5AQW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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:  
    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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEAT SHOCK 70 KDA PROTEIN 1AA394Homo sapiensMutation(s): 0 
Gene Names: HSPA1AHSP72HSPA1HSX70
EC: 3.6.3.51
UniProt & NIH Common Fund Data Resources
Find proteins for P0DMV8 (Homo sapiens)
Explore P0DMV8 
Go to UniProtKB:  P0DMV8
PHAROS:  P0DMV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DMV8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5P7
Query on 5P7

Download Ideal Coordinates CCD File 
B [auth A](1S,2R,3R,5R)-3-(hydroxymethyl)-5-(quinazolin-4-ylamino)cyclopentane-1,2-diol
C14 H17 N3 O3
CXHFBVLYDOBWST-STRQVWJDSA-N
 Ligand Interaction
DTV
Query on DTV

Download Ideal Coordinates CCD File 
D [auth A](2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
C4 H10 O2 S2
VHJLVAABSRFDPM-QWWZWVQMSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
Q [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.942α = 90
b = 70.207β = 90
c = 84.769γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

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
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation