9EXW: PWWP1 domain of NSD2 bound by compound 17

Crystal structure of the PWWP1 domain of NSD2 bound by compound 17. Determined by X-ray diffraction at 2.43 Å resolution. Released 29 May 2024.

Method: X-ray diffraction
Resolution: 2.43 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,265
Mol. weight: 39.93 kDa
Ligands: A1H7X
Released: 29 May 2024

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

Secondary structure: helices and β-sheets

9EXW contains 16 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: 9 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	289-299	11
α-helix	304-311	8
α-helix	313-314	2
α-helix	317-333	17
α-helix	337-344	8
β-strand	347-349	3	2
β-strand	352-354	3	2
α-helix	357-363	7

Chain B: 7 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
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

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

>9EXW_1 Histone-lysine N-methyltransferase NSD2 (chains A, B)
MGGGPNTGRDKDHLLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQKKSARQYH
VQFFGDAPERAWIFEKSLVAFEGEGQFEKLCQESAKQAPTKAEKIKLLKPISGKLRAQWE
MGIVQAEEAASMSVEERKAKFTFLYVGDQLHLNPQVAKEAGIAAEGGGENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
A1H7X	7-[3-methyl-5-[2-methyl-5-[(pyridin-3-ylamino)methyl]phenyl]imidazol-4-yl]-4~{H…	C25 H23 N5 O2	2

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
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

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