5FV7

Human Fen1 in complex with an N-hydroxyurea compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Cellular Active N-Hydroxyurea Fen1 Inhibitors Block Substrate Entry to the Active Site

Exell, J.C.Thompson, M.J.Finger, L.D.Shaw, S.K.Abbott, W.M.Mcwhirter, C.Debreczeni, J.E.Jones, C.D.Nissink, J.W.M.Ward, T.A.Sioberg, C.W.L.Molina, D.M.Durant, S.T.Grasby, J.A.

(2016) Nat.Chem.Biol. 12: 815

  • DOI: 10.1038/nchembio.2148

  • PubMed Abstract: 
  • The structure-specific nuclease human flap endonuclease-1 (hFEN1) plays a key role in DNA replication and repair and may be of interest as an oncology target. We present the crystal structure of inhibitor-bound hFEN1, which shows a cyclic N-hydroxyur ...

    The structure-specific nuclease human flap endonuclease-1 (hFEN1) plays a key role in DNA replication and repair and may be of interest as an oncology target. We present the crystal structure of inhibitor-bound hFEN1, which shows a cyclic N-hydroxyurea bound in the active site coordinated to two magnesium ions. Three such compounds had similar IC50 values but differed subtly in mode of action. One had comparable affinity for protein and protein-substrate complex and prevented reaction by binding to active site catalytic metal ions, blocking the necessary unpairing of substrate DNA. Other compounds were more competitive with substrate. Cellular thermal shift data showed that both inhibitor types engaged with hFEN1 in cells, and activation of the DNA damage response was evident upon treatment with inhibitors. However, cellular EC50 values were significantly higher than in vitro inhibition constants, and the implications of this for exploitation of hFEN1 as a drug target are discussed.


    Organizational Affiliation

    Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FLAP ENDONUCLEASE 1
A, B
353Homo sapiensMutation(s): 0 
Gene Names: FEN1 (RAD2)
EC: 3.1.-.-
Find proteins for P39748 (Homo sapiens)
Go to Gene View: FEN1
Go to UniProtKB:  P39748
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R3Z
Query on R3Z

Download SDF File 
Download CCD File 
A, B
1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione
C15 H12 N2 O5 S
MXQGCMQXTPTJJT-VIFPVBQESA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
R3ZIC50: 0 - 46.4 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.234 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 43.339α = 102.06
b = 50.193β = 94.01
c = 66.945γ = 90.74
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-08-24
    Type: Database references
  • Version 1.2: 2016-10-05
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Data collection