5WBZ

Structure of human Ketohexokinase complexed with hits from fragment screening

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

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

  • 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, ident ...

    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: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ketohexokinase A, B313Homo sapiensMutation(s): 0 
Gene Names: KHK
EC: 2.7.1.3
Find proteins for P50053 (Homo sapiens)
Explore P50053 
Go to UniProtKB:  P50053
NIH Common Fund Data Resources
PHAROS:  P50053
GTEx:  ENSG00000138030
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A4J
Query on A4J
Download Ideal Coordinates CCD File 
A, B
6-[(3S,4S)-3,4-dihydroxypyrrolidin-1-yl]-2-[(3S)-3-hydroxy-3-methylpyrrolidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile
C16 H19 F3 N4 O3
FAXXYODRCHXHTQ-HUBLWGQQSA-N		 Ligand Interaction
CIT
Query on CIT
Download Ideal Coordinates CCD File 
A, B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A4JIC50:  340   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.18α = 90
b = 86.38β = 90
c = 137.62γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2017-06-29 
  • Released Date: 2017-09-13 
    • Deposition Author(s): Pandit, J.

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Database references