Structure of KHK in complex with compound 4 (6-[(1~{S},5~{R})-6-(hydroxymethyl)-3-azabicyclo[3.1.0]hexan-3-yl]-2-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile)

Experimental Data Snapshot

  • Resolution: 2.38 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history


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.

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
GTEx:  ENSG00000138030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50053
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on S6J

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C17 H19 F3 N4 O2
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
S6J Binding MOAD:  6W0X IC50: 140 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.38 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.79α = 90
b = 85.82β = 90
c = 137.76γ = 90
Software Package:
Software NamePurpose
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