MolNFT v1 · #121002 · protein

Co-crystal structure of human SMYD3 with an aza-sah compound

5HI7 · Histone-lysine N-methyltransferase SMYD3: “Co-crystal structure of human SMYD3 with an aza-sah compound”. X-ray diffraction, 3 ligands (62X, ZN, MG), 1 pocket (best druggability 0.81). MolNFT v1 #121002 on GenesisL1: 3D structure…

PDB: 5HI7
Type: protein
Length: 426 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone-lysine N-methyltransferase SMYD3
EC: 2.1.1.43
UniProt: Q9H7B4
Ligands: 62X, ZN, MG
Pockets: 1 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone-lysine N-methyltransferase SMYD3 (EC 2.1.1.43)	protein	426	50% helix, 13% strand	Q9H7B4

Ligands and binding sites

62X · 5'-{[(3S)-3-amino-3-carboxypropyl][3-(dimethylamino) propyl]amino}-5'-deoxyadenosine · ligand · chains A
ZN · Zinc ion · metal · 3 copies · chains A
MG · Magnesium ion · metal · 2 copies · chains A
DMS · Dimethyl sulfoxide · additive · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1005	0.81	0.82	107	MG, DMS, 62X

Compared structures

Q9H7B4 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SMYD3 (Q9H7B4) · 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 Q9H7B4
Elsewhere: RCSB PDB 5HI7 · PDBe 5HI7 · UniProt Q9H7B4

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