6W0Z

Structure of KHK in complex with compound 8 (2-[(1~{S},5~{R})-3-[2-[(2~{S})-2-methylazetidin-1-yl]-6-(trifluoromethyl)pyrimidin-4-yl]-3-azabicyclo[3.1.0]hexan-6-yl]ethanoic acid)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Discovery of PF-06835919: A Potent Inhibitor of Ketohexokinase (KHK) for the Treatment of Metabolic Disorders Driven by the Overconsumption of Fructose.

Futatsugi, K.Smith, A.C.Tu, M.Raymer, B.Ahn, K.Coffey, S.B.Dowling, M.S.Fernando, D.P.Gutierrez, J.A.Huard, K.Jasti, J.Kalgutkar, A.S.Knafels, J.D.Pandit, J.Parris, K.D.Perez, S.Pfefferkorn, J.A.Price, D.A.Ryder, T.Shavnya, A.Stock, I.A.Tsai, A.S.Tesz, G.J.Thuma, B.A.Weng, Y.Wisniewska, H.M.Xing, G.Zhou, J.Magee, T.V.

(2020) J Med Chem 63: 13546-13560

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00944
  • Primary Citation of Related Structures:  
    6W0N, 6W0W, 6W0X, 6W0Y, 6W0Z

  • PubMed Abstract: 

    Increased fructose consumption and its subsequent metabolism have been implicated in metabolic disorders such as nonalcoholic fatty liver disease and steatohepatitis (NAFLD/NASH) and insulin resistance. Ketohexokinase (KHK) converts fructose to fructose-1-phosphate (F1P) in the first step of the metabolic cascade. Herein we report the discovery of a first-in-class KHK inhibitor, PF-06835919 ( 8 ), currently in phase 2 clinical trials. The discovery of 8 was built upon our originally reported, fragment-derived lead 1 and the recognition of an alternative, rotated binding mode upon changing the ribose-pocket binding moiety from a pyrrolidinyl to an azetidinyl ring system. This new binding mode enabled efficient exploration of the vector directed at the Arg-108 residue, leading to the identification of highly potent 3-azabicyclo[3.1.0]hexane acetic acid-based KHK inhibitors by combined use of parallel medicinal chemistry and structure-based drug design.


  • Organizational Affiliation

    Pfizer Inc. Medicine Design, 1 Portland Street, Cambridge, Massachusetts 02139, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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: 2.30 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.415α = 90
b = 82.883β = 90
c = 137.186γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2020-09-23 
  • Deposition Author(s): Jasti, J.

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2020-12-09
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description