{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T03:25:32Z","timestamp":1776050732112,"version":"3.50.1"},"reference-count":60,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,19]],"date-time":"2023-05-19T00:00:00Z","timestamp":1684454400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"MSCA ITN ALLODD","award":["956314"],"award-info":[{"award-number":["956314"]}]},{"name":"National Research Development and Innovation Office of Hungary","award":["K135150"],"award-info":[{"award-number":["K135150"]}]},{"name":"National Research Development and Innovation Office of Hungary","award":["RRF-2.3.1-21-2022-00015"],"award-info":[{"award-number":["RRF-2.3.1-21-2022-00015"]}]},{"DOI":"10.13039\/501100003825","name":"Hungarian Academy of Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003825","id-type":"DOI","asserted-by":"publisher"}]},{"name":"\u00daNKP-22-5 New National Excellence Program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>SH2 domains are key mediators of phosphotyrosine-based signalling, and therapeutic targets for diverse, mostly oncological, disease indications. They have a highly conserved structure with a central beta sheet that divides the binding surface of the protein into two main pockets, responsible for phosphotyrosine binding (pY pocket) and substrate specificity (pY\u00a0+\u00a03 pocket). In recent years, structural databases have proven to be invaluable resources for the drug discovery community, as they contain highly relevant and up-to-date information on important protein classes. Here, we present SH2db, a comprehensive structural database and webserver for SH2 domain structures. To organize these protein structures efficiently, we introduce (i) a generic residue numbering scheme to enhance the comparability of different SH2 domains, (ii) a structure-based multiple sequence alignment of all 120 human wild-type SH2 domain sequences and their PDB and AlphaFold structures. The aligned sequences and structures can be searched, browsed and downloaded from the online interface of SH2db (http:\/\/sh2db.ttk.hu), with functions to conveniently prepare multiple structures into a Pymol session, and to export simple charts on the contents of the database. Our hope is that SH2db can assist researchers in their day-to-day work by becoming a one-stop shop for SH2 domain related research.<\/jats:p>","DOI":"10.1093\/nar\/gkad420","type":"journal-article","created":{"date-parts":[[2023,5,19]],"date-time":"2023-05-19T20:23:26Z","timestamp":1684527806000},"page":"W542-W552","source":"Crossref","is-referenced-by-count":9,"title":["SH2db, an information system for the SH2 domain"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4277-9481","authenticated-orcid":false,"given":"D\u00e1vid","family":"Bajusz","sequence":"first","affiliation":[{"name":"Medicinal Chemistry Research Group\u00a0and National Laboratory for Drug Researchand Development,\u00a0Research Centre for Natural Sciences , Magyar tud\u00f3sok krt. 2, 1117 Budapest , Hungary"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7697-2696","authenticated-orcid":false,"given":"G\u00e1sp\u00e1r","family":"P\u00e1ndy-Szekeres","sequence":"additional","affiliation":[{"name":"Medicinal Chemistry Research Group\u00a0and National Laboratory for Drug Researchand Development,\u00a0Research Centre for Natural Sciences , Magyar tud\u00f3sok krt. 2, 1117 Budapest , Hungary"},{"name":"Department of Drug Design and Pharmacology, University of Copenhagen , Universitetsparken 2, 2100 Copenhagen, Denmark"}]},{"given":"\u00c1gnes","family":"Tak\u00e1cs","sequence":"additional","affiliation":[{"name":"Medicinal Chemistry Research Group\u00a0and National Laboratory for Drug Researchand Development,\u00a0Research Centre for Natural Sciences , Magyar tud\u00f3sok krt. 2, 1117 Budapest , Hungary"}]},{"given":"Elvin D","family":"de\u00a0Araujo","sequence":"additional","affiliation":[{"name":"Centre for Medicinal Chemistry, University of Toronto at Mississauga , Mississauga , ON L5L 1C6 , Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1039-7809","authenticated-orcid":false,"given":"Gy\u00f6rgy M","family":"Keser\u0171","sequence":"additional","affiliation":[{"name":"Medicinal Chemistry Research Group\u00a0and National Laboratory for Drug Researchand Development,\u00a0Research Centre for Natural Sciences , Magyar tud\u00f3sok krt. 2, 1117 Budapest , Hungary"},{"name":"Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics , M\u0171egyetem rkp. 3, 1111 Budapest , Hungary"}]}],"member":"286","published-online":{"date-parts":[[2023,5,19]]},"reference":[{"key":"2023070505022403900_B1","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1126\/science.1708916","article-title":"SH2 and SH3 domains: elements that control interactions of cytoplasmic signaling proteins","volume":"252","author":"Koch","year":"1991","journal-title":"Science"},{"key":"2023070505022403900_B2","doi-asserted-by":"crossref","first-page":"9680","DOI":"10.1073\/pnas.0803161105","article-title":"Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages","volume":"105","author":"Pincus","year":"2008","journal-title":"Proc. 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