3FCI

Complex of UNG2 and a fragment-based designed inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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:  
    3FCI, 3FCK, 3FCL, 3FCF

  • 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: 
    • 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
    • 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
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uracil-DNA glycosylaseA223Homo sapiensMutation(s): 0 
Gene Names: UNG, DGU, UNG1, UNG15
EC: 3.2.2 (PDB Primary Data), 3.2.2.27 (UniProt)
Find proteins for P13051 (Homo sapiens)
Explore P13051 
Go to UniProtKB:  P13051
NIH Common Fund Data Resources
PHAROS  P13051
GTEx  ENSG00000076248
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3FI
Query on 3FI
Download Ideal Coordinates CCD File 
A
3-{(E)-[(3-{[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methyl]amino}propoxy)imino]methyl}benzoic acid
C16 H18 N4 O5
DNNMFLCWPRQYIC-GIJQJNRQSA-N		 Ligand Interaction
SCN
Query on SCN
Download Ideal Coordinates CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3FIIC50:  1300   nM  BindingDB
3FIIC50 :  1300   nM  PDBBind
3FIIC50:  1300   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.014α = 90
b = 68.476β = 90
c = 69.674γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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: Refinement description