GL1X · GenesisL1 explorer

Research workbench

Crystal structure of SETD2 bound to compound 57

Analyse Crystal structure of SETD2 bound to compound 57 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
7LZF
Type
protein
Length
239 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Histone-lysine N-methyltransferase SETD2
EC
2.1.1.359, 2.1.1.-
UniProt
Q9BYW2
Ligands
SAM, YHV, ZN
Pockets
2 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 26% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AHistone-lysine N-methyltransferase SETD2 (EC 2.1.1.359, 2.1.1.-)protein23918% helix, 26% strandQ9BYW2

Ligands and binding sites

  • SAM · S-adenosylmethionine · ligand · chains A
  • YHV · 4-fluoro-N-[(1R,3S)-3-{(3S)-3-[(methanesulfonyl) (methyl)amino]pyrrolidin-1-yl}cyclohexyl]-7-methyl-1H-indole-2-carboxamide · ligand · chains A
  • ZN · Zinc ion · metal · 3 copies · chains A
  • EDO · 1,2-ethanediol · additive · 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, 2 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14370.760.8447SAM, YHV
21330.520.8119empty

Compared structures

  • 7LZF · Crystal Structure of SETD2 bound to Compound 57 · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9BYW2 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETD2 (Q9BYW2) · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.