7QFV

Crystal structure of KLK6 in complex with compound 17a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A KLK6 Activity-Based Probe Reveals a Role for KLK6 Activity in Pancreatic Cancer Cell Invasion.

Zhang, L.Lovell, S.De Vita, E.Jagtap, P.K.A.Lucy, D.Goya Grocin, A.Kjaer, S.Borg, A.Hennig, J.Miller, A.K.Tate, E.W.

(2022) J Am Chem Soc 144: 22493-22504

  • DOI: https://doi.org/10.1021/jacs.2c07378
  • Primary Citation of Related Structures:  
    7QFT, 7QFV

  • PubMed Abstract: 

    Pancreatic cancer has the lowest survival rate of all common cancers due to late diagnosis and limited treatment options. Serine hydrolases are known to mediate cancer progression and metastasis through initiation of signaling cascades and cleavage of extracellular matrix proteins, and the kallikrein-related peptidase (KLK) family of secreted serine proteases have emerging roles in pancreatic ductal adenocarcinoma (PDAC). However, the lack of reliable activity-based probes (ABPs) to profile KLK activity has hindered progress in validation of these enzymes as potential targets or biomarkers. Here, we developed potent and selective ABPs for KLK6 by using a positional scanning combinatorial substrate library and characterized their binding mode and interactions by X-ray crystallography. The optimized KLK6 probe IMP-2352 ( k obs / I = 11,000 M -1 s -1 ) enabled selective detection of KLK6 activity in a variety of PDAC cell lines, and we observed that KLK6 inhibition reduced the invasiveness of PDAC cells that secrete active KLK6. KLK6 inhibitors were combined with N-terminomics to identify potential secreted protein substrates of KLK6 in PDAC cells, providing insights into KLK6-mediated invasion pathways. These novel KLK6 ABPs offer a toolset to validate KLK6 and associated signaling partners as targets or biomarkers across a range of diseases.


  • Organizational Affiliation

    Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kallikrein-6
A, B
223Homo sapiensMutation(s): 3 
Gene Names: KLK6PRSS18PRSS9
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q92876 (Homo sapiens)
Explore Q92876 
Go to UniProtKB:  Q92876
PHAROS:  Q92876
GTEx:  ENSG00000167755 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92876
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
KLK6 Activity-Based Probe (Ahx-DPhe-Ser(Z)-Dht-Arg-DPP)
C, D
5synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEM
Query on SEM
C, D
L-PEPTIDE LINKINGC10 H13 N O3SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.43α = 82.08
b = 40.08β = 84.95
c = 65.21γ = 70.87
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2024-01-31
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Source and taxonomy, Structure summary