2YJA

Stapled Peptides binding to Estrogen Receptor alpha.

• PDB DOI: https://doi.org/10.2210/pdb2YJA/pdb

• Classification: HORMONE RECEPTOR/PEPTIDE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-19 Released: 2011-08-03 
• Deposition Author(s): Phillips, C., Roberts, L.R., Schade, M., Bazin, R., Bent, A., Davies, N.L., Irving, S.L., Moore, R., Pannifer, A.D., Brown, D.G., Pickford, A.R., Scott, A., Xu, B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.234 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Literature

Design and Structure of Stapled Peptides Binding to Estrogen Receptors.

Phillips, C., Roberts, L.R., Schade, M., Bazin, R., Bent, A., Davies, N.L., Moore, R., Pannifer, A.D., Pickford, A.R., Prior, S.H., Read, C.M., Scott, A., Brown, D.G., Xu, B., Irving, S.L.

(2011) J Am Chem Soc 133: 9696

• PubMed: 21612236 
• DOI: https://doi.org/10.1021/ja202946k
• Primary Citation of Related Structures:  
  2LDA, 2LDC, 2LDD, 2YJA, 2YJD


• PubMed Abstract: 
  

  Synthetic peptides that specifically bind nuclear hormone receptors offer an alternative approach to small molecules for the modulation of receptor signaling and subsequent gene expression. Here we describe the design of a series of novel stapled peptides that bind the coactivator peptide site of estrogen receptors. Using a number of biophysical techniques, including crystal structure analysis of receptor-stapled peptide complexes, we describe in detail the molecular interactions and demonstrate that all-hydrocarbon staples modulate molecular recognition events. The findings have implications for the design of stapled peptides in general.

---

Organizational Affiliation: 

Department of Chemistry, Pfizer, Sandwich CT13 9NJ, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 30.78 kDa 
• Atom Count: 2,198 
• Modelled Residue Count: 258 
• Deposited Residue Count: 268 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STAPLED PEPTIDE	A	13	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTROGEN RECEPTOR	B	255	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EST	C [auth B]	ESTRADIOL C18 H24 O2 VOXZDWNPVJITMN-ZBRFXRBCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MK8	A	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Binding Affinity Annotations
ID	Source	Binding Affinity
EST	BindingDB:  2YJA	Ki: min: 0.11, max: 100 (nM) from 14 assay(s)
		Kd: min: 0.2, max: 3.5 (nM) from 3 assay(s)
		IC50: min: 1.00e-2, max: 46 (nM) from 50 assay(s)
		EC50: min: 4.00e-3, max: 10 (nM) from 53 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.234 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.032	α = 90
b = 110.407	β = 90
c = 65.192	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Phillips, C., Roberts, L.R., Schade, M., Bazin, R., Bent, A., Davies, N.L., Irving, S.L., Moore, R., Pannifer, A.D., Brown, D.G., Pickford, A.R., Scott, A., Xu, B.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary