GL1X · GenesisL1 explorer

MolNFT v1 · #124588 · protein

SMYD2 in complex with AZ370

5KJK · N-lysine methyltransferase SMYD2: “SMYD2 in complex with AZ370”. X-ray diffraction, 3 ligands (SAM, 6T1, ZN), 3 pockets (best druggability 0.77). MolNFT v1 #124588 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5KJK
Type
protein
Length
429 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
N-lysine methyltransferase SMYD2
EC
2.1.1.-, 2.1.1.43
UniProt
Q9NRG4
Ligands
SAM, 6T1, ZN
Pockets
3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AN-lysine methyltransferase SMYD2 (EC 2.1.1.-, 2.1.1.43)protein42951% helix, 14% strandQ9NRG4

Ligands and binding sites

  • SAM · S-adenosylmethionine · ligand · chains A
  • 6T1 · 2-[2-[1-[2-(3,4-dichlorophenyl)ethyl]azetidin-3-yl]oxyphenyl]-~{N}-(3-pyrrolidin-1-ylpropyl)pyridine-4-carboxamide · ligand · chains A
  • ZN · Zinc ion · metal · 3 copies · chains A
  • BU3 · (R,R)-2,3-butanediol · additive · 4 copies · chains A

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

Pockets

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

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111360.770.79108SAM, 6T1
21030.390.7520empty
3560.250.7212empty

Compared structures

  • 5KJK · SMYD2 in complex with AZ370 · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9NRG4 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase SMYD2 (Q9NRG4) · a predicted model of the same protein · chain A against A, TM-score 1.00

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