MolNFT v1 · #140019 · protein

Crystal structure of SMYD3 in complex with covalent inhibitor 1

5XXD · SMYD3 methyltransferase: “Crystal structure of SMYD3 in complex with covalent inhibitor 1”. X-ray diffraction, 3 ligands (SAM, 8NR, ZN), 4 pockets (best druggability 0.79). MolNFT v1 #140019 on GenesisL1: 3D structure, binding sites…

PDB: 5XXD
Type: protein
Length: 423 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SMYD3 methyltransferase
Ligands: SAM, 8NR, ZN
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SMYD3 methyltransferase	protein	423	49% helix, 13% strand	—

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · chains A
8NR · Ethyl 4-(5,6,7,8-tetrahydroacridin-3-ylcarbonyl) piperazine-1-carboxylate · 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

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1057	0.79	0.81	101	SAM, 8NR
2	201	0.53	0.78	31	empty
3	94	0.42	0.78	23	empty
4	50	0.31	0.77	13	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5XXD · Crystal structure of SmyD3 in complex with covalent inhibitor 1 · the same entry in another collection · 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
Elsewhere: RCSB PDB 5XXD · PDBe 5XXD

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