4EGH

Hsp90-alpha ATPase domain in complex with (4-Hydroxyphenyl)morpholin-4-yl methanone

• PDB DOI: https://doi.org/10.2210/pdb4EGH/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-30 Released: 2012-05-23 
• Deposition Author(s): Chen, W.J., Wood, S.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.226 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

Fragment screening using capillary electrophoresis (CEfrag) for hit identification of heat shock protein 90 ATPase inhibitors.

Austin, C., Pettit, S.N., Magnolo, S.K., Sanvoisin, J., Chen, W., Wood, S.P., Freeman, L.D., Pengelly, R.J., Hughes, D.E.

(2012) J Biomol Screen 17: 868-876

• PubMed: 22573733 
• DOI: https://doi.org/10.1177/1087057112445785
• Primary Citation of Related Structures:  
  4EGH, 4EGI, 4EGK


• PubMed Abstract: 
  

  CEfrag is a new fragment screening technology based on affinity capillary electrophoresis (ACE). Here we report on the development of a mobility shift competition assay using full-length human heat shock protein 90α (Hsp90α), radicicol as the competitor probe ligand, and successful screening of the Selcia fragment library. The CEfrag assay was able to detect weaker affinity (IC(50) >500 µM) fragments than were detected by a fluorescence polarization competition assay using FITC-labeled geldanamycin. The binding site of selected fragments was determined by co-crystallization with recombinant Hsp90α N-terminal domain and X-ray analysis. The results of this study confirm that CEfrag is a sensitive microscale technique enabling detection of fragments binding to the biological target in near-physiological solution.

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Organizational Affiliation: 

Discovery, Selcia Ltd, Fyfield Business and Research Park, Ongar, UK. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.3 kDa 
• Atom Count: 1,920 
• Modelled Residue Count: 209 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	232	Homo sapiens	Mutation(s): 0  Gene Names: HSP90AA1, HSP90A, HSPC1, HSPCA EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens) Explore P07900  Go to UniProtKB:  P07900
PHAROS:  P07900 GTEx:  ENSG00000080824

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0OY	C [auth A]	(4-hydroxyphenyl)(morpholin-4-yl)methanone C11 H13 N O3 GJHYHTYGGHFYNN-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0OY	PDBBind:  4EGH	IC50: 5.50e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.226 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.87	α = 90
b = 89.66	β = 90
c = 100.12	γ = 90

Software Package:

Software Name	Purpose
PROTEUM2	data collection
PHASER	phasing
REFMAC	refinement
PROTEUM2	data reduction
PROTEUM2	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Chen, W.J., Wood, S.P.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2012-10-17
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations