5MKS

HSP72-NBD bound to compound TCI 8 - Tyr15 in down-conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

An Irreversible Inhibitor of HSP72 that Unexpectedly Targets Lysine-56.

Pettinger, J.Le Bihan, Y.V.Widya, M.van Montfort, R.L.Jones, K.Cheeseman, M.D.

(2017) Angew Chem Int Ed Engl 56: 3536-3540

  • DOI: 10.1002/anie.201611907
  • Primary Citation of Related Structures:  
    5MKR, 5MKS

  • PubMed Abstract: 
  • The stress-inducible molecular chaperone, HSP72, is an important therapeutic target in oncology, but inhibiting this protein with small molecules has proven particularly challenging. Validating HSP72 inhibitors in cells is difficult owing to competition with the high affinity and abundance of its endogenous nucleotide substrates ...

    The stress-inducible molecular chaperone, HSP72, is an important therapeutic target in oncology, but inhibiting this protein with small molecules has proven particularly challenging. Validating HSP72 inhibitors in cells is difficult owing to competition with the high affinity and abundance of its endogenous nucleotide substrates. We hypothesized this could be overcome using a cysteine-targeted irreversible inhibitor. Using rational design, we adapted a validated 8-N-benzyladenosine ligand for covalent bond formation and confirmed targeted irreversible inhibition. However, no cysteine in the protein was modified; instead, we demonstrate that lysine-56 is the key nucleophilic residue. Targeting this lysine could lead to a new design paradigm for HSP72 chemical probes and drugs.


    Organizational Affiliation

    Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK.



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: HSPA1AHSPA1HSX70HSP72
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TI8
Query on TI8

Download Ideal Coordinates CCD File 
B [auth A]3-[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-[(4-chlorophenyl)methylamino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propyl prop-2-enoate
C22 H25 Cl N6 O5
XOSUZIPWVSJZRF-HAXDFEGKSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TI8 Binding MOAD:  5MKS Ki: 1.70e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.637α = 90
b = 83.672β = 90
c = 99.21γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC309/A8274
Cancer Research UKUnited KingdomC309/A11566

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-03-29
    Changes: Database references