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Crystal structure of KDM4D with tetrazole ligand GF049

Analyse Crystal structure of KDM4D with tetrazole ligand GF049 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6F5S
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: CQT, ZN, NI, SO4, CL
Pockets: 1 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 4D (EC 1.14.11.-)	protein	330	33% helix, 26% strand	Q6B0I6

Ligands and binding sites

CQT · ~{N}-(3-morpholin-4-ylpropyl)-4-(2~{H}-1,2,3,4-tetrazol-5-yl)pyridine-2-carboxamide · ligand · chains A
ZN · Zinc ion · metal · chains A
NI · Nickel (II) ion · metal · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A
CL · Chloride ion · ion · chains A
EDO · 1,2-ethanediol · additive · 5 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	549	0.77	0.84	60	NI, CQT

Compared structures

6F5S · Crystal Structure of KDM4D with tetrazole ligand GF049 · 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 6F5S · PDBe 6F5S · UniProt Q6B0I6

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