9EXX: PWWP1 domain of NSD2 bound by compound 18

Crystal structure of the PWWP1 domain of NSD2 bound by compound 18. Determined by X-ray diffraction at 1.94 Å resolution. Released 29 May 2024.

Method: X-ray diffraction
Resolution: 1.94 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,408
Mol. weight: 40.22 kDa
Ligands: A1H7Y, EOH
Released: 29 May 2024

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

Secondary structure: helices and β-sheets

9EXX contains 20 α-helices and 14 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: 11 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
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	304-311	8
α-helix	313-314	2
α-helix	316-333	18
α-helix	337-344	8
α-helix	346	1
β-strand	347-349	3	2
β-strand	352-354	3	2
α-helix	357-363	7

Chain B: 9 helices, 6 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	272-277	6	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	316-333	18
α-helix	337-344	8
α-helix	346-347	2

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>9EXX_1 Histone-lysine N-methyltransferase NSD2 (chains A, B)
MGGGPNTGRDKDHLLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQKKSARQYH
VQFFGDAPERAWIFEKSLVAFEGEGQFEKLCQESAKQAPTKAEKIKLLKPISGKLRAQWE
MGIVQAEEAASMSVEERKAKFTFLYVGDQLHLNPQVAKEAGIAAEGGGENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
A1H7Y	4-methyl-3-[1-methyl-5-(3-oxidanylidene-4~{H}-1,4-benzoxazin-7-yl)imidazol-4-yl…	C26 H22 N4 O3	2
EOH	Ethanol	C2 H6 O	3

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

Primary citation

Identification of Novel Potent NSD2-PWWP1 Ligands Using Structure-Based Design and Computational Approaches. Carlino, L., Astles, P.C., Ackroyd, B. et al. J Med Chem (2024) 67:8962-8987. DOI 10.1021/acs.jmedchem.4c00215 · 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
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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