5HES

Human leucine zipper- and sterile alpha motif-containing kinase (ZAK, MLT, HCCS-4, MRK, AZK, MLTK) in complex with vemurafenib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure of the Human Protein Kinase ZAK in Complex with Vemurafenib.

Mathea, S.Abdul Azeez, K.R.Salah, E.Tallant, C.Wolfreys, F.Konietzny, R.Fischer, R.Lou, H.J.Brennan, P.E.Schnapp, G.Pautsch, A.Kessler, B.M.Turk, B.E.Knapp, S.

(2016) ACS Chem Biol 11: 1595-1602

  • DOI: https://doi.org/10.1021/acschembio.6b00043
  • Primary Citation of Related Structures:  
    5HES

  • PubMed Abstract: 

    The mixed lineage kinase ZAK is a key regulator of the MAPK pathway mediating cell survival and inflammatory response. ZAK is targeted by several clinically approved kinase inhibitors, and inhibition of ZAK has been reported to protect from doxorubicin-induced cardiomyopathy. On the other hand, unintended targeting of ZAK has been linked to severe adverse effects such as the development of cutaneous squamous cell carcinoma. Therefore, both specific inhibitors of ZAK, as well as anticancer drugs lacking off-target activity against ZAK, may provide therapeutic benefit. Here, we report the first crystal structure of ZAK in complex with the B-RAF inhibitor vemurafenib. The cocrystal structure displayed a number of ZAK-specific features including a highly distorted P loop conformation enabling rational inhibitor design. Positional scanning peptide library analysis revealed a unique substrate specificity of the ZAK kinase including unprecedented preferences for histidine residues at positions -1 and +2 relative to the phosphoacceptor site. In addition, we screened a library of clinical kinase inhibitors identifying several inhibitors that potently inhibit ZAK, demonstrating that this kinase is commonly mistargeted by currently used anticancer drugs.


  • Organizational Affiliation

    Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford , Oxford, OX37DQ, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase MLT
A, B
307Homo sapiensMutation(s): 0 
Gene Names: ZAKMLTKHCCS4
EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYL2 (Homo sapiens)
Explore Q9NYL2 
Go to UniProtKB:  Q9NYL2
PHAROS:  Q9NYL2
GTEx:  ENSG00000091436 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NYL2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
032
Query on 032

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
N-(3-{[5-(4-chlorophenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]carbonyl}-2,4-difluorophenyl)propane-1-sulfonamide
C23 H18 Cl F2 N3 O3 S
GPXBXXGIAQBQNI-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
032 BindingDB:  5HES IC50: min: 23, max: 31 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.180 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.712α = 90
b = 78.712β = 90
c = 133.345γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-04-06
    Changes: Database references
  • Version 1.2: 2016-06-29
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Structure summary
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-23
    Changes: Structure summary