3FZK

Crystal Structures of Hsc70/Bag1 in Complex with Small Molecule Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Novel adenosine-derived inhibitors of 70 kDa heat shock protein, discovered through structure-based design

Williamson, D.S.Borgognoni, J.Clay, A.Daniels, Z.Dokurno, P.Drysdale, M.J.Foloppe, N.Francis, G.L.Graham, C.J.Howes, R.Macias, A.T.Murray, J.B.Parsons, R.Shaw, T.Surgenor, A.E.Terry, L.Wang, Y.Wood, M.Massey, A.J.

(2009) J Med Chem 52: 1510-1513

  • DOI: https://doi.org/10.1021/jm801627a
  • Primary Citation of Related Structures:  
    3FZF, 3FZH, 3FZK, 3FZL, 3FZM

  • PubMed Abstract: 

    The design and synthesis of novel adenosine-derived inhibitors of HSP70, guided by modeling and X-ray crystallographic structures of these compounds in complex with HSC70/BAG-1, is described. Examples exhibited submicromolar affinity for HSP70, were highly selective over HSP90, and some displayed potency against HCT116 cells. Exposure of compound 12 to HCT116 cells caused significant reduction in cellular levels of Raf-1 and Her2 at concentrations similar to that which caused cell growth arrest.


  • Organizational Affiliation

    Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, United Kingdom. d.williamson@vernalis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock cognate 71 kDa protein381Homo sapiensMutation(s): 0 
Gene Names: HSPA8HSC70HSP73HSPA10
UniProt & NIH Common Fund Data Resources
Find proteins for P11142 (Homo sapiens)
Explore P11142 
Go to UniProtKB:  P11142
PHAROS:  P11142
GTEx:  ENSG00000109971 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11142
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BAG family molecular chaperone regulator 1114Homo sapiensMutation(s): 0 
Gene Names: BAG1HAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q99933 (Homo sapiens)
Explore Q99933 
Go to UniProtKB:  Q99933
PHAROS:  Q99933
GTEx:  ENSG00000107262 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99933
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3BK
Query on 3BK

Download Ideal Coordinates CCD File 
E [auth A](2R,3R,4S,5R)-2-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol
C17 H18 Cl2 N6 O4
VBJKVZXRYLCYGQ-XNIJJKJLSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
C [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
3BK BindingDB:  3FZK Ki: 4310 (nM) from 1 assay(s)
Kd: min: 3500, max: 3548 (nM) from 2 assay(s)
IC50: 9100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.504α = 90
b = 119.896β = 106.52
c = 53.047γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description