Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 28.64 kDa 
• Atom Count: 1613 
• Residue Count: 187 
• Unique protein chains: 1

4DUM

Co-crystal structure of eIF4E with inhibitor

• DOI: 10.2210/pdb4DUM/pdb

• Classification: TRANSLATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-22 Released: 2012-04-11 
• Deposition Author(s): Min, X., Johnstone, S., Walker, N., Wang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.271 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Literature

Structure-Guided Design, Synthesis, and Evaluation of Guanine-Derived Inhibitors of the eIF4E mRNA-Cap Interaction.

Chen, X., Kopecky, D.J., Mihalic, J., Jeffries, S., Min, X., Heath, J., Deignan, J., Lai, S., Fu, Z., Guimaraes, C., Shen, S., Li, S., Johnstone, S., Thibault, S., Xu, H., Cardozo, M., Shen, W., Walker, N., Kayser, F., Wang, Z.

(2012) J Med Chem 55: 3837-3851

• PubMed: 22458568 
• DOI: 10.1021/jm300037x
• Primary Citation of Related Structures:  
  4DT6, 4DUM


• PubMed Abstract: 
  

The eukaryotic initiation factor 4E (eIF4E) plays a central role in the initiation of gene translation and subsequent protein synthesis by binding the 5' terminal mRNA cap structure. We designed and synthesized a series of novel compounds that display potent binding affinity against eIF4E despite their lack of a ribose moiety, phosphate, and positive charge as present in m7-GMP. The biochemical activity of compound 33 is 95 nM for eIF4E in an SPA binding assay. More importantly, the compound has an IC(50) of 2.5 μM for inhibiting cap-dependent mRNA translation in a rabbit reticular cell extract assay (RRL-IVT). This series of potent, truncated analogues could serve as a promising new starting point toward the design of neutral eIF4E inhibitors with physicochemical properties suitable for cellular activity assessment.

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Organizational Affiliation: 

Department of Chemistry Research & Discovery, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, California 94080, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 4E	A	240	Homo sapiens	Mutation(s): 0  Gene Names: EIF4E, EIF4EL1, EIF4F
Find proteins for P06730 (Homo sapiens) Explore P06730  Go to UniProtKB:  P06730
NIH Common Fund Data Resources
PHAROS  P06730 GTEx  ENSG00000151247

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HLI	A	(4-{7-[2-(4-chlorophenoxy)ethyl]-2-(methylamino)-6-oxo-6,7-dihydro-1H-purin-8-yl}phenyl)phosphonic acid C20 H19 Cl N5 O5 P MCYZBWKMUOPJOU-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
HLI	IC50 :  95   nM  PDBBind
HLI	IC50:  95   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.271 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.225	α = 90
b = 58.766	β = 90
c = 125.442	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-22 
• Released Date: 2012-04-11 
Deposition Author(s): Min, X., Johnstone, S., Walker, N., Wang, Z.

Revision History 

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2012-05-02
  Changes: Database references
• Version 1.2: 2012-06-27
  Changes: Database references