SMTL ID : 7ty3.1

Crystal Structure of SETD2 Bound to an Indole-based Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.66, C.68, C.83, C.87 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.68, A:C.83, A:C.87 ZN.2: 5 residues within 4Å: Chain A: C.83, C.96, C.100, C.106 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.83, A:C.96, A:C.100, A:C.106 ZN.3: 4 residues within 4Å: Chain A: C.198, C.245, C.247, C.252 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.198, A:C.245, A:C.247, A:C.252

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.4: 19 residues within 4Å: Chain A: K.127, G.128, W.129, I.169, H.170, Y.171, Y.172, R.192, F.193, M.194, N.195, H.196, Q.243, K.244, C.245, F.246, C.247, L.256 Ligands: KRF.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:W.129, A:W.129, A:I.169, A:Y.171, A:Y.171, A:N.195, A:H.196, A:H.196, A:Q.243, A:F.246 Salt bridges: A:H.170

1 x KRF: N-[(1R,3R)-3-(4-acetylpiperazin-1-yl)cyclohexyl]-4-fluoro-7-methyl-1H-indole-2-carboxamide(Non-covalent)

KRF.5: 17 residues within 4Å: Chain A: Y.146, Y.171, Y.172, F.173, M.174, M.194, H.196, F.231, Y.233, F.235, Q.236, R.237, Y.238, E.241, Q.243, L.256 Ligands: SAM.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.146, A:Y.171, A:F.231, A:F.235, A:Y.238 Hydrogen bonds: A:F.173, A:F.173 pi-Stacking: A:Y.233, A:Y.233 pi-Cation interactions: A:Y.171

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

EDO.6: 6 residues within 4Å: Chain A: M.174, A.175, D.232, Y.233, Q.234, F.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.175, A:D.232, A:Q.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alford, J.S. et al., Conformational-Design-Driven Discovery of EZM0414: A Selective, Potent SETD2 Inhibitor for Clinical Studies. Acs Med.Chem.Lett. (2022)

Release Date

2022-08-31

Peptides

Histone-lysine N-methyltransferase SETD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SETD2

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