7QI0

Crystal structure of KLK6 in complex with compound DKFZ918

• PDB DOI: https://doi.org/10.2210/pdb7QI0/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2021-12-14 Released: 2022-11-23 
• Deposition Author(s): Jagtap, P.K.A., Baumann, A., Lohbeck, J., Isak, D., Miller, A., Hennig, J.
• Funding Organization(s): Not funded

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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 

Starting Model: experimental

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

• PubMed: 36320846 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Cancer Drug Development Group, German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg Germany [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.67 kDa 
• Atom Count: 3,503 
• Modelled Residue Count: 439 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kallikrein-6	A, B	223	Homo sapiens	Mutation(s): 3  Gene Names: KLK6, PRSS18, PRSS9 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C9I (Subject of Investigation/LOI)	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

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 = 62.41	α = 90
b = 46.86	β = 92.32
c = 68.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Jagtap, P.K.A., Baumann, A., Lohbeck, J., Isak, D., Miller, A., Hennig, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary