Complex of UNG2 and a fragment-based design inhibitor

Experimental Data Snapshot

  • Resolution: 1.64 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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This is version 1.3 of the entry. See complete history


Impact of linker strain and flexibility in the design of a fragment-based inhibitor

Chung, S.Parker, J.B.Bianchet, M.Amzel, L.M.Stivers, J.T.

(2009) Nat Chem Biol 5: 407-413

  • DOI: https://doi.org/10.1038/nchembio.163
  • Primary Citation of Related Structures:  
    3FCF, 3FCI, 3FCK, 3FCL

  • PubMed Abstract: 

    The linking together of molecular fragments that bind to adjacent sites on an enzyme can lead to high-affinity inhibitors. Ideally, this strategy would use linkers that do not perturb the optimal binding geometries of the fragments and do not have excessive conformational flexibility that would increase the entropic penalty of binding. In reality, these aims are seldom realized owing to limitations in linker chemistry. Here we systematically explore the energetic and structural effects of rigid and flexible linkers on the binding of a fragment-based inhibitor of human uracil DNA glycosylase. Analysis of the free energies of binding in combination with cocrystal structures shows that the flexibility and strain of a given linker can have a substantial impact on binding affinity even when the binding fragments are optimally positioned. Such effects are not apparent from inspection of structures and underscore the importance of linker optimization in fragment-based drug discovery efforts.

  • Organizational Affiliation

    Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uracil-DNA glycosylaseA [auth B]223Homo sapiensMutation(s): 0 
EC: 3.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P13051 (Homo sapiens)
Explore P13051 
Go to UniProtKB:  P13051
PHAROS:  P13051
GTEx:  ENSG00000076248 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13051
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FCK

Download Ideal Coordinates CCD File 
3-({[3-({[(1E)-(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methylidene]amino}oxy)propyl]amino}methyl)benzoic acid
C16 H18 N4 O5
Binding Affinity Annotations 
IDSourceBinding Affinity
FCK PDBBind:  3FCK IC50: 1.00e+5 (nM) from 1 assay(s)
BindingDB:  3FCK IC50: 1.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.64 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.18α = 90
b = 69.149β = 90
c = 70.037γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-12-27
    Changes: Advisory, Data collection, Database references, Derived calculations