GPMDB00235OtherAdachi J, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Human_female25230287jun_adachi@nibio.go.jphttp://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004776http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004775http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004778http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004777http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004779http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004759http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004790http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004770http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004792http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004791http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004772http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004794http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004793http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004771http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004774http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004773http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004795http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004765http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004787http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004764http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004786http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004767http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004789http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004788http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004766http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004769http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004768http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004780http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004761http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004783http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004760http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004782http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004785http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004763http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004762http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004784Laboratory of Proteome Research, National Institute of Biomedical Innovation , Ibaraki, OsakaNot availableGPMDBATP-binding proteins, including protein kinases, play essential roles in many biological and pathological processes and thus these proteins are attractive as drug targets. Acyl-ATP probes have been developed as efficient probes for kinase enrichment, and these probes have also been used to enrich other ATP-binding proteins. However, a robust method to identify ATP-binding proteins with systematic elimination of nonspecific binding proteins has yet to be established. Here, we describe an ATP competition assay that permitted establishment of a rigorous ATP-binding protein list with virtual elimination of nonspecific proteins. A total of 539 ATP-binding protein candidates were identified, including 178 novel candidates. In informatics analysis, ribosomal proteins were overrepresented in the list of novel candidates. We also found multiple ATP-competitive sites for several kinases, including epidermal growth factor receptor, serine/threonine-protein kinase PRP4 homologue, cyclin-dependent kinase 12, eukaryotic elongation factor 2 kinase, ribosomal protein S6 kinase alpha-1, and SRSF protein kinase 1. Using our cataloged ATP-binding protein list, a selectivity profiling method that covers the kinome and ATPome was established to identify off-target binding sites of ATP-competitive kinase inhibitors, staurosporine and crizotinib.Proteome-wide discovery of unknown ATP-binding proteins and kinase inhibitor target proteins using an ATP probe.Adachi Jun J,Kishida Marina M,Watanabe Shio S,Hashimoto Yuuki Y,Fukamizu Kazuna K,Tomonaga Takeshi T,Adachi Jun J, Kishida Marina M, Watanabe Shio S, Hashimoto Yuuki Y, Fukamizu Kazuna K, Tomonaga Takeshi TProtein Gene Products, Gene., Gene Proteins, polypeptide, wide, wide/broad, down regulation of kinase activity, inhibition of kinase activity, ligand, Protein, Gene Products, Proteins, kinase inhibitor, Gene, proteins, broad, Proteomes, down-regulation of kinase activity, downregulation of kinase activityprojections, Gene., measuring, data, Plays, anatomical protrusion, PLXN5, Procedures, lamellae, anatomical process, drug, Proteins, lamina, Nl1, flanges, Gene, PLEXIN-B1, Mell1, Procedure, process of organ, Phosphotransferases, SeP, protrusion, polypeptide, lamella, any method, method, CEH, MMEL2, Playthings and Play, Method, method used in an