Structure of human Ketohexokinase complexed with hits from fragment screening

Experimental Data Snapshot

  • Resolution: 2.74 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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Discovery of Fragment-Derived Small Molecules for in Vivo Inhibition of Ketohexokinase (KHK).

Huard, K.Ahn, K.Amor, P.Beebe, D.A.Borzilleri, K.A.Chrunyk, B.A.Coffey, S.B.Cong, Y.Conn, E.L.Culp, J.S.Dowling, M.S.Gorgoglione, M.F.Gutierrez, J.A.Knafels, J.D.Lachapelle, E.A.Pandit, J.Parris, K.D.Perez, S.Pfefferkorn, J.A.Price, D.A.Raymer, B.Ross, T.T.Shavnya, A.Smith, A.C.Subashi, T.A.Tesz, G.J.Thuma, B.A.Tu, M.Weaver, J.D.Weng, Y.Withka, J.M.Xing, G.Magee, T.V.

(2017) J Med Chem 60: 7835-7849

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00947
  • Primary Citation of Related Structures:  
    5WBM, 5WBO, 5WBP, 5WBQ, 5WBR, 5WBZ

  • PubMed Abstract: 

    Increased fructose consumption and its subsequent metabolism have been implicated in hepatic steatosis, dyslipidemia, obesity, and insulin resistance in humans. Since ketohexokinase (KHK) is the principal enzyme responsible for fructose metabolism, identification of a selective KHK inhibitor may help to further elucidate the effect of KHK inhibition on these metabolic disorders. Until now, studies on KHK inhibition with small molecules have been limited due to the lack of viable in vivo pharmacological tools. Herein we report the discovery of 12, a selective KHK inhibitor with potency and properties suitable for evaluating KHK inhibition in rat models. Key structural features interacting with KHK were discovered through fragment-based screening and subsequent optimization using structure-based drug design, and parallel medicinal chemistry led to the identification of pyridine 12.

  • Organizational Affiliation

    Medicine Design, Pfizer Inc. , Eastern Point Road, Groton, Connecticut 06340, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
313Homo sapiensMutation(s): 0 
Gene Names: KHK
UniProt & NIH Common Fund Data Resources
Find proteins for P50053 (Homo sapiens)
Explore P50053 
Go to UniProtKB:  P50053
PHAROS:  P50053
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50053
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.74 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.91α = 90
b = 85.02β = 90
c = 138.78γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2017-09-13 
  • Deposition Author(s): Pandit, J.

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description