7VLN: NSD2-PWWP1 domain

NSD2-PWWP1 domain bound with an imidazol-5-yl benzonitrile compound. Determined by X-ray diffraction at 3.09 Å resolution. Released 6 Jul 2022.

Method: X-ray diffraction
Resolution: 3.09 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,074
Mol. weight: 45.77 kDa
Ligands: 7QC
Released: 6 Jul 2022

Explore 7VLN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VLN contains 19 α-helices and 18 β-strands across 3 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: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	225-228	4	1
β-strand	236-240	5	1
β-strand	250	1	1
β-strand	261-266	6	1
β-strand	272-277	6	1
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

Chain B: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	225-228	4	2
β-strand	236-240	5	2
β-strand	250-251	2	2
β-strand	261-266	6	2
β-strand	272-277	6	2
α-helix	278-280	3
β-strand	281-283	3	2
α-helix	287-289	3
α-helix	290-299	10
α-helix	305-311	7
α-helix	317-333	17
α-helix	337-344	8
α-helix	345-347	3

Chain C: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	225-230	6	3
β-strand	233-240	8	3
β-strand	250-252	3	3
β-strand	260-266	7	3
β-strand	274-277	4	3
β-strand	281-283	3	3
α-helix	287-289	3
α-helix	290-299	10
α-helix	305-309	5
α-helix	313-314	2
α-helix	316-333	18
α-helix	338-344	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase NSD2	A, B, C	protein	132	Homo sapiens	O96028 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>7VLN_1 Histone-lysine N-methyltransferase NSD2 (chains A, B, C)
LLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQKKSARQYHVQFFGDAPERAWI
FEKSLVAFEGEGQFEKLCQESAKQAPTKAEKIKLLKPISGKLRAQWEMGIVQAEEAASMS
VEERKAKFTFLY

Ligands and cofactors

ID	Name	Formula	Copies
7QC	4-[5-[4-(aminomethyl)-2,6-dimethoxy-phenyl]-3-methyl-imidazol-4-yl]benzenecarbo…	C20 H20 N4 O2	1

Primary citation

Structure-Based Discovery of a Series of NSD2-PWWP1 Inhibitors. Li, N., Yang, H., Liu, K. et al. J Med Chem (2022) 65:9459-9477. DOI 10.1021/acs.jmedchem.2c00709 · 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

Browse structure collections

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