5FV7

Human Fen1 in complex with an N-hydroxyurea compound

Summary for 5FV7

• Entry DOI: 10.2210/pdb5fv7/pdb
• Descriptor: FLAP ENDONUCLEASE 1, MAGNESIUM ION, 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione, ... (4 entities in total)
• Functional Keywords: hydrolase
• Biological source: HOMO SAPIENS (HUMAN)
• Cellular location: Isoform 1: Nucleus, nucleolus. Isoform FENMIT: Mitochondrion : P39748
• Total number of polymer chains: 2
• Total formula weight: 80355.02

Authors

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. (deposition date: 2016-02-03, release date: 2016-08-17, Last modification date: 2024-05-08)

Primary citation

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.
Cellular Active N-Hydroxyurea Fen1 Inhibitors Block Substrate Entry to the Active Site
Nat.Chem.Biol., 12:815-, 2016

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. 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.

PubMed: 27526030
DOI: 10.1038/NCHEMBIO.2148

Experimental method

X-RAY DIFFRACTION (2.84 Å)