3RO4

X-ray Structure of Ketohexokinase in complex with an indazole compound derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Optimization of a pyrazole hit from FBDD into a novel series of indazoles as ketohexokinase inhibitors.

Zhang, X.Song, F.Kuo, G.H.Xiang, A.Gibbs, A.C.Abad, M.C.Sun, W.Kuo, L.C.Sui, Z.

(2011) Bioorg Med Chem Lett 21: 4762-4767

  • DOI: 10.1016/j.bmcl.2011.06.067
  • Primary Citation of Related Structures:  
    3RO4

  • PubMed Abstract: 
  • A series of indazoles have been discovered as KHK inhibitors from a pyrazole hit identified through fragment-based drug discovery (FBDD). The optimization process guided by both X-ray crystallography and solution activity resulted in lead-like compounds ...

    A series of indazoles have been discovered as KHK inhibitors from a pyrazole hit identified through fragment-based drug discovery (FBDD). The optimization process guided by both X-ray crystallography and solution activity resulted in lead-like compounds with good pharmaceutical properties.


    Organizational Affiliation

    Johnson & Johnson Pharmaceutical Research and Development, Welsh & McKean Roads, PO Box 776, Spring House, PA 19477, United States. xzhang5@its.jnj.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ketohexokinase AB313Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LJ9
Query on LJ9

Download Ideal Coordinates CCD File 
B
3-ethyl-6-[(3aR,6aS)-hexahydropyrrolo[3,4-c]pyrrol-2(1H)-yl]-1-phenyl-1H-indazole
C21 H24 N4
JRGJWNYNELQBIY-IYBDPMFKSA-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 %)
LJ9IC50:  590   nM  BindingDB
LJ9IC50:  5360   nM  BindingDB
LJ9IC50 :  590   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.61α = 90
b = 86.034β = 90
c = 139.792γ = 90
Software Package:
Software NamePurpose
JDirectordata collection
PHENIXmodel building
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2012-05-23
    Changes: Database references
  • Version 1.2: 2012-12-05
    Changes: Other
  • Version 1.3: 2017-11-08
    Changes: Refinement description