9FOE: PWWP1 domain of NSD2 bound by compound 7

Crystal structure of the PWWP1 domain of NSD2 bound by compound 7. Determined by X-ray diffraction at 1.96 Å resolution. Released 3 Sept 2025.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,010
Mol. weight: 19.46 kDa
Ligands: A1IEF
Released: 3 Sept 2025

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

Secondary structure: helices and β-sheets

9FOE contains 5 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: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	225-228	4	1
β-strand	236-240	5	1
β-strand	243	1	2
β-strand	248	1	2
β-strand	250-251	2	1
β-strand	261-266	6	1
β-strand	272-277	6	1
α-helix	278-280	3
β-strand	281-283	3	1
α-helix	305-307	3
α-helix	316-333	18
α-helix	337-344	8
β-strand	347-349	3	3
β-strand	352-354	3	3
α-helix	357-360	4

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

>9FOE_1 Histone-lysine N-methyltransferase NSD2 (chains A)
MGGGPNTGRDKDHLLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQAASARQYH
VQFFGDAPERAWIFEKSLVAFAGEGQFAKLCQESAKQAPTAAEKIKLLAPISGKLRAQWE
MGIVQAEEAASMSVEERKAKFTFLYVGAQLHLNPQVAKEAGIAAEGGGENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
A1IEF	1-[[(2~{S})-1-[4-[ethyl(pyridin-4-ylmethyl)amino]-6-methyl-pyrimidin-2-yl]pyrro…	C19 H27 N7 O	1

Primary citation

Structural and Molecular Insight into the PWWP1 Domain of NSD2 from the Discovery of Novel Binders Via DNA-Encoded Library Screening. Collie, G.W., Ackroyd, B., Corbishley, C. et al. ACS Med Chem Lett (2025) 16:1703-1708. DOI 10.1021/acsmedchemlett.5c00396 · 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.
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

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