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X-ray structure of NSD3-PWWP1 in complex with compound 5

Analyse X-ray structure of NSD3-PWWP1 in complex with compound 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6G27
Type: protein
Length: 119 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone-lysine N-methyltransferase NSD3
EC: 2.1.1.43
UniProt: Q9BZ95
Ligands: EHE
Pockets: 2 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43)	protein	119	32% helix, 24% strand	Q9BZ95

Ligands and binding sites

EHE · 5-methyl-6-phenyl-2-piperidin-4-yl-pyridazin-3-one · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	77	0.44	0.80	14	EHE
2	111	0.43	0.77	18	empty

Compared structures

6G27 · X-ray structure of NSD3-PWWP1 in complex with compound 5 · the same entry in another collection · chain A against A, TM-score 1.00
Q9BZ95 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase NSD3 (Q9BZ95) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9BZ95
Elsewhere: RCSB PDB 6G27 · PDBe 6G27 · UniProt Q9BZ95

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