SMTL ID : 9cr7.1

Structure of human SETD8 in complex with covalent inhibitor AM2928

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

1 x E1J: N-(3-{[7-(2-aminoethoxy)-6-methoxy-2-(pyrrolidin-1-yl)quinazolin-4-yl]amino}propyl)prop-2-enamide(Covalent)

E1J.1: 15 residues within 4Å: Chain A: C.107 Chain B: Y.82, C.107, Y.108, M.109, Y.110, R.132, L.133, I.134, N.135, T.144, L.155, Y.171, Y.173 Ligands: H81.2 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.82, B:Y.108, B:T.144, B:L.155, B:Y.171 Hydrogen bonds: B:C.107 Water bridges: B:Y.108

1 x H81: N-(3-{[7-(2-aminoethoxy)-6-methoxy-2-(pyrrolidin-1-yl)quinazolin-4-yl]amino}propyl)prop-2-ynamide(Covalent)

H81.2: 15 residues within 4Å: Chain A: Y.82, C.107, Y.108, M.109, Y.110, R.132, L.133, I.134, N.135, T.144, L.155, Y.171, Y.173 Chain B: C.107 Ligands: E1J.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.108, A:T.144, A:L.155, A:Y.171 Hydrogen bonds: A:C.107, A:M.109 Water bridges: A:R.65, A:N.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, A. et al., Structure-Activity relationship studies of SETD8 covalent inhibitors. To be published

Release Date

2025-07-30

Peptides

N-lysine methyltransferase KMT5A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-lysine methyltransferase KMT5A