MolNFT v1 · #119584 · protein

Crystal structure of danio rerio HDAC6 CD1 and CD2 (linker intact) in complex with nexturastat a

5G0J: “Crystal structure of danio rerio HDAC6 CD1 and CD2 (linker intact) in complex with nexturastat a”. X-ray diffraction, 4 ligands (N4R, K, ZN), 4 pockets (best druggability 0.59). MolNFT v1 #119584 on GenesisL1: 3D structure, binding…

PDB: 5G0J
Type: protein
Length: 756 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HDAC6
UniProt: F8W4B7
Ligands: N4R, K, ZN, CL
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HDAC6	protein	756	40% helix, 12% strand	F8W4B7

Ligands and binding sites

N4R · Nexturastat A · ligand · chains A
K · Potassium ion · metal · 5 copies · chains A
ZN · Zinc ion · metal · chains A
CL · Chloride ion · ion · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	143	0.59	0.84	34	empty
2	222	0.47	0.74	26	empty
3	96	0.43	0.78	24	empty
4	52	0.34	0.78	11	empty

Compared structures

5G0J · Crystal structure of Danio rerio HDAC6 CD1 and CD2 (linker intact) in complex with… · the same entry in another collection · chain A 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 F8W4B7
Elsewhere: RCSB PDB 5G0J · PDBe 5G0J · UniProt F8W4B7

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