MolNFT v1 · #140022 · protein

Crystal structure of SMYD3 in complex with covalent inhibitor 2

5XXG: “Crystal structure of SMYD3 in complex with covalent inhibitor 2”. X-ray diffraction, 3 ligands (8HR, SAM, ZN), 4 pockets (best druggability 0.79). MolNFT v1 #140022 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XXG
Type: protein
Length: 423 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SMYD3
Ligands: 8HR, 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

8HR · Propyl 4-(4-chloranyl-2-phenyl-quinolin-7-yl) carbonylpiperazine-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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	906	0.79	0.81	84	8HR
2	204	0.58	0.80	31	SAM
3	182	0.53	0.79	31	empty
4	114	0.43	0.77	27	empty

Modifications

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

Compared structures

5XXG · Crystal structure of SmyD3 in complex with covalent inhibitor 2 · 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 5XXG · PDBe 5XXG

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