MolNFT v1 · #140025 · protein

Crystal structure of SMYD3 in complex with covalent inhibitor 3

5XXJ: “Crystal structure of SMYD3 in complex with covalent inhibitor 3”. X-ray diffraction, 3 ligands (8HF, SAM, ZN), 4 pockets (best druggability 0.79). MolNFT v1 #140025 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SMYD3	protein	423	51% helix, 13% strand	—

Ligands and binding sites

8HF · propyl (2~{R})-4-[4-chloranyl-2-[4-(2-oxidanylpropan-2-yl)phenyl]quinolin-7-yl]carbonyl-2-methyl-piperazine-1-carboxylate · ligand · chains A
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

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	1156	0.79	0.81	102	8HF, SAM
2	177	0.54	0.79	33	empty
3	111	0.47	0.79	23	empty
4	55	0.33	0.77	13	empty

Modifications

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

Compared structures

5XXJ · Crystal structure of SmyD3 in complex with covalent inhibitor 3 · 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 5XXJ · PDBe 5XXJ

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