MolNFT v1 · #124589 · protein

SMYD2 in complex with AZ378

5KJL · N-lysine methyltransferase SMYD2: “SMYD2 in complex with AZ378”. X-ray diffraction, 2 ligands (SAM, ZN), 3 pockets (best druggability 0.77). MolNFT v1 #124589 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KJL
Type: protein
Length: 428 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, ZN
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	N-lysine methyltransferase SMYD2 (EC 2.1.1.-, 2.1.1.43)	protein	428	50% helix, 14% strand	Q9NRG4

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · chains A
ZN · Zinc ion · metal · 3 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1067	0.77	0.79	109	SAM
2	66	0.38	0.79	16	empty
3	86	0.38	0.76	17	empty

Compared structures

5KJL · SMYD2 in complex with AZ378 · 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

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 Q9NRG4
Elsewhere: RCSB PDB 5KJL · PDBe 5KJL · UniProt Q9NRG4

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