Research workbench

Crystal structure of KDM4D with GF026 ligand

Analyse Crystal structure of KDM4D with GF026 ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6F5Q
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.-
UniProt: Q6B0I6
Ligands: CTK, ZN, NI, SO4, CL
Pockets: 2 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 4D (EC 1.14.11.-)	protein	330	31% helix, 26% strand	Q6B0I6

Ligands and binding sites

CTK · 2-[2-(methylsulfonylamino)ethylamino]pyridine-4-carboxylic acid · ligand · chains A
ZN · Zinc ion · metal · chains A
NI · Nickel (II) ion · metal · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A
CL · Chloride ion · ion · chains A
EDO · 1,2-ethanediol · additive · 9 copies · chains A

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

Pockets

2 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	480	0.78	0.86	53	EDO, NI, CTK
2	53	0.32	0.77	19	EDO

Compared structures

6F5Q · Crystal Structure of KDM4D with GF026 ligand · 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 6F5Q · PDBe 6F5Q · UniProt Q6B0I6

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