3PP0

Crystal Structure of the Kinase domain of Human HER2 (erbB2).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Analysis of the Mechanism of Inhibition and Allosteric Activation of the Kinase Domain of HER2 Protein.

Aertgeerts, K.Skene, R.Yano, J.Sang, B.C.Zou, H.Snell, G.Jennings, A.Iwamoto, K.Habuka, N.Hirokawa, A.Ishikawa, T.Tanaka, T.Miki, H.Ohta, Y.Sogabe, S.

(2011) J.Biol.Chem. 286: 18756-18765

  • DOI: 10.1074/jbc.M110.206193
  • Primary Citation of Related Structures:  3POZ

  • PubMed Abstract: 
  • Aberrant signaling of ErbB family members human epidermal growth factor 2 (HER2) and epidermal growth factor receptor (EGFR) is implicated in many human cancers, and HER2 expression is predictive of human disease recurrence and prognosis. Small molec ...

    Aberrant signaling of ErbB family members human epidermal growth factor 2 (HER2) and epidermal growth factor receptor (EGFR) is implicated in many human cancers, and HER2 expression is predictive of human disease recurrence and prognosis. Small molecule kinase inhibitors of EGFR and of both HER2 and EGFR have received approval for the treatment of cancer. We present the first high resolution crystal structure of the kinase domain of HER2 in complex with a selective inhibitor to understand protein activation, inhibition, and function at the molecular level. HER2 kinase domain crystallizes as a dimer and suggests evidence for an allosteric mechanism of activation comparable with previously reported activation mechanisms for EGFR and HER4. A unique Gly-rich region in HER2 following the α-helix C is responsible for increased conformational flexibility within the active site and could explain the low intrinsic catalytic activity previously reported for HER2. In addition, we solved the crystal structure of the kinase domain of EGFR in complex with a HER2/EGFR dual inhibitor (TAK-285). Comparison with previously reported inactive and active EGFR kinase domain structures gave insight into the mechanism of HER2 and EGFR inhibition and may help guide the design and development of new cancer drugs with improved potency and selectivity.


    Organizational Affiliation

    Takeda San Diego Inc, 10410 Science Center Drive, San Diego, California 92121, USA. kaertgeerts@takedasd.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor tyrosine-protein kinase erbB-2
A, B
338Homo sapiensGene Names: ERBB2 (HER2, MLN19, NEU, NGL)
EC: 2.7.10.1
Find proteins for P04626 (Homo sapiens)
Go to Gene View: ERBB2
Go to UniProtKB:  P04626
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
03Q
Query on 03Q

Download SDF File 
Download CCD File 
A, B
2-{2-[4-({5-chloro-6-[3-(trifluoromethyl)phenoxy]pyridin-3-yl}amino)-5H-pyrrolo[3,2-d]pyrimidin-5-yl]ethoxy}ethanol
C22 H19 Cl F3 N5 O3
XPUIECRALWERTL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
03QIC50: 11 nM (95) BINDINGDB
03QIC50: 11 nM BINDINGMOAD
03QIC50: 11 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.705α = 90.00
b = 78.951β = 90.00
c = 152.675γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description