MolNFT v1 · #25265 · protein

Crystal structure of human HDAC8 complexed with cra-19156

1VKG · Histone deacetylase 8: “Crystal structure of human HDAC8 complexed with cra-19156”. X-ray diffraction, 3 ligands (CRI, ZN, NA), 2 pockets (best druggability 0.83). MolNFT v1 #25265 on GenesisL1: 3D structure, binding sites and…

PDB: 1VKG
Type: protein
Length: 696 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone deacetylase 8
UniProt: Q9BY41
Ligands: CRI, ZN, NA
Pockets: 2 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Histone deacetylase 8	protein	348	39% helix, 15% strand	Q9BY41

Ligands and binding sites

CRI · 5-(4-methyl-benzoylamino)-biphenyl-3,4'-dicarboxylic acid 3-dimethylamide-4'-hydroxyamide · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 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	1059	0.83	0.83	123	CRI
2	98	0.43	0.78	24	empty

Interfaces

1 interface between chains.

A–B · 697 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1VKG · Crystal Structure of Human HDAC8 complexed with CRA-19156 · the same entry in another collection · chain A against A, TM-score 1.00
Q9BY41 · AlphaFold monomer V2.0 prediction for histone deacetylase 8 (Q9BY41) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9BY41
Elsewhere: RCSB PDB 1VKG · PDBe 1VKG · UniProt Q9BY41

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