7QI0

Crystal structure of KLK6 in complex with compound DKFZ918


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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Literature

Scalable synthesis and structural characterization of reversible KLK6 inhibitors.

Baumann, A.Isak, D.Lohbeck, J.Jagtap, P.K.A.Hennig, J.Miller, A.K.

(2022) RSC Adv 12: 26989-26993

  • DOI: 10.1039/d2ra04670a
  • Primary Citation of Related Structures:  
    7QHZ, 7QI0

  • PubMed Abstract: 
  • Scalable asymmetric syntheses of two kallikrein-related protease 6 (KLK6) inhibitors are reported. The inhibitors are assembled by linking enantiomerically enriched fragments via amide bond formation, followed by conversion of a cyano group to an amidine ...

    Scalable asymmetric syntheses of two kallikrein-related protease 6 (KLK6) inhibitors are reported. The inhibitors are assembled by linking enantiomerically enriched fragments via amide bond formation, followed by conversion of a cyano group to an amidine. One fragment, an amine, was prepared using the Ellman auxiliary, and a lack of clarity in the literature regarding the stereochemical outcome of this reaction was solved via X-ray crystallographic analysis of two derivatives. Complexes of the inhibitors bound to human KLK6 were solved by X-ray crystallography, revealing the binding poses.


    Organizational Affiliation

    German Cancer Consortium (DKTK) Im Neuenheimer Feld 280 69120 Heidelberg Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kallikrein-6A, B223Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92876
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C9I (Subject of Investigation/LOI)
Query on C9I

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(5~{R})-3-(6-carbamimidoylpyridin-3-yl)-~{N}-[(1~{S})-1-naphthalen-1-ylpropyl]-2-oxidanylidene-1,3-oxazolidine-5-carboxamide
C23 H23 N5 O3
QAGBDIKHIHPMIP-AZUAARDMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.41α = 90
b = 46.86β = 92.32
c = 68.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release