MolNFT v1 · #176816 · protein

Histone lysine demethylase 4D (KDM4D) in complex with the inhibitor 2- (1H-pyrazol-3-YL)ISONICOTINIC acid

7DYG · Lysine-specific demethylase 4D: “Histone lysine demethylase 4D (KDM4D) in complex with the inhibitor 2- (1H-pyrazol-3-YL)ISONICOTINIC acid”. X-ray diffraction, 2 ligands (0WS, FE), 3 pockets (best druggability 0.75). MolNFT v1…

PDB: 7DYG
Type: protein
Length: 330 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific demethylase 4D
EC: 1.14.11.66
UniProt: Q6B0I6
Ligands: 0WS, FE
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 4D (EC 1.14.11.66)	protein	330	32% helix, 26% strand	Q6B0I6

Ligands and binding sites

0WS · 2-(1H-pyrazol-3-yl)pyridine-4-carboxylic acid · ligand · chains A
FE · Fe (III) ion · metal · chains A

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

Pockets

3 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	408	0.75	0.85	43	0WS, FE
2	53	0.49	0.86	19	empty
3	57	0.30	0.75	19	empty

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7DYG · Histone lysine demethylase 4D (KDM4D) in complex with the inhibitor… · 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 Q6B0I6
Elsewhere: RCSB PDB 7DYG · PDBe 7DYG · UniProt Q6B0I6

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.