Research workbench

HDAC2 with ligand BRD4884

Analyse HDAC2 with ligand BRD4884 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IWG
Type: protein
Length: 1,100 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: IWX, CA, ZN
Pockets: 7 · best druggability 0.73

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	368	41% helix, 13% strand	Q92769
B, C	Histone deacetylase 2 (EC 3.5.1.98)	protein	366	42% helix, 13% strand	Q92769

Ligands and binding sites

IWX · N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)oxane-4-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
PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains B, C, A
PGE · Triethylene glycol · additive · 2 copies · chains A
PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · chains A
PG4 · Tetraethylene glycol · additive · chains B, C

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

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	816	0.73	0.78	79	PEG
2	104	0.68	0.91	28	ZN, IWX
3	111	0.66	0.89	29	ZN, IWX
4	523	0.65	0.77	48	empty
5	104	0.65	0.89	27	ZN, IWX

Interfaces

3 interfaces between chains.

A–C · 641 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 562 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 377 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5IWG · HDAC2 with ligand BRD4884 · 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 5IWG · PDBe 5IWG · UniProt Q92769

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