9FOC: PWWP1 domain of NSD2 bound by compound 11

Crystal structure of the PWWP1 domain of NSD2 bound by compound 11. Determined by X-ray diffraction at 1.62 Å resolution. Released 3 Sept 2025.

Method: X-ray diffraction
Resolution: 1.62 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,461
Mol. weight: 40.77 kDa
Ligands: A1IFS, A1IEG
Released: 3 Sept 2025

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

Secondary structure: helices and β-sheets

9FOC contains 17 α-helices and 16 β-strands across 2 chains. 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	225-228	4	1
β-strand	236-240	5	1
β-strand	250-252	3	1
α-helix	253-255	3
β-strand	260-266	7	1
β-strand	273-277	5	1
α-helix	278-280	3
β-strand	281-283	3	1
α-helix	287-289	3
α-helix	290-294	5
α-helix	317-333	17
α-helix	337-344	8
α-helix	346	1
β-strand	347-349	3	2
β-strand	352-354	3	2
α-helix	357-362	6

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	225-228	4	3
β-strand	236-240	5	3
β-strand	250-252	3	3
β-strand	260-266	7	3
α-helix	267	1
β-strand	273-277	5	3
α-helix	278-280	3
β-strand	281-283	3	3
α-helix	287-289	3
α-helix	290-299	10
α-helix	304-311	8
α-helix	313-314	2
α-helix	316-334	19
α-helix	337-344	8
α-helix	345-346	2
β-strand	347-349	3	4
β-strand	352-354	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase NSD2	A, B	protein	176	Homo sapiens	O96028 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9FOC_1 Histone-lysine N-methyltransferase NSD2 (chains A, B)
MGGGPNTGRDKDHLLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQKKSARQYH
VQFFGDAPERAWIFEKSLVAFEGEGQFEKLCQESAKQAPTKAEKIKLLKPISGKLRAQWE
MGIVQAEEAASMSVEERKAKFTFLYVGDQLHLNPQVAKEAGIAAEGGGENLYFQGS

Ligands and cofactors

ID	Name	Formula	Copies
A1IFS	(2S)-1-[4-[[(3R)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-meth…	C17 H27 N5 O3 S	2
A1IEG	(2S)-1-[4-[[(3S)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-meth…	C17 H27 N5 O3 S	2

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:

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.
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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