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 

Starting Model: experimental
View more details

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