9Y60: NSD2 PWWP1 domain

Crystal structure of NSD2 PWWP1 domain in complex with (6R)-6-(3,5-dichlorophenyl)morpholin-3-one (ligand 2). Determined by X-ray diffraction at 2.02 Å resolution. Released 15 Jul 2026.

Method: X-ray diffraction
Resolution: 2.02 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,380
Mol. weight: 20.01 kDa
Ligands: A1CSP
Released: 15 Jul 2026

Explore 9Y60 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Y60 contains 9 α-helices and 10 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	206	1	1
β-strand	217	1	1
β-strand	225-228	4	2
β-strand	236-240	5	2
β-strand	250-252	3	2
α-helix	253-255	3
β-strand	260-266	7	2
α-helix	267	1
β-strand	272-277	6	2
α-helix	278-280	3
β-strand	281-283	3	2
α-helix	289-300	12
α-helix	304-310	7
α-helix	316-334	19
α-helix	337-344	8
α-helix	346	1
β-strand	347-349	3	3
β-strand	352-354	3	3
α-helix	357-369	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase NSD2	A	protein	174	Homo sapiens	O96028 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9Y60_1 Histone-lysine N-methyltransferase NSD2 (chains A)
MAKKESCPNTGRDKDHLLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQKKSAR
QYHVQFFGDAPERAWIFEKSLVAFEGEGQFEKLCQESAKQAPTKAEKIKLLKPISGKLRA
QWEMGIVQAEEAASMSVEERKAKFTFLYVGDQLHLNPQVAAEAGIAAEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1CSP	(6R)-6-(3,5-dichlorophenyl)morpholin-3-one	C10 H9 Cl2 N O2	1

Primary citation

NSD2 Degradation Remediates the Oncogenic Cistrome in t(4;14) Multiple Myeloma. Hu, B., Edwards, J., Modi, H. et al. Blood (2026). DOI 10.1182/blood.2025031998 · PubMed

Other PDB entries of the same protein (UniProt O96028 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9FOC 1.62 Å, Crystal structure of the PWWP1 domain of NSD2 bound by compound 11.
6XCG 1.64 Å, Histone-lysine N-methyltransferase NSD2-PWWP1 with compound UNC6934
9EXY 1.7 Å, Crystal structure of the PWWP1 domain of NSD2 bound by compound 34.
9GBF 1.76 Å, X-RAY structure of PHDvC5HCH tandem domain of NSD2
5VC8 1.8 Å, Crystal structure of the WHSC1 PWWP1 domain
9KNB 1.84 Å, NSD2-PWWP1 domain bound with compound 9
9EXX 1.94 Å, Crystal structure of the PWWP1 domain of NSD2 bound by compound 18.
9FOE 1.96 Å, Crystal structure of the PWWP1 domain of NSD2 bound by compound 7.
9KN9 2.0 Å, NSD2-PWWP1 domain bound with compound 1.
5LSU 2.14 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
7LMT 2.27 Å, Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a
6UE6 2.4 Å, PWWP1 domain of NSD2 in complex with MR837

Browse structure collections

About this viewer

MolViewer shows 9Y60 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.