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 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    5FV7

  • 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-hydroxyurea bound in the active site coordinated to two magnesium ions ...

    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

    Bioscience, Oncology Innovative Medicines and Early Development Biotech Unit, Cambridge, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FLAP ENDONUCLEASE 1A, B353Homo sapiensMutation(s): 0 
Gene Names: FEN1RAD2
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P39748 (Homo sapiens)
Explore P39748 
Go to UniProtKB:  P39748
PHAROS:  P39748
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39748
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R3Z
Query on R3Z

Download Ideal Coordinates CCD File 
E [auth A],
H [auth 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 Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth B],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
R3Z BindingDB:  5FV7 IC50: min: 0.01, max: 46.4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • 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



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

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