Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  (To be retired June 1st  )
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 77.45 kDa 
• Atom Count: 4924 
• Residue Count: 582 
• Unique protein chains: 1

3PP0

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

• DOI: 10.2210/pdb3PP0/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Antheraea
• Mutation(s): Yes 


• Deposited: 2010-11-23 Released: 2011-03-30 
• Deposition Author(s): Skene, R.J., Aertgeerts, K., Sogabe, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.260 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 

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

• PubMed: 21454582 
• DOI: 10.1074/jbc.M110.206193
• Structures With Same Primary Citation


• 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 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.

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Organizational Affiliation: 

Takeda San Diego Inc, 10410 Science Center Drive, San Diego, California 92121, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Receptor tyrosine-protein kinase erbB-2	A, B	338	Homo sapiens	Mutation(s): 3  Gene Names: ERBB2, HER2, MLN19, NEU, NGL EC: 2.7.10.1
Find proteins for P04626 (Homo sapiens) Go to UniProtKB:  P04626
NIH Common Fund Data Resources
PHAROS  P04626

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
03Q	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
03Q	IC50:  11   nM  BindingDB
03Q	IC50:  11   nM  Binding MOAD
03Q	IC50:  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 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.705	α = 90
b = 78.951	β = 90
c = 152.675	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-23 
• Released Date: 2011-03-30 
Deposition Author(s): Skene, R.J., Aertgeerts, K., Sogabe, S.

Revision History 

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