MolNFT v1 · #122694 · protein

HDAC2 with ligand BRD7232

5IX0 · Histone deacetylase 2: “HDAC2 with ligand BRD7232”. X-ray diffraction, 3 ligands (6EZ, CA, ZN), 5 pockets (best druggability 0.74). MolNFT v1 #122694 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IX0
Type: protein
Length: 1,101 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone deacetylase 2
EC: 3.5.1.98
UniProt: Q92769
Ligands: 6EZ, CA, ZN
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone deacetylase 2 (EC 3.5.1.98)	protein	369	41% helix, 13% strand	Q92769
B, C	Histone deacetylase 2 (EC 3.5.1.98)	protein	366	40% helix, 13% strand	Q92769

Ligands and binding sites

6EZ · (3-exo)-N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)-8-oxabicyclo[3.2.1]octane-3-carboxamide · ligand · 3 copies · chains A, B, C
CA · Calcium ion · metal · 6 copies · chains A, B, C
ZN · Zinc ion · metal · 3 copies · chains A, B, C
PGE · Triethylene glycol · additive · 9 copies · chains A, B, C
PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C
PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · 3 copies · chains A, B, C
PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 2 copies · chains B, C

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	740	0.74	0.79	92	ZN, 6EZ
2	851	0.74	0.78	77	PG5, PGE
3	111	0.65	0.89	28	6EZ
4	121	0.63	0.87	31	6EZ
5	231	0.56	0.78	21	empty

Interfaces

3 interfaces between chains.

A–C · 664 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 613 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 378 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5IX0 · HDAC2 with ligand BRD7232 · the same entry in another collection · chain A against A, TM-score 1.00
Q92769 · AlphaFold monomer V2.0 prediction for histone deacetylase 2 (Q92769) · a predicted model of the same protein · chain B 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 Q92769
Elsewhere: RCSB PDB 5IX0 · PDBe 5IX0 · UniProt Q92769

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