PDBsum entry 3fcf

Hydrolase

PDB id: 3fcf

Contents

Protein chain

223 a.a. *

Ligands

FCF

SCN ×2

Waters ×179

* Residue conservation analysis

PDB id:

3fcf

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

Resolution:

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

Date:

21-Nov-08 Release date: 28-Apr-09

Protein chain

P13051  (UNG_HUMAN) -  Uracil-DNA glycosylase from Homo sapiens

Seq: 313 a.a.

Struc: 223 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.2.27 - uracil-DNA glycosylase.

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.

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. 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.