6QFG

Crystal Structure of Human Kallikrein 6 (I218Y) in complex with GSK144


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Evaluation of a crystallographic surrogate for kallikrein 5 in the discovery of novel inhibitors for Netherton syndrome.

Thorpe, J.H.Edgar, E.V.Smith, K.J.Lewell, X.Q.Rella, M.White, G.V.Polyakova, O.Nassau, P.Walker, A.L.Holmes, D.S.Pearce, A.C.Wang, Y.Liddle, J.Hovnanian, A.

(2019) Acta Crystallogr F Struct Biol Commun 75: 385-391

  • DOI: 10.1107/S2053230X19003169
  • Primary Citation of Related Structures:  
    6QFF, 6QFE, 6QFH, 6QFG

  • PubMed Abstract: 
  • The inhibition of kallikrein 5 (KLK5) has been identified as a potential strategy for treatment of the genetic skin disorder Netherton syndrome, in which loss-of-function mutations in the SPINK5 gene lead to down-regulation of the endogenous inhibitor LEKTI-1 and profound skin-barrier defects with severe allergic manifestations ...

    The inhibition of kallikrein 5 (KLK5) has been identified as a potential strategy for treatment of the genetic skin disorder Netherton syndrome, in which loss-of-function mutations in the SPINK5 gene lead to down-regulation of the endogenous inhibitor LEKTI-1 and profound skin-barrier defects with severe allergic manifestations. To aid in the development of a medicine for this target, an X-ray crystallographic system was developed to facilitate fragment-guided chemistry and knowledge-based drug-discovery approaches. Here, the development of a surrogate crystallographic system in place of KLK5, which proved to be challenging to crystallize, is described. The biochemical robustness of the crystallographic surrogate and the suitability of the system for the study of small nonpeptidic fragments and lead-like molecules are demonstrated.


    Organizational Affiliation

    INSERM UMR1163 Laboratory of Genetic Skin Diseases, Imagine Institute and Université Paris Descartes-Sorbonne Paris Cité, Paris, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kallikrein-6A, B223Homo sapiensMutation(s): 4 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J08 (Subject of Investigation/LOI)
Query on J08

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]4-[(5-phenyl-1~{H}-imidazol-2-yl)methylamino]-2-(pyridin-3-ylmethoxy)benzenecarboximidamide
C23 H22 N6 O
ZDLCAMFQMDNCSU-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
J08 Binding MOAD:  6QFG IC50: 3010 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.4α = 90
b = 45.9β = 93.64
c = 89.35γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2019-01-10 
  • Released Date: 2019-05-08 
  • Deposition Author(s): Thorpe, J.H.

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references