SH2db, an information system for the SH2 domain
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SH2 domains are key mediators of phosphotyrosinebased 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 + 3 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.
Original language | English |
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Book series | Nucleic acids symposium series |
Volume | 51 |
Issue number | W1 |
Pages (from-to) | W542–W552 |
ISSN | 0305-1048 |
DOIs | |
Publication status | Published - 2023 |
- ACCURATE DOCKING, PROTEIN, SEQUENCE, DATABASE, LEUKEMIA, TARGETS, BINDING, MODELS, GPCRDB, GLIDE
Research areas
ID: 357281133