9KNB: NSD2-PWWP1 domain

NSD2-PWWP1 domain bound with compound 9. Determined by X-ray diffraction at 1.84 Å resolution. Released 26 Nov 2025.

Method: X-ray diffraction
Resolution: 1.84 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,080
Mol. weight: 15.79 kDa
Ligands: A1EF7
Released: 26 Nov 2025

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

Secondary structure: helices and β-sheets

9KNB contains 8 α-helices and 6 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	225-228	4	1
β-strand	236-240	5	1
β-strand	250-251	2	1
β-strand	261-266	6	1
α-helix	267	1
β-strand	272-277	6	1
α-helix	278-280	3
β-strand	281-283	3	1
α-helix	287-289	3
α-helix	290-299	10
α-helix	306-309	4
α-helix	316-334	19
α-helix	337-344	8
α-helix	345-347	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase NSD2	A	protein	133	Homo sapiens	O96028 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9KNB_1 Histone-lysine N-methyltransferase NSD2 (chains A)
LLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQKKSARQYHVQFFGDAPERAWI
FEKSLVAFEGEGQFEKLCQESAKQAPTKAEKIKLLKPISGKLRAQWEMGIVQAEEAASMS
VEERKAKFTFLYV

Ligands and cofactors

ID	Name	Formula	Copies
A1EF7	N-(2-methoxyphenyl)-2-selanyl-benzamide	C14 H13 N O2 Se	1

Water and common crystallization additives (EPE) are not listed.

Primary citation

Fragment-Based Screening of NSD2-PWWP1 Identifies Novel Covalent Allosteric Ligands That Diminish Methyllysine and DNA Binding Abilities of NSD2. Huang, Y., Li, Y., Chen, X. et al. J Med Chem (2025) 68:24953-24967. DOI 10.1021/acs.jmedchem.5c01902 · 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
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.
9Y60 2.02 Å, Crystal structure of NSD2 PWWP1 domain in complex with (6R)-6-(3,5-dichlorophenyl)morphol…
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

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