SH2db, an information system for the SH2 domain
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SH2db, an information system for the SH2 domain. / Bajusz, David; Pandy-Szekeres, Gaspar; Takacs, Agnes; de Araujo, Elvin D.; Keseru, Gyorgy M.
In: Nucleic acids symposium series, Vol. 51, No. W1, 2023, p. W542–W552.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - SH2db, an information system for the SH2 domain
AU - Bajusz, David
AU - Pandy-Szekeres, Gaspar
AU - Takacs, Agnes
AU - de Araujo, Elvin D.
AU - Keseru, Gyorgy M.
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
KW - ACCURATE DOCKING
KW - PROTEIN
KW - SEQUENCE
KW - DATABASE
KW - LEUKEMIA
KW - TARGETS
KW - BINDING
KW - MODELS
KW - GPCRDB
KW - GLIDE
U2 - 10.1093/nar/gkad420
DO - 10.1093/nar/gkad420
M3 - Journal article
C2 - 37207333
VL - 51
SP - W542–W552
JO - Nucleic acids symposium series
JF - Nucleic acids symposium series
SN - 0261-3166
IS - W1
ER -
ID: 357281133