GL1X · GenesisL1 explorer

Research workbench

SETD8 in complex with a covalent inhibitor

Analyse SETD8 in complex with a covalent inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5W1Y
Type
protein
Length
314 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
N-lysine methyltransferase KMT5A
EC
2.1.1.-, 2.1.1.43
UniProt
Q9NQR1
Ligands
9SV, UNX
Pockets
1 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 35% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AN-lysine methyltransferase KMT5A (EC 2.1.1.-, 2.1.1.43)protein16229% helix, 35% strandQ9NQR1
BN-lysine methyltransferase KMT5A (EC 2.1.1.-, 2.1.1.43)protein15223% helix, 36% strandQ9NQR1

Ligands and binding sites

  • 9SV · 2-(4-methylpiperazin-1-yl)-3-(phenylsulfanyl) naphthalene-1,4-dione · ligand · 2 copies · chains A, B
  • UNX · Unknown atom or ion · ion · 36 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111990.850.86599SV, UNX

Interfaces

1 interface between chains.

  • A–B · 971 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

  • 5W1Y · SETD8 in complex with a covalent inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9NQR1 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase KMT5A (Q9NQR1) · a predicted model of the same protein · chain B against A, TM-score 0.88

Analyse

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