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 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


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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:  
    5AQF, 5AQG, 5AQH, 5AQI, 5AQJ, 5AQK, 5AQL, 5AQM, 5AQN, 5AQO, 5AQP, 5AQQ, 5AQR, 5AQS, 5AQT, 5AQU, 5AQV, 5AQW, 5AQX, 5AQY

  • 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 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 ...

    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: 

    Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEAT SHOCK COGNATE 71 KDA PROTEINA, C, E386Homo sapiensMutation(s): 0 
Gene Names: HSPA8, HSC70, HSP73, HSPA10
EC: 3.6.3.51
UniProt & NIH Common Fund Data Resources
Find proteins for P11142 (Homo sapiens)
Explore P11142 
Go to UniProtKB:  P11142
PHAROS:  P11142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11142
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1B, D, F118Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99933
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JG8
Query on JG8
Download Ideal Coordinates CCD File 
G [auth A],
N [auth C],
U [auth E]		BENZOFURO[3,2-D]PYRIMIDIN-4(3H)-ONE
C10 H6 N2 O2
PCCWPSFTRGJXEF-UHFFFAOYSA-N		 Ligand Interaction
TRS
Query on TRS
Download Ideal Coordinates CCD File 
K [auth A],
Q [auth C],
W [auth E]		2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
M [auth B],
O [auth C],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
O [auth C],
P [auth C],
T [auth D],
V [auth E],
Y [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
L [auth A],
R [auth C],
X [auth E]		DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
S [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 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 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 233.29α = 90
b = 41.03β = 123.13
c = 205.25γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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