experiment, Protein, shelf, Gene Products, Studies, Plaything, NEPII, NL1, NL2, Kinase, SEH, flange, organ process, SEP, Toy, Transphosphorylases, Playthings, Kinases, ligand, shelves, Toys, proteins, ridges, Methodological, projection, Methodological Study, study assay, ATP-protein phosphotransferase, ridge, sEP, Protein Gene Products, plan specification, Study, Gene Proteins, process, processes, drugs, Puppets, Methodological Studies, spine, medicine, scientific observation, papilla, SELP, Play, processus, Eph2, ATP Phosphotransferases, laminae, Protein Kinase, Proteomes, NEP2, Puppet, ATPProtein Gene Products, Gene., Gene Proteins, polypeptide, wide, wide/broad, down regulation of kinase activity, inhibition of kinase activity, ligand, Protein, Gene Products, Proteins, kinase inhibitor, Gene, proteins, broad, Proteomes, down-regulation of kinase activity, downregulation of kinase activityprojections, receptor tyrosine-protein kinase erbB-1, cyclin, 16-hexahydro-5H, 1-3H3, Plays, HPRP4P, cyclin-dependent protein kinase regulator activity, Procedures, proto-oncogene c-ErbB-1, Calmodulin Dependent Protein Kinase III, PF02341066., determination, 7b, lamellae, Gene, Ribosomal Protein, L-Threonine, CN[C@@H]1C[C@H]2O[C@@](C)([C@@H]1OC)n1c3ccccc3c3c4CNC(=O)c4c4c5ccccc5n2c4c13, process of organ, eEF 2 Specific Ca and Calmodulin Dependent Protein Kinase III, Staurosporin, 10, protrusion, (H, 11, lamella, g)cyclonona(cde)trinden-1-one, method, 15, 33)/t17-, EF-2, 14H-5, 17, PRP4K, PF 02341066, Method, method used in an experiment, PRP4H, Sites, Gene Products, Studies, Kinase CPK3, G1/S-specific cyclin, 2, PR4H, 3, Kinase, 7, 8, 9, InChIKey=HKSZLNNOFSGOKW-PULLEYNNDJ, 12alpha)-(+)-, 20, Toy, cyclin-dependent protein kinase, Prp4, Site, PRP4, Ribosomal, 9-epoxy-4b, 26, 9a, Playthings, 9R)-6-methoxy-5-methyl-7-methylamino-6, 12-13H2, ligand, Xalkori, proteins, Prp4p, ridges, L Threonine, cbp143, Prp4k, study assay, ATP-protein phosphotransferase, (8alpha, 30, Study, Combining Site, EF-2 Kinase, drugs, Puppets, Methodological Studies, 26-, medicine, scientific observation, papilla, Play, E-2 Kinase, Eukaryotic Elongation Factor-2 Kinase, ATP Phosphotransferases, laminae, Combining Sites, h]cyclonona[1, Puppet, ATP, InChI=1/C28H26N4O3/c1-28-26(34-3)17(29-2)12-20(35-28)31-18-10-6-4-8-14(18)22-23-16(13-30-27(23)33)21-15-9-5-7-11-19(15)32(28)25(21)24(22)31/h4-11, measuring, 2610037H07, 12-hexahydro-9-methoxy-8-methyl-10-(methylamino)-, Calmodulin-Dependent Protein Kinase III, C28H26N4O3, anatomical protrusion, anatomical process, 12a-triazadibenzo(a, drug, Proteins, lamina, flanges, Protein S6, Cam PK III, CAM Kinase III, Binding Site, Procedure, Phosphotransferases, Binding, polypeptide, any method, Playthings and Play, eEF-2-Specific Ca and Calmodulin-Dependent Protein Kinase III, Protein, chemical analysis, shelf, 20-, 8H-2, Plaything, RP70, HPRP4, SNRNP60, Prpk, flange, Calcium Calmodulin Dependent Protein Kinase Type 3, organ process, Calcium-Calmodulin-Dependent Protein Kinase Type 3, Transphosphorylases, PCNA, PF-02341066, Cyclin, Kinases, shelves, EGFR, Toys, Combining, ERBB1, Methodological, projection, Methodological Study, intrinsic regulator activity, ridge, 6R, G2/M-specific cyclin, 28+/m1/s1/f/h30H, 15-triazadibenzo[b, Protein Gene Products, plan specification, 10beta, 29H, Gene Proteins, process, processes, Eukaryotic Elongation Factor 2 Kinase, (5S, 12-Epoxy-1H, spine, PF-2341066, EF 2 Kinase, 4-jkl]cyclopenta[e]-as-indacen-14-one, processus, Protein Kinase CPK3, assay, threonine, 9beta, dJ1013A10.1, Protein Kinase, 7R, E 2 Kinase2305http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310004771dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0embl-pathogen~0project~0pride~1human_diseases~0geo_datasets~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.0070943861813695250.01.0falseProteome-Wide Discovery of Unknown ATP-Binding Proteins and Kinase Inhibitor Target Proteins Using an ATP Probe.Data from ProteomeXchange, PXD ID: PXD001200. File: 1300809_AAS2set_10uM.mzml. Data publsihed as part of J Proteome Res. 2014 Sep 30 . From the Abstract: {{i}} ATP-binding proteins, including protein kinases, play essential roles in many biological and pathological processes and thus these proteins are attractive as drug targets. Acyl-ATP probes have been developed as efficient probes for kinase enrichment, and these probes have also been used to enrich other ATP-binding proteins. However, a robust method to identify ATP-binding proteins with systematic elimination of nonspecific binding proteins has yet to be established. Here, we describe an ATP competition assay that permitted establishment of a rigorous ATP-binding protein list with virtual elimination of nonspecific proteins. {{/i}}2014-10-26GPM3231000477125230287PXD001200PXD001200