SMTL ID : 6boz.1

Structure of human SETD8 in complex with covalent inhibitor MS4138

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: C.107, M.109, Y.111 Chain B: C.107, M.109, Y.111 Ligands: E1J.3 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:E.96, A:M.109, A:Y.111, B:E.96, B:Y.111

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

E1J.2: 20 residues within 4Å: Chain A: Y.82, G.106, C.107, Y.108, M.109, Y.110, R.132, L.133, I.134, N.135, T.144, L.155, L.157, Y.171, Y.173 Chain B: E.96, Q.101, P.103, C.107, M.109 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.82, A:Y.82, A:Y.108, A:T.144, A:L.155, A:L.157, A:Y.171, A:Y.171, B:P.103 Hydrogen bonds: A:C.107, A:Y.108, A:Y.173, B:E.96, B:E.96 Water bridges: A:R.132, A:N.135 E1J.3: 20 residues within 4Å: Chain A: E.96, Q.101, P.103, C.107 Chain B: Y.82, G.106, C.107, Y.108, M.109, Y.110, R.132, L.133, I.134, N.135, T.144, L.155, L.157, Y.171, Y.173 Ligands: EDO.1 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:E.96, A:P.103, B:Y.82, B:Y.108, B:Y.110, B:T.144, B:L.155, B:L.157, B:Y.171, B:Y.171 Hydrogen bonds: A:E.96, B:C.107 Water bridges: B:Y.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S. et al., The dynamic conformational landscape of the protein methyltransferase SETD8. Elife (2019)

Release Date

2019-05-01

Peptides

N-lysine methyltransferase KMT5A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-lysine methyltransferase KMT5A