5AQN

Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

A fragment-based approach applied to a highly flexible target: Insights and challenges towards the inhibition of HSP70 isoforms.

Jones, A.M., Westwood, I.M., Osborne, J.D., Matthews, T.P., Cheeseman, M.D., Rowlands, M.G., Jeganathan, F., Burke, R., Lee, D., Kadi, N., Liu, M., Richards, M., McAndrew, C., Yahya, N., Dobson, S.E., Jones, K., Workman, P., Collins, I., van Montfort, R.L.

(2016) Sci Rep 6: 34701-34701

  • DOI: 10.1038/srep34701
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The heat shock protein 70s (HSP70s) are molecular chaperones implicated in many cancers and of significant interest as targets for novel cancer therapies. Several HSP70 inhibitors have been reported, but because the majority have poor physicochemical ...

    The heat shock protein 70s (HSP70s) are molecular chaperones implicated in many cancers and of significant interest as targets for novel cancer therapies. Several HSP70 inhibitors have been reported, but because the majority have poor physicochemical properties and for many the exact mode of action is poorly understood, more detailed mechanistic and structural insight into ligand-binding to HSP70s is urgently needed. Here we describe the first comprehensive fragment-based inhibitor exploration of an HSP70 enzyme, which yielded an amino-quinazoline fragment that was elaborated to a novel ATP binding site ligand with different physicochemical properties to known adenosine-based HSP70 inhibitors. Crystal structures of amino-quinazoline ligands bound to the different conformational states of the HSP70 nucleotide binding domain highlighted the challenges of a fragment-based approach when applied to this particular flexible enzyme class with an ATP-binding site that changes shape and size during its catalytic cycle. In these studies we showed that Ser275 is a key residue in the selective binding of ATP. Additionally, the structural data revealed a potential functional role for the ATP ribose moiety in priming the protein for the formation of the ATP-bound pre-hydrolysis complex by influencing the conformation of one of the phosphate binding loops.

    Organizational Affiliation: 

    Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London SM2 5NG, United Kingdom.,Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEAT SHOCK COGNATE 71 KDA PROTEIN
A, C, E
386Homo sapiensMutation(s): 0 
Gene Names: HSPA8 (HSC70, HSP73, HSPA10)
Find proteins for P11142 (Homo sapiens)
Go to Gene View: HSPA8
Go to UniProtKB:  P11142
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
B, D, F
118Homo sapiensMutation(s): 0 
Gene Names: BAG1 (HAP)
Find proteins for Q99933 (Homo sapiens)
Go to Gene View: BAG1
Go to UniProtKB:  Q99933
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JG8
Query on JG8
Download SDF File 
Download CCD File 
A, C, E
BENZOFURO[3,2-D]PYRIMIDIN-4(3H)-ONE
C10 H6 N2 O2
PCCWPSFTRGJXEF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B, C, D, E, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS
Download SDF File 
Download CCD File 
A, C, E
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS
Download SDF File 
Download CCD File 
A, C, E
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 233.290α = 90.00
b = 41.030β = 123.13
c = 205.250γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Data collection, Database references