2YEJ

HSP90 inhibitors and drugs from fragment and virtual screening

• PDB DOI: https://doi.org/10.2210/pdb2YEJ/pdb

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


• Deposited: 2011-03-25 Released: 2011-06-15 
• Deposition Author(s): Roughley, S.D., Hubbard, R.E., Baker, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.349 
• R-Value Work: 0.246 
• R-Value Observed: 0.251 

Starting Model: experimental

Literature

How Well Can Fragments Explore Accessed Chemical Space? a Case Study from Heat Shock Protein 90.

Roughley, S.D., Hubbard, R.E.

(2011) J Med Chem 54: 3989

• PubMed: 21561141 
• DOI: https://doi.org/10.1021/jm200350g
• Primary Citation of Related Structures:  
  2YE2, 2YE3, 2YE4, 2YE5, 2YE6, 2YE7, 2YE8, 2YE9, 2YEA, 2YEB, 2YEC, 2YED, 2YEE, 2YEF, 2YEG, 2YEH, 2YEI, 2YEJ

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Organizational Affiliation: 

Vernalis (R&D) Ltd., Granta Park, Abington, Cambridge, CB21 6GB, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 28.92 kDa 
• Atom Count: 1,829 
• Modelled Residue Count: 209 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT SHOCK PROTEIN HSP 90-ALPHA	A	252	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens) Explore P07900  Go to UniProtKB:  P07900
GTEx:  ENSG00000080824

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XQK	C [auth A]	METHYL 5-ISOXAZOL-5-YL-3-METHYL-1H-PYRAZOLE-4-CARBOXYLATE C9 H9 N3 O3 ATKIWUMRVKGZOO-UHFFFAOYSA-N
ZZ3	D [auth A]	4-METHYL-6-(METHYLSULFANYL)-1,3,5-TRIAZIN-2-AMINE C5 H8 N4 S CQORBMDQIUWHGC-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZZ3	BindingDB:  2YEJ	IC50: 3.50e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.349 
• R-Value Work: 0.246 
• R-Value Observed: 0.251 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.038	α = 90
b = 90.352	β = 90
c = 98.858	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-15 
Deposition Author(s): Roughley, S.D., Hubbard, R.E., Baker, L.M.

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-06-23
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description