3FZL

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

• PDB DOI: https://doi.org/10.2210/pdb3FZL/pdb

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


• Deposited: 2009-01-26 Released: 2009-03-17 
• Deposition Author(s): Dokurno, P., Williamson, D.S., Murray, J.B., Surgenor, A.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.304 
• R-Value Work: 0.210 
• R-Value Observed: 0.217 

Starting Model: experimental

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

• PubMed: 19256508 
• 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.

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Organizational Affiliation: 

Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, United Kingdom. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.92 kDa 
• Atom Count: 4,171 
• Modelled Residue Count: 488 
• Deposited Residue Count: 495 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock cognate 71 kDa protein	A	381	Homo sapiens	Mutation(s): 0  Gene Names: HSPA8, HSC70, HSP73, HSPA10 EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P11142 (Homo sapiens) Explore P11142  Go to UniProtKB:  P11142
PHAROS:  P11142 GTEx:  ENSG00000109971

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BAG family molecular chaperone regulator 1	B	114	Homo sapiens	Mutation(s): 0  Gene Names: BAG1, HAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q99933 (Homo sapiens) Explore Q99933  Go to UniProtKB:  Q99933
PHAROS:  Q99933 GTEx:  ENSG00000107262

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3FD	D [auth A]	4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile C25 H23 Cl2 N7 O4 ZXGGCBQORXDVTE-UMCMBGNQSA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
3FD	BindingDB:  3FZL	Ki: min: 120, max: 200 (nM) from 3 assay(s)
		Kd: 300 (nM) from 1 assay(s)
		IC50: min: 500, max: 1.04e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.304 
• R-Value Work: 0.210 
• R-Value Observed: 0.217 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.601	α = 90
b = 120.384	β = 106.57
c = 53.128	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Dokurno, P., Williamson, D.S., Murray, J.B., Surgenor, A.E.

Revision History  

• 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
• Version 1.3: 2024-10-30
  Changes: Structure summary