SMTL ID : 9foc.1 (1 other biounit)

Crystal structure of the PWWP1 domain of NSD2 bound by compound 11.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

1 x 01: (2S)-1-[4-[[(3R)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide

01.1: 11 residues within 4Å: Chain A: Y.30, W.33, F.63, F.64, G.65, D.66, A.67, P.68, E.69, Q.118 Ligands: 02.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.63, A:F.63, A:F.63, A:E.69 Hydrogen bonds: A:E.69 Water bridges: A:Y.30, A:Y.30, A:Q.118, A:Q.118 Salt bridges: A:E.69 pi-Cation interactions: A:Y.30

1 x 02: (2S)-1-[4-[[(3S)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide

02.2: 11 residues within 4Å: Chain A: Y.30, W.33, F.63, F.64, G.65, D.66, A.67, P.68, E.69, Q.118 Ligands: 01.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.33, A:F.63, A:F.63, A:F.63, A:E.69, A:E.69 Hydrogen bonds: A:E.69 Water bridges: A:Y.30, A:Y.30, A:Q.118, A:Q.118 Salt bridges: A:E.69 pi-Cation interactions: A:Y.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Collie, G.W. et al., Structural and Molecular Insight into the PWWP1 Domain of NSD2 from the Discovery of Novel Binders Via DNA-Encoded Library Screening. Acs Med.Chem.Lett. (2025)

Release Date

2025-09-03

Peptides

Histone-lysine N-methyltransferase NSD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase NSD2

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