6W0X

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KetohexokinaseA, B313Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S6J (Subject of Investigation/LOI)
Query on S6J

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

Download Ideal Coordinates CCD File 
E [auth B], F [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2020-03-03 
  • 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