3BBT

crystal structure of the ErbB4 kinase in complex with lapatinib

• PDB DOI:  https://doi.org/10.2210/pdb3BBT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2007-11-11 Released: 2008-02-12 
• Deposition Author(s): Qiu, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.289 
• R-Value Work: 0.251 
• R-Value Observed: 0.253 

Literature

Mechanism of Activation and Inhibition of the HER4/ErbB4 Kinase.

Qiu, C., Tarrant, M.K., Choi, S.H., Sathyamurthy, A., Bose, R., Banjade, S., Pal, A., Bornmann, W.G., Lemmon, M.A., Cole, P.A., Leahy, D.J.

(2008) Structure 16: 460-467

• PubMed: 18334220 
• DOI: https://doi.org/10.1016/j.str.2007.12.016
• Primary Citation of Related Structures:  
  3BBT, 3BBW, 3BCE


• PubMed Abstract: 
  

HER4/ErbB4 is a ubiquitously expressed member of the EGF/ErbB family of receptor tyrosine kinases that is essential for normal development of the heart, nervous system, and mammary gland. We report here crystal structures of the ErbB4 kinase domain in active and lapatinib-inhibited forms. Active ErbB4 kinase adopts an asymmetric dimer conformation essentially identical to that observed to be important for activation of the EGF receptor/ErbB1 kinase. Mutagenesis studies of intact ErbB4 in Ba/F3 cells confirm the importance of this asymmetric dimer for activation of intact ErbB4. Lapatinib binds to an inactive form of the ErbB4 kinase in a mode equivalent to its interaction with the EGF receptor. All ErbB4 residues contacted by lapatinib are conserved in the EGF receptor and HER2/ErbB2, which lapatinib also targets. These results demonstrate that key elements of kinase activation and inhibition are conserved among ErbB family members.

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Organizational Affiliation: 

Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.15 kDa 
• Atom Count: 4,431 
• Modelled Residue Count: 533 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-4	A [auth B], B [auth D]	328	Homo sapiens	Mutation(s): 0  Gene Names: ERBB4, HER4 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15303 (Homo sapiens) Explore Q15303  Go to UniProtKB:  Q15303
PHAROS:  Q15303

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMM	C [auth B], D	N-{3-CHLORO-4-[(3-FLUOROBENZYL)OXY]PHENYL}-6-[5-({[2-(METHYLSULFONYL)ETHYL]AMINO}METHYL)-2-FURYL]-4-QUINAZOLINAMINE C29 H26 Cl F N4 O4 S BCFGMOOMADDAQU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FMM	PDBBind:  3BBT	Ki: 700 (nM) from 1 assay(s)
	BindingDB:  3BBT	Kd: 54 (nM) from 1 assay(s)
		IC50: min: 7.6, max: 1000 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.289 
• R-Value Work: 0.251 
• R-Value Observed: 0.253 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.682	α = 90
b = 102.682	β = 90
c = 185.124	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-12 
Deposition Author(s): Qiu, C.

Revision History  

• Version 1.0: 2008-02-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description