MolNFT v1 · #104426 · protein

Crystal structure of A188T HDAC8 in complex with M344

4QA1 · Histone deacetylase 8: “Crystal structure of A188T HDAC8 in complex with M344”. X-ray diffraction, 3 ligands (B3N, K, ZN), 9 pockets (best druggability 0.81). MolNFT v1 #104426 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4QA1
Type: protein
Length: 1,447 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone deacetylase 8
EC: 3.5.1.98
UniProt: Q9BY41
Ligands: B3N, K, ZN
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone deacetylase 8 (EC 3.5.1.98)	protein	354	41% helix, 13% strand	Q9BY41
B, D	Histone deacetylase 8 (EC 3.5.1.98)	protein	370	39% helix, 13% strand	Q9BY41
C	Histone deacetylase 8 (EC 3.5.1.98)	protein	353	41% helix, 13% strand	Q9BY41

Ligands and binding sites

B3N · 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide · ligand · 4 copies · chains A, B, C, D
K · Potassium ion · metal · 8 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 4 copies · chains A, B, C, D

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

Pockets

9 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	999	0.81	0.82	92	ZN, B3N, GOL
2	1196	0.80	0.81	108	B3N, GOL
3	215	0.50	0.76	36	empty
4	204	0.50	0.76	23	empty
5	167	0.49	0.77	22	empty

Interfaces

5 interfaces between chains.

A–B · 821 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 814 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 372 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 336 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 163 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4QA1 · Crystal structure of A188T HDAC8 in complex with M344 · 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 C 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
Every structure of UniProt Q9BY41
Elsewhere: RCSB PDB 4QA1 · PDBe 4QA1 · UniProt Q9BY41

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