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PDBsum entry 2j5e

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protein metals links
Transferase PDB id
2j5e
Jmol
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00533  (EGFR_HUMAN) -  Epidermal growth factor receptor
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1210 a.a.
310 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* 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.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
ATP
+ [protein]-L-tyrosine
= ADP
+ [protein]-L-tyrosine phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein phosphorylation   1 term 
  Biochemical function     transferase activity, transferring phosphorus-containing groups     4 terms  

 

 
    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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22218294 E.Deu, M.Verdoes, and M.Bogyo (2012).
New approaches for dissecting protease functions to improve probe development and drug discovery.
  Nat Struct Mol Biol, 19, 9.  
21049105 A.Crespo, A.Coelho, P.M.Diz, F.Fernández, H.Novoa de Armas, and E.Sotelo (2011).
Convergent assembly of structurally diverse quinazolines.
  Org Biomol Chem, 9, 351-357.  
21190999 D.B.Yap, J.Chu, T.Berg, M.Schapira, S.W.Cheng, A.Moradian, R.D.Morin, A.J.Mungall, B.Meissner, M.Boyle, V.E.Marquez, M.A.Marra, R.D.Gascoyne, R.K.Humphries, C.H.Arrowsmith, G.B.Morin, and S.A.Aparicio (2011).
Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation.
  Blood, 117, 2451-2459.  
20938978 M.Mustafa, A.Mirza, and N.Kannan (2011).
Conformational regulation of the EGFR kinase core by the juxtamembrane and C-terminal tail: a molecular dynamics study.
  Proteins, 79, 99.  
21383145 T.F.Chou, S.J.Brown, D.Minond, B.E.Nordin, K.Li, A.C.Jones, P.Chase, P.R.Porubsky, B.M.Stoltz, F.J.Schoenen, M.P.Patricelli, P.Hodder, H.Rosen, and R.J.Deshaies (2011).
Reversible inhibitor of p97, DBeQ, impairs both ubiquitin-dependent and autophagic protein clearance pathways.
  Proc Natl Acad Sci U S A, 108, 4834-4839.  
20886146 W.P.Heal, T.H.Dang, and E.W.Tate (2011).
Activity-based probes: discovering new biology and new drug targets.
  Chem Soc Rev, 40, 246-257.  
20306284 A.Del Rio, M.Sgobba, M.D.Parenti, G.Degliesposti, R.Forestiero, C.Percivalle, P.F.Conte, M.Freccero, and G.Rastelli (2010).
A computational workflow for the design of irreversible inhibitors of protein kinases.
  J Comput Aided Mol Des, 24, 183-194.  
19942586 D.Huang, T.Zhou, K.Lafleur, C.Nevado, and A.Caflisch (2010).
Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis.
  Bioinformatics, 26, 198-204.  
  20640225 D.S.Johnson, E.Weerapana, and B.F.Cravatt (2010).
Strategies for discovering and derisking covalent, irreversible enzyme inhibitors.
  Future Med Chem, 2, 949-964.  
20126732 K.A.Kalesh, D.S.Sim, J.Wang, K.Liu, Q.Lin, and S.Q.Yao (2010).
Small molecule probes that target Abl kinase.
  Chem Commun (Camb), 46, 1118-1120.  
20179705 P.I.Poulikakos, C.Zhang, G.Bollag, K.M.Shokat, and N.Rosen (2010).
RAF inhibitors transactivate RAF dimers and ERK signalling in cells with wild-type BRAF.
  Nature, 464, 427-430.  
21080395 S.Klüter, J.R.Simard, H.B.Rode, C.Grütter, V.Pawar, H.C.Raaijmakers, T.A.Barf, M.Rabiller, W.A.van Otterlo, and D.Rauh (2010).
Characterization of irreversible kinase inhibitors by directly detecting covalent bond formation: a tool for dissecting kinase drug resistance.
  Chembiochem, 11, 2557-2566.
PDB code: 3lok
20485436 S.Lourido, J.Shuman, C.Zhang, K.M.Shokat, R.Hui, and L.D.Sibley (2010).
Calcium-dependent protein kinase 1 is an essential regulator of exocytosis in Toxoplasma.
  Nature, 465, 359-362.  
19830290 H.S.Ban, T.Usui, W.Nabeyama, H.Morita, K.Fukuzawa, and H.Nakamura (2009).
Discovery of boron-conjugated 4-anilinoquinazoline as a prolonged inhibitor of EGFR tyrosine kinase.
  Org Biomol Chem, 7, 4415-4427.  
19822424 J.Li, T.S.Kaoud, C.Laroche, K.N.Dalby, and S.M.Kerwin (2009).
Synthesis and biological evaluation of p38alpha kinase-targeting dialkynylimidazoles.
  Bioorg Med Chem Lett, 19, 6293-6297.  
  19527888 O.Billker, S.Lourido, and L.D.Sibley (2009).
Calcium-dependent signaling and kinases in apicomplexan parasites.
  Cell Host Microbe, 5, 612-622.  
18493974 A.Wissner, and T.S.Mansour (2008).
The development of HKI-272 and related compounds for the treatment of cancer.
  Arch Pharm (Weinheim), 341, 465-477.  
18366325 B.F.Cravatt, A.T.Wright, and J.W.Kozarich (2008).
Activity-based protein profiling: from enzyme chemistry to proteomic chemistry.
  Annu Rev Biochem, 77, 383-414.  
18287036 E.R.Wood, L.M.Shewchuk, B.Ellis, P.Brignola, R.L.Brashear, T.R.Caferro, S.H.Dickerson, H.D.Dickson, K.H.Donaldson, M.Gaul, R.J.Griffin, A.M.Hassell, B.Keith, R.Mullin, K.G.Petrov, M.J.Reno, D.W.Rusnak, S.M.Tadepalli, J.C.Ulrich, C.D.Wagner, D.E.Vanderwall, A.G.Waterson, J.D.Williams, W.L.White, and D.E.Uehling (2008).
6-Ethynylthieno[3,2-d]- and 6-ethynylthieno[2,3-d]pyrimidin-4-anilines as tunable covalent modifiers of ErbB kinases.
  Proc Natl Acad Sci U S A, 105, 2773-2778.
PDB code: 2r4b
18937562 M.Fonović, and M.Bogyo (2008).
Activity-based probes as a tool for functional proteomic analysis of proteases.
  Expert Rev Proteomics, 5, 721-730.  
18022565 J.L.Snead, M.Sullivan, D.M.Lowery, M.S.Cohen, C.Zhang, D.H.Randle, J.Taunton, M.B.Yaffe, D.O.Morgan, and K.M.Shokat (2007).
A coupled chemical-genetic and bioinformatic approach to Polo-like kinase pathway exploration.
  Chem Biol, 14, 1261-1272.  
17514789 N.Rusk (2007).
Kinase clamping.
  Nat Methods, 4, 382-383.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.