PDBsum entry 3svv

Transferase/transferase inhibitor

PDB id: 3svv

Contents

Protein chains

261 a.a.

Ligands

VSP ×2

Waters ×234

PDB id:

3svv

Name:

Transferase/transferase inhibitor

Title:

Crystal structure of t338c c-src covalently bound to vinylsulfonamide- pyrazolopyrimidine 9

Structure:

Proto-oncogene tyrosine-protein kinase src. Chain: a, b. Fragment: kinase domain, unp residues 251-533. Synonym: proto-oncogenE C-src, pp60c-src, p60-src. Engineered: yes. Mutation: yes

Source:

Gallus gallus. Bantam,chickens. Organism_taxid: 9031. Gene: src. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.20Å R-factor: 0.178 R-free: 0.215

Authors:

A.L.Garske,U.Peters,A.Cortesi,J.Perez,K.M.Shokat

Key ref:

A.L.Garske et al. (2011). Chemical genetic strategy for targeting protein kinases based on covalent complementarity. Proc Natl Acad Sci U S A, 108, 15046-15052. PubMed id: 21852571

Date:

12-Jul-11 Release date: 17-Aug-11

Protein chains

P00523  (SRC_CHICK) -  Proto-oncogene tyrosine-protein kinase Src from Gallus gallus

Seq: 533 a.a.

Struc: 261 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.7.10.2 - non-specific protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Proc Natl Acad Sci U S A 108:15046-15052 (2011)

PubMed id: 21852571

Chemical genetic strategy for targeting protein kinases based on covalent complementarity.

A.L.Garske, U.Peters, A.T.Cortesi, J.L.Perez, K.M.Shokat.

ABSTRACT

The conserved nature of the ATP-binding site of the > 500 human kinases renders the development of specific inhibitors a challenging task. A widely used chemical genetic strategy to overcome the specificity challenge exploits a large-to-small mutation of the gatekeeper residue (a conserved hydrophobic amino acid) and the use of a bulky inhibitor to achieve specificity via shape complementarity. However, in a number of cases, introduction of a glycine or alanine gatekeeper results in diminished kinase activity and ATP affinity. A new chemical genetic approach based on covalent complementarity between an engineered gatekeeper cysteine and an electrophilic inhibitor was developed to address these challenges. This strategy was evaluated with Src, a proto-oncogenic tyrosine kinase known to lose some enzymatic activity using the shape complementarity chemical genetic strategy. We found that Src with a cysteine gatekeeper recapitulates wild type activity and can be irreversibly inhibited both in vitro and in cells. A cocrystal structure of T338C c-Src with a vinylsulfonamide-derivatized pyrazolopyrimidine inhibitor was solved to elucidate the inhibitor binding mode. A panel of electrophilic inhibitors was analyzed against 307 kinases and MOK (MAPK/MAK/MRK overlapping kinase), one of only two human kinases known to have an endogenous cysteine gatekeeper. This analysis revealed remarkably few off-targets, making these compounds the most selective chemical genetic inhibitors reported to date. Protein engineering studies demonstrated that it is possible to increase inhibitor potency through secondary-site mutations. These results suggest that chemical genetic strategies based on covalent complementarity should be widely applicable to the study of protein kinases.