5WBO | pdb_00005wbo

Structure of human Ketohexokinase complexed with hits from fragment screening


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.223 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.7b00947
  • Primary Citation 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. , 1 Portland Street, Cambridge, Massachusetts 02139, United States.

Macromolecule Content 

  • Total Structure Weight: 69.35 kDa 
  • Atom Count: 4,815 
  • Modeled Residue Count: 597 
  • Deposited Residue Count: 626 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1Y

Query on A1Y



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
4,6-dimethyl-2-(morpholin-4-yl)pyridine-3-carbonitrile
C12 H15 N3 O
LUTZBWBXBMVIOV-UHFFFAOYSA-N
CIT

Query on CIT



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
A1Y BindingDB:  5WBO Kd: 6.20e+4 (nM) from 1 assay(s)
IC50: min: 3.16e+5, max: 3.19e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.223 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.98α = 90
b = 85.9β = 90
c = 138.35γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

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: 2024-03-13
    Changes: Data collection, Database references