SMTL ID : 5w1y.1

SETD8 in complex with a covalent inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 9SV: 2-(4-methylpiperazin-1-yl)-3-(phenylsulfanyl)naphthalene-1,4-dione(Covalent)

9SV.1: 11 residues within 4Å: Chain A: E.73, Y.76, D.79, P.80, T.82, G.83, C.84, L.164 Chain B: C.84 Ligands: UNX.5, 9SV.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.164 Hydrogen bonds: A:T.82 9SV.17: 9 residues within 4Å: Chain A: C.84 Chain B: Y.76, D.79, P.80, T.82, G.83, C.84, H.161 Ligands: 9SV.1 No protein-ligand interaction detected (PLIP)

36 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 3 residues within 4Å: Chain A: S.116, G.117, R.138 Ligand excluded by PLIP UNX.3: 3 residues within 4Å: Chain A: M.86, R.153 Ligands: UNX.5 Ligand excluded by PLIP UNX.4: 3 residues within 4Å: Chain A: L.123, H.124, D.125 Ligand excluded by PLIP UNX.5: 4 residues within 4Å: Chain A: C.84, R.153 Ligands: 9SV.1, UNX.3 Ligand excluded by PLIP UNX.6: 3 residues within 4Å: Chain A: D.149, G.151, D.152 Ligand excluded by PLIP UNX.7: 2 residues within 4Å: Chain A: F.89 Ligands: UNX.8 Ligand excluded by PLIP UNX.8: 4 residues within 4Å: Chain A: Y.87, T.121, D.152 Ligands: UNX.7 Ligand excluded by PLIP UNX.9: 2 residues within 4Å: Chain A: Q.13, S.14 Ligand excluded by PLIP UNX.10: 4 residues within 4Å: Chain A: R.52, G.53, A.136, S.137 Ligand excluded by PLIP UNX.11: 7 residues within 4Å: Chain A: E.29, V.57, E.58, H.60, R.106, L.107, G.108 Ligand excluded by PLIP UNX.12: 6 residues within 4Å: Chain A: E.58, Y.59, V.98, H.131, L.132 Ligands: UNX.13 Ligand excluded by PLIP UNX.13: 4 residues within 4Å: Chain A: L.63, P.130, H.131 Ligands: UNX.12 Ligand excluded by PLIP UNX.14: 5 residues within 4Å: Chain A: Y.85, R.109, Y.150, R.153 Ligands: UNX.15 Ligand excluded by PLIP UNX.15: 4 residues within 4Å: Chain A: C.84, Y.85, R.153 Ligands: UNX.14 Ligand excluded by PLIP UNX.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNX.18: 3 residues within 4Å: Chain B: T.82, T.101 Ligands: UNX.19 Ligand excluded by PLIP UNX.19: 4 residues within 4Å: Chain B: Y.76, T.82, T.101 Ligands: UNX.18 Ligand excluded by PLIP UNX.20: 3 residues within 4Å: Chain B: M.86, R.153, S.157 Ligand excluded by PLIP UNX.21: 3 residues within 4Å: Chain B: D.62, R.102 Ligands: UNX.25 Ligand excluded by PLIP UNX.22: 5 residues within 4Å: Chain B: R.17, D.21, H.124, D.125, I.126 Ligand excluded by PLIP UNX.23: 3 residues within 4Å: Chain A: G.39 Chain B: E.103 Ligands: UNX.32 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain B: S.81, E.103 Ligand excluded by PLIP UNX.25: 5 residues within 4Å: Chain B: D.99, A.100, T.101, R.102 Ligands: UNX.21 Ligand excluded by PLIP UNX.26: 4 residues within 4Å: Chain B: N.118, E.145, L.147 Ligands: UNX.27 Ligand excluded by PLIP UNX.27: 3 residues within 4Å: Chain B: E.144, E.145 Ligands: UNX.26 Ligand excluded by PLIP UNX.28: 1 residues within 4Å: Chain B: D.125 Ligand excluded by PLIP UNX.29: 3 residues within 4Å: Chain B: R.52, G.53, D.54 Ligand excluded by PLIP UNX.30: 4 residues within 4Å: Chain A: I.34, R.42 Chain B: D.38, G.39 Ligand excluded by PLIP UNX.31: 3 residues within 4Å: Chain B: K.115, D.149, G.151 Ligand excluded by PLIP UNX.32: 4 residues within 4Å: Chain A: G.39 Chain B: I.34, R.42 Ligands: UNX.23 Ligand excluded by PLIP UNX.33: 2 residues within 4Å: Chain B: G.83, C.84 Ligand excluded by PLIP UNX.34: 3 residues within 4Å: Chain B: V.129, H.131 Ligands: UNX.35 Ligand excluded by PLIP UNX.35: 4 residues within 4Å: Chain B: I.126, D.127, V.129 Ligands: UNX.34 Ligand excluded by PLIP UNX.36: 2 residues within 4Å: Chain B: N.112, H.113 Ligand excluded by PLIP UNX.37: 5 residues within 4Å: Chain B: I.66, A.69, K.70, E.73, Y.88 Ligand excluded by PLIP UNX.38: 2 residues within 4Å: Chain B: K.33, I.34 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tempel, W. et al., SETD8 in complex with a covalent inhibitor. to be published

Release Date

2017-06-21

Peptides

N-lysine methyltransferase KMT5A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-lysine methyltransferase KMT5A