3NC9

X-ray structure of ketohexokinase complexed with an indazole compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Electron density guided fragment-based lead discovery of ketohexokinase inhibitors.

Gibbs, A.C.Abad, M.C.Zhang, X.Tounge, B.A.Lewandowski, F.A.Struble, G.T.Sun, W.Sui, Z.Kuo, L.C.

(2010) J.Med.Chem. 53: 7979-7991

  • DOI: 10.1021/jm100677s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A fragment-based drug design paradigm has been successfully applied in the discovery of lead series of ketohexokinase inhibitors. The paradigm consists of three iterations of design, synthesis, and X-ray crystallographic screening to progress low mol ...

    A fragment-based drug design paradigm has been successfully applied in the discovery of lead series of ketohexokinase inhibitors. The paradigm consists of three iterations of design, synthesis, and X-ray crystallographic screening to progress low molecular weight fragments to leadlike compounds. Applying electron density of fragments within the protein binding site as defined by X-ray crystallography, one can generate target specific leads without the use of affinity data. Our approach contrasts with most fragment-based drug design methodology where solution activity is a main design guide. Herein we describe the discovery of submicromolar ketohexokinase inhibitors with promising druglike properties.


    Organizational Affiliation

    Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ketohexokinase
A, B
313Homo sapiensMutation(s): 0 
Gene Names: KHK
EC: 2.7.1.3
Find proteins for P50053 (Homo sapiens)
Go to Gene View: KHK
Go to UniProtKB:  P50053
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TR3
Query on TR3

Download SDF File 
Download CCD File 
B
N-[3-(methylsulfanyl)-1-phenyl-1H-indazol-6-yl]piperidine-4-carboxamide
C20 H22 N4 O S
DHDKYDLNUPJXFQ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TR3IC50: 330 - 590 nM (100) BINDINGDB
TR3IC50: 330 nM BINDINGMOAD
TR3IC50: 330 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.696α = 90.00
b = 85.692β = 90.00
c = 136.852γ = 90.00
Software Package:
Software NamePurpose
JDirectordata collection
d*TREKdata scaling
PHENIXrefinement
PHENIXphasing
d*TREKdata reduction
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-02-22
    Type: Structure summary
  • Version 1.3: 2017-11-08
    Type: Advisory, Refinement description