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 

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
A
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN
Download SDF File 
Download CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
3FI
Query on 3FI
Download SDF File 
Download 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3FIIC50: 1300 nM (100) BINDINGDB
3FIIC50: 1300 nM BINDINGMOAD
3FIIC50: 1300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.014α = 90.00
b = 68.476β = 90.00
c = 69.674γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
DENZOdata reduction
ADSCdata collection
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


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
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description