3FCK

Complex of UNG2 and a fragment-based design inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1038/nchembio.163
  • Primary Citation of Related Structures:  

  • 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 ex ...

    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.


    Related Citations: 
    • Mimicking damaged DNA with a small molecule inhibitor of human UNG2.
      Krosky, D.J.,Bianchet, M.A.,Seiple, L.,Chung, S.,Amzel, L.M.,Stivers, J.T.
      (2006) Nucleic Acids Res. 34: 5872
    • Uracil-directed ligand tethering: an efficient strategy for uracil DNA glycosylase (UNG) inhibitor development
      Jiang, T.L.,Krosky, D.J.,Seiple, L.,Stivers, J.T.
      (2005) J.Am.Chem.Soc. 127: 17412


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase
B
223Homo sapiensMutation(s): 0 
Gene Names: UNG (DGU, UNG1, UNG15)
EC: 3.2.2.27
Find proteins for P13051 (Homo sapiens)
Go to Gene View: UNG
Go to UniProtKB:  P13051
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FCK
Query on FCK

Download SDF File 
Download CCD File 
B
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
CZTGLADCGFOCLD-VCHYOVAHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FCKIC50: 100000 nM (100) BINDINGDB
FCKIC50: 100000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.180α = 90.00
b = 69.149β = 90.00
c = 70.037γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Advisory, Refinement description