3FCF

Complex of UNG2 and a fragment-based designed inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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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:  
    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 ...

    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)  |  3D 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)
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FCF
Query on FCF
Download Ideal Coordinates CCD File 
B [auth A]3-[(1E,7E)-8-(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)-3,6-dioxa-2,7-diazaocta-1,7-dien-1-yl]benzoic acid
C15 H14 N4 O6
TUYDQQMKXSQIQG-GONBZBRSSA-N		 Ligand Interaction
SCN
Query on SCN
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FCF Binding MOAD:  3FCF IC50: 4.00e+4 (nM) from 1 assay(s)
PDBBind:  3FCF IC50: 4.00e+4 (nM) from 1 assay(s)
BindingDB:  3FCF IC50: 4.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.251α = 90
b = 69.26β = 90
c = 70.097γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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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: Refinement description