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MolNFT v1 · #104427 · protein

Crystal structure of I243N HDAC8 in complex with saha

4QA2 · Histone deacetylase 8: “Crystal structure of I243N HDAC8 in complex with saha”. X-ray diffraction, 3 ligands (SHH, K, ZN), 1 pocket (best druggability 0.82). MolNFT v1 #104427 on GenesisL1: 3D structure, binding sites and pockets in…

PDB
4QA2
Type
protein
Length
721 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Histone deacetylase 8
EC
3.5.1.98
UniProt
Q9BY41
Ligands
SHH, K, ZN
Pockets
1 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 13% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AHistone deacetylase 8 (EC 3.5.1.98)protein35640% helix, 13% strandQ9BY41
BHistone deacetylase 8 (EC 3.5.1.98)protein36538% helix, 13% strandQ9BY41

Ligands and binding sites

  • SHH · Octanedioic acid hydroxyamide phenylamide · ligand · 2 copies · chains A, B
  • K · Potassium ion · metal · 4 copies · chains A, B
  • ZN · Zinc ion · metal · 2 copies · chains A, B
  • GOL · Glycerol · additive · 2 copies · chains A, B

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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111290.820.83128SHH

Interfaces

1 interface between chains.

  • A–B · 853 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

  • 4QA2 · Crystal structure of I243N HDAC8 in complex with SAHA · 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

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