SMTL ID : 9cvd.1

SET Domain of Histone-Lysine N-Methyltransferase NSD2 in Complex with Selective Inhibitor

Coordinates

PDB Format Compare

Method

SOLUTION NMR

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.161, C.208, C.210, C.215, S.216, G.217 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.161, A:C.208, A:C.210, A:C.215 ZN.2: 5 residues within 4Å: Chain A: C.33, C.35, C.43, C.49 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.33, A:C.35, A:C.43, A:C.49 ZN.3: 8 residues within 4Å: Chain A: C.33, C.43, C.58, C.63, A.65, C.69, N.71 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.43, A:C.58, A:C.63, A:C.69

1 x 01: 9-{[(2M)-5-[(3R)-3-amino-3-(pyridin-2-yl)piperidin-1-yl]-2-(3,4-difluorophenyl)pyridin-4-yl]methyl}-9H-purin-6-amine

01.4: 21 residues within 4Å: Chain A: P.6, K.86, K.90, G.91, W.92, F.134, Y.135, R.155, F.156, M.157, N.158, H.159, S.160, Y.196, N.203, T.206, V.207, C.208, R.209, C.210, L.219 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.6, A:F.134, A:Y.196, A:T.206, A:L.219 Hydrogen bonds: A:W.92, A:W.92, A:H.159, A:H.159, A:R.209 pi-Stacking: A:F.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szczepski, K. et al., Selective NSD2 Inhibition Reveals an Epigenetic Dependency of KRAS-Driven Cancers. Nature (2025)

Release Date

2025-04-30

Peptides

Histone-lysine N-methyltransferase NSD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase NSD2