MolNFT v1 · #84534 · protein

HDAC7 bound with inhibitor TMP269

3ZNR · Histone deacetylase 7: “HDAC7 bound with inhibitor TMP269”. X-ray diffraction, 3 ligands (NU9, ZN, K), 7 pockets (best druggability 0.61). MolNFT v1 #84534 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3ZNR
Type: protein
Length: 1,108 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone deacetylase 7
EC: 3.5.1.98
UniProt: Q8WUI4
Ligands: NU9, ZN, K
Pockets: 7 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone deacetylase 7 (EC 3.5.1.98)	protein	368	39% helix, 14% strand	Q8WUI4
B	Histone deacetylase 7 (EC 3.5.1.98)	protein	381	40% helix, 14% strand	Q8WUI4
C	Histone deacetylase 7 (EC 3.5.1.98)	protein	359	39% helix, 14% strand	Q8WUI4

Ligands and binding sites

NU9 · N-{[4-(4-phenyl-1,3-thiazol-2-yl)tetrahydro-2H-pyran-4-yl]methyl}-3-[5-(trifluoromethyl)-1,2,4-oxadiazol-3-yl]benzamide · ligand · chains A
ZN · Zinc ion · metal · 6 copies · chains A, B, C
K · Potassium ion · metal · 6 copies · chains A, 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	119	0.61	0.86	22	empty
2	159	0.60	0.83	23	NU9
3	493	0.59	0.74	57	empty
4	141	0.58	0.83	25	empty
5	282	0.53	0.75	37	empty

Interfaces

3 interfaces between chains.

A–B · 504 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 274 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 57 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3ZNR · HDAC7 bound with inhibitor TMP269 · the same entry in another collection · chain A against A, TM-score 1.00
Q8WUI4 · AlphaFold monomer V2.0 prediction for histone deacetylase 7 (Q8WUI4) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q8WUI4
Elsewhere: RCSB PDB 3ZNR · PDBe 3ZNR · UniProt Q8WUI4

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