2YEJ

HSP90 inhibitors and drugs from fragment and virtual screening


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEAT SHOCK PROTEIN HSP 90-ALPHA252Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
PHAROS:  P07900
GTEx:  ENSG00000080824 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07900
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XQK
Query on XQK

Download Ideal Coordinates CCD File 
C [auth A]METHYL 5-ISOXAZOL-5-YL-3-METHYL-1H-PYRAZOLE-4-CARBOXYLATE
C9 H9 N3 O3
ATKIWUMRVKGZOO-UHFFFAOYSA-N
ZZ3
Query on ZZ3

Download Ideal Coordinates CCD File 
D [auth A]4-METHYL-6-(METHYLSULFANYL)-1,3,5-TRIAZIN-2-AMINE
C5 H8 N4 S
CQORBMDQIUWHGC-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding 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 = 67.038α = 90
b = 90.352β = 90
c = 98.858γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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