PDBsum entry 3fcf

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protein ligands links
Hydrolase PDB id
Protein chain
223 a.a. *
SCN ×2
Waters ×179
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Complex of ung2 and a fragment-based designed inhibitor
Structure: Uracil-DNA glycosylase. Chain: a. Synonym: udg. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ung, dgu, ung1, ung15. Expressed in: escherichia coli. Expression_system_taxid: 562
1.84Å     R-factor:   0.200     R-free:   0.248
Authors: M.A.Bianchet,S.Chung,J.B.Parker,L.M.Amzel,J.T.Stivers
Key ref:
S.Chung et al. (2009). Impact of linker strain and flexibility in the design of a fragment-based inhibitor. Nat Chem Biol, 5, 407-413. PubMed id: 19396178 DOI: 10.1038/nchembio.163
21-Nov-08     Release date:   28-Apr-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P13051  (UNG_HUMAN) -  Uracil-DNA glycosylase
313 a.a.
223 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Uracil-DNA glycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   2 terms 
  Biochemical function     hydrolase activity, hydrolyzing N-glycosyl compounds     2 terms  


DOI no: 10.1038/nchembio.163 Nat Chem Biol 5:407-413 (2009)
PubMed id: 19396178  
Impact of linker strain and flexibility in the design of a fragment-based inhibitor.
S.Chung, J.B.Parker, M.Bianchet, L.M.Amzel, J.T.Stivers.
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.
  Selected figure(s)  
Figure 1.
(a) The method involves linking a substrate-derived aldehyde fragment to a library of aldehydes using bivalent oxyamine linkers (n = 2–6). The tethering reactions are performed in high-throughput and high-yield (>90%) using 96-well plates^5, ^6, ^7. Without the need for purification, the libraries are directly screened against a desired enzyme target to rapidly identify inhibitors. (b) Substrate fragment tethering using 6-formyluracil (11) as the substrate fragment yielded the first small-molecule inhibitor of the DNA repair enzyme human UNG2 (13, K[d] = 6 M). The interactions of the uracil and library fragments of dioxime 13 with human UNG2 are shown (Protein Data Bank ID 2HXM). The tether does not directly interact with the enzyme and has an unusual kinked conformation (see text).
Figure 4.
Difference free energies are in kcal mol^-1 relative to the DA (27) compound. The individual NH linkages that are changed when switching from DA (27) to MA1 (6), DO (14) or MA2 (22) are numbered as indicated (see text for further details).
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2009, 5, 407-413) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20471246 C.W.Murray, and T.L.Blundell (2010).
Structural biology in fragment-based drug design.
  Curr Opin Struct Biol, 20, 497-507.  
19909758 D.O.Zharkov, G.V.Mechetin, and G.A.Nevinsky (2010).
Uracil-DNA glycosylase: Structural, thermodynamic and kinetic aspects of lesion search and recognition.
  Mutat Res, 685, 11-20.  
20350805 F.Liu, R.M.Hakami, B.Dyas, M.Bahta, G.T.Lountos, D.S.Waugh, R.G.Ulrich, and T.R.Burke (2010).
A rapid oxime linker-based library approach to identification of bivalent inhibitors of the Yersinia pestis protein-tyrosine phosphatase, YopH.
  Bioorg Med Chem Lett, 20, 2813-2816.  
20520657 R.Huang, I.Martinez-Ferrando, and P.A.Cole (2010).
Enhanced interrogation: emerging strategies for cell signaling inhibition.
  Nat Struct Mol Biol, 17, 646-649.  
20165808 R.Moumné, V.Larue, B.Seijo, T.Lecourt, L.Micouin, and C.Tisné (2010).
Tether influence on the binding properties of tRNALys3 ligands designed by a fragment-based approach.
  Org Biomol Chem, 8, 1154-1159.  
19929835 C.L.Verlinde, E.Fan, S.Shibata, Z.Zhang, Z.Sun, W.Deng, J.Ross, J.Kim, L.Xiao, T.L.Arakaki, J.Bosch, J.M.Caruthers, E.T.Larson, I.Letrong, A.Napuli, A.Kelly, N.Mueller, F.Zucker, W.C.Van Voorhis, E.A.Merritt, and W.G.Hol (2009).
Fragment-based cocktail crystallography by the medical structural genomics of pathogenic protozoa consortium.
  Curr Top Med Chem, 9, 1678-1687.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.