Human PFKFB3 in complex with an indole inhibitor 5

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 

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Structure-Based Design of Potent and Selective Inhibitors of the Metabolic Kinase Pfkfb3.

Boyd, S.Brookfield, J.L.Critchlow, S.E.Cumming, I.A.Curtis, N.J.Debreczeni, J.Degorce, S.L.Donald, C.Evans, N.J.Groombridge, S.Hopcroft, P.Jones, N.P.Kettle, J.G.Lamont, S.Lewis, H.J.Macfaull, P.Mcloughlin, S.B.Rigoreau, L.J.M.Smith, J.M.St-Gallay, S.Stock, J.K.Turnbull, A.P.Wheatley, E.R.Winter, J.Wingfield, J.

(2015) J Med Chem 58: 3611

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00352
  • Primary Citation of Related Structures:  
    5AJV, 5AJW, 5AJX, 5AJY, 5AJZ, 5AK0

  • PubMed Abstract: 

    A weak screening hit with suboptimal physicochemical properties was optimized against PFKFB3 kinase using critical structure-guided insights. The resulting compounds demonstrated high selectivity over related PFKFB isoforms and modulation of the target in a cellular context. A selected example demonstrated exposure in animals following oral dosing. Examples from this series may serve as useful probes to understand the emerging biology of this metabolic target.

  • Organizational Affiliation

    ‡CRT Discovery Laboratories, Jonas Webb Building (B910), Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16875 (Homo sapiens)
Explore Q16875 
Go to UniProtKB:  Q16875
PHAROS:  Q16875
GTEx:  ENSG00000170525 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16875
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
MJP BindingDB:  5AJZ IC50: 2010 (nM) from 1 assay(s)
Binding MOAD:  5AJZ IC50: 2010 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.48α = 90
b = 102.48β = 90
c = 258.96γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary