MolNFT v1 · #169507 · protein

Structure of human HDAC2 in complex with ketone inhibitor (compound O)

6XEC · Histone deacetylase 2: “Structure of human HDAC2 in complex with ketone inhibitor (compound O)”. X-ray diffraction, 4 ligands (V1S, CA, ZN), 6 pockets (best druggability 0.72). MolNFT v1 #169507 on GenesisL1: 3D structure, binding…

PDB: 6XEC
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: V1S, CA, ZN, SO4
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone deacetylase 2 (EC 3.5.1.98)	protein	368	39% 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

V1S · (1S)-N-{(1S)-1-[5-cyano-2-(4-fluorophenyl)-1H-imidazol-4-yl]-7,7-dihydroxynonyl}-6-methyl-6-azaspiro[2.5]octane-1-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
SO4 · Sulfate ion · ion · 10 copies · chains A, B, C
PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C

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

Pockets

6 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	756	0.72	0.78	76	SO4
2	545	0.63	0.75	57	empty
3	220	0.52	0.77	21	SO4
4	51	0.46	0.85	19	ZN, V1S
5	52	0.46	0.85	18	V1S

Interfaces

3 interfaces between chains.

A–C · 611 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 557 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 357 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6XEC · Structure of human HDAC2 in complex with ketone inhibitor (compound O) · 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 6XEC · PDBe 6XEC · UniProt Q92769

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