8OMF

Crystal structure of hKHK-C in complex with compound-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

Starting Model: experimental
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Literature

Crystal structures of human and mouse ketohexokinase provide a structural basis for species- and isoform-selective inhibitor design.

Ebenhoch, R.Bauer, M.Romig, H.Gottschling, D.Kley, J.T.Heine, N.Weber, A.Uphues, I.Nar, H.Pautsch, A.

(2023) Acta Crystallogr D Struct Biol 79: 871-880

  • DOI: https://doi.org/10.1107/S2059798323006137
  • Primary Citation of Related Structures:  
    8OMD, 8OME, 8OMF, 8OMG

  • PubMed Abstract: 

    A molecular understanding of the proteins involved in fructose metabolism is essential for controlling the current spread of fructose-related obesity, diabetes and related adverse metabolic states in Western populations. Fructose catabolism starts with the phosphorylation of D-fructose to fructose 1-phosphate by ketohexokinase (KHK). KHK exists in two alternatively spliced isoforms: the hepatic and intestinal isoform KHK-C and the peripheral isoform KHK-A. Here, the structure of apo murine KHK (mKHK), which differs from structures of human KHK in overall conformation, is reported. An isoform-selective ligand, which offers a 50-fold higher potency on mKHK and human KHK-A compared with KHK-C, is further characterized. In mKHK, large-scale conformational changes are observed upon ligand binding. The structures suggest a combined strategy for the design of species- and isoform-selective KHK inhibitors.


  • Organizational Affiliation

    Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstrasse 67, 88400 Biberach an der Riss, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ketohexokinase
A, B
313Homo sapiensMutation(s): 0 
Gene Names: KHK
EC: 2.7.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P50053 (Homo sapiens)
Explore P50053 
Go to UniProtKB:  P50053
PHAROS:  P50053
GTEx:  ENSG00000138030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50053
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.36α = 90
b = 86.89β = 90
c = 137.91γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
BALBESphasing

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: 2023-09-27
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Database references