Human Hsp90-alpha with 8-(2-chloro-3,4,5-trimethoxy-benzyl)-2-fluoro-9-pent-4-ylnyl-9H-purin-6-ylamine

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Structure-Activity Relationships in Purine-Based Inhibitor Binding to Hsp90 Isoforms

Wright, L.Barril, X.Dymock, B.Sheridan, L.Surgenor, A.Beswick, M.Drysdale, M.Collier, A.Massey, A.Davies, N.Fink, A.Fromont, C.Aherne, W.Boxall, K.Sharp, S.Workman, P.Hubbard, R.E.

(2004) Chem Biol 11: 775

  • DOI: https://doi.org/10.1016/j.chembiol.2004.03.033
  • Primary Citation of Related Structures:  
    1UY6, 1UY7, 1UY8, 1UY9, 1UYC, 1UYD, 1UYE, 1UYF, 1UYG, 1UYH, 1UYI, 1UYK, 1UYL, 1UYM

  • PubMed Abstract: 

    Inhibition of the ATPase activity of the chaperone protein HSP90 is a potential strategy for treatment of cancers. We have determined structures of the HSP90alpha N-terminal domain complexed with the purine-based inhibitor, PU3, and analogs with enhanced potency both in enzyme and cell-based assays. The compounds induce upregulation of HSP70 and downregulation of the known HSP90 client proteins Raf-1, CDK4, and ErbB2, confirming that the molecules inhibit cell growth by a mechanism dependent on HSP90 inhibition. We have also determined the first structure of the N-terminal domain of HSP90beta, complexed with PU3. The structures allow a detailed rationale to be developed for the observed affinity of the PU3 class of compounds for HSP90 and also provide a structural framework for design of compounds with improved binding affinity and drug-like properties.

  • Organizational Affiliation

    Vernalis (R&D) Ltd., Granta Park, Abington, Cambridge CB1 6GB, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEAT SHOCK PROTEIN HSP 90-ALPHA236Homo 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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PU1

Download Ideal Coordinates CCD File 
C20 H21 Cl F N5 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
PU1 PDBBind:  1UYF IC50: 3.00e+4 (nM) from 1 assay(s)
BindingDB:  1UYF IC50: min: 660, max: 3.00e+4 (nM) from 3 assay(s)
EC50: min: 1200, max: 1700 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.79α = 90
b = 91.509β = 90
c = 99.173γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-01
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Advisory, Data collection, Database references, Other, Refinement description