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

Crystal structure of the PWWP1 domain of NSD2 bound by compound 17.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: W.72, I.73, F.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.74 EDO.2: 3 residues within 4Å: Chain A: V.27, Y.30 Ligands: 01.3 No protein-ligand interaction detected (PLIP)

1 x 01: 7-[3-methyl-5-[2-methyl-5-[(pyridin-3-ylamino)methyl]phenyl]imidazol-4-yl]-4~{H}-1,4-benzoxazin-3-one

01.3: 15 residues within 4Å: Chain A: V.27, Y.30, W.33, F.63, F.64, G.65, D.66, A.67, P.68, E.69, R.70, A.71, L.115, Q.118 Ligands: EDO.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.33, A:F.63, A:F.63, A:E.69, A:A.71, A:L.115 Hydrogen bonds: A:A.67, A:E.69, A:E.69, A:Q.118 pi-Stacking: A:Y.30, A:W.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carlino, L. et al., Identification of Novel Potent NSD2-PWWP1 Ligands Using Structure-Based Design and Computational Approaches. J.Med.Chem. (2024)

Release Date

2024-05-29

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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