PDBsum entry 2j5e

Transferase

PDB id: 2j5e

Contents

Protein chain

310 a.a. *

Metals

_CL

Waters ×60

* Residue conservation analysis

PDB id:

2j5e

Name:

Transferase

Title:

Crystal structure of egfr kinase domain in complex with an irreversible inhibitor 13-jab

Structure:

Epidermal growth factor receptor. Chain: a. Fragment: kinase domain, residues 696-1022. Synonym: receptor tyrosine-protein kinase erbb-1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9.

Resolution:

3.10Å R-factor: 0.191 R-free: 0.255

Authors:

C.-H.Yun,M.J.Eck

Key ref:

J.A.Blair et al. (2007). Structure-guided development of affinity probes for tyrosine kinases using chemical genetics. Nat Chem Biol, 3, 229-238. PubMed id: 17334377 DOI: 10.1038/nchembio866

Date:

14-Sep-06 Release date: 27-Feb-07

Protein chain

P00533  (EGFR_HUMAN) -  Epidermal growth factor receptor from Homo sapiens

Seq: 1210 a.a.

Struc: 310 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.7.10.1 - receptor 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

DOI no: 10.1038/nchembio866

Nat Chem Biol 3:229-238 (2007)

PubMed id: 17334377

Structure-guided development of affinity probes for tyrosine kinases using chemical genetics.

J.A.Blair, D.Rauh, C.Kung, C.H.Yun, Q.W.Fan, H.Rode, C.Zhang, M.J.Eck, W.A.Weiss, K.M.Shokat.

ABSTRACT

As key components in nearly every signal transduction pathway, protein kinases are attractive targets for the regulation of cellular signaling by small-molecule inhibitors. We report the structure-guided development of 6-acrylamido-4-anilinoquinazoline irreversible kinase inhibitors that potently and selectively target rationally designed kinases bearing two selectivity elements that are not found together in any wild-type kinase: an electrophile-targeted cysteine residue and a glycine gatekeeper residue. Cocrystal structures of two irreversible quinazoline inhibitors bound to either epidermal growth factor receptor (EGFR) or engineered c-Src show covalent inhibitor binding to the targeted cysteine (Cys797 in EGFR and Cys345 in engineered c-Src). To accommodate the new covalent bond, the quinazoline core adopts positions that are different from those seen in kinase structures with reversible quinazoline inhibitors. Based on these structures, we developed a fluorescent 6-acrylamido-4-anilinoquinazoline affinity probe to report the fraction of kinase necessary for cellular signaling, and we used these reagents to quantitate the relationship between EGFR stimulation by EGF and its downstream outputs-Akt, Erk1 and Erk2.

Selected figure(s)

Figure 3.
ESI-oa-TOF of control and drug-treated c-Src kinases are shown.

Figure 4.
The experimental electron densities of EGFR and c-Src-cys at 2.95 Å and 2.48 Å resolution, respectively, are shown (2F[o] – F[c] map contoured at 1 ). (a) Optimized EGFR inhibitor 2 (PD 168393)^13 (green ball and sticks) in complex with the EGFR kinase domain shows clear electron density between the targeted Cys797 and the acrylamide Michael acceptor on 2. The inhibitor makes a direct hydrogen bond between its quinazoline N1 and the main chain amide of Met793, which is a common recognition motif among reversible anilinoquinazolines and several protein kinase domains^16, ^20, ^21, ^22, ^23, ^24. We find the cocrystal complex in an active conformation of EGFR: a conserved salt bridge found only in active EGFR conformations between the catalytic Lys745 and helix C Glu762 remains intact. The m-bromine group sits adjacent (within 3.4 Å) to the gatekeeper residue, Thr790. (b) Notably, structures of 2 in complex with c-Src-cys show an inhibitor binding mode distinct from any reported for anilinoquinazolines with a protein kinase. In molecule B of the c-Src-cys–2 complex, 2 (green ball and sticks) forms a water-mediated (W1) hydrogen bond via its N1 of the quinazoline core to the backbone amide of Met341.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2007, 3, 229-238) copyright 2007.

Figures were selected by an automated process.