Height bmse000879 1 7 4.24 Height bmse000879 1 8 3.99 Height bmse000879 1 9 2.22 Height bmse000879 1 10 5.76 Height bmse000879 1 11 5.99 Height bmse000879 1 12 8.77 Height bmse000879 1 13 15.00 Height bmse000879 1 14 8.21 Height bmse000879 1 15 2.13 Height bmse000879 1 16 3.35 Height bmse000879 1 17 4.79 Height bmse000879 1 18 4.06 Height bmse000879 1 19 2.54 Height bmse000879 1 20 2.74 Height bmse000879 1 21 3.03 Height bmse000879 1 22 3.29 Height bmse000879 1 23 3.17 Height bmse000879 1 24 2.67 Height bmse000879 1 25 2.71 Height bmse000879 1 26 2.55 Height bmse000879 1 27 2.36 Height bmse000879 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 8.1283 bmse000879 1 2 1 6.2569 bmse000879 1 3 1 6.2455 bmse000879 1 4 1 6.2340 bmse000879 1 5 1 4.7139 bmse000879 1 6 1 4.7086 bmse000879 1 7 1 4.7038 bmse000879 1 8 1 4.6989 bmse000879 1 9 1 4.6936 bmse000879 1 10 1 4.2276 bmse000879 1 11 1 4.2220 bmse000879 1 12 1 3.9667 bmse000879 1 13 1 3.9590 bmse000879 1 14 1 3.9513 bmse000879 1 15 1 2.7863 bmse000879 1 16 1 2.7749 bmse000879 1 17 1 2.7633 bmse000879 1 18 1 2.7514 bmse000879 1 19 1 2.7405 bmse000879 1 20 1 2.5487 bmse000879 1 21 1 2.5429 bmse000879 1 22 1 2.5384 bmse000879 1 23 1 2.5325 bmse000879 1 24 1 2.5256 bmse000879 1 25 1 2.5197 bmse000879 1 26 1 2.5152 bmse000879 1 27 1 2.5093 bmse000879 1 stop_ save_