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Crystal structure of histone lysine demethylase 4D (KDM4D) in complex with the inhibitor 5-hydroxy-2-METHYLPYRAZOLO[1,5-A]PYRIDO[3,2- E]PYRIMIDINE-3-carbonitrile

Analyse Crystal structure of histone lysine demethylase 4D (KDM4D) in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DYQ
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: HR0, FE
Pockets: 2 · best druggability 0.78

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

HR0 · 5-hydroxy-2-methylpyrazolo[1,5-a]pyrido[3,2-e]pyrimidine-3-carbonitrile · 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

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	458	0.78	0.86	62	HR0, FE
2	84	0.39	0.77	23	empty

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7DYQ · Crystal structure of histone lysine demethylase 4D (KDM4D) in complex with the inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00

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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 7DYQ · PDBe 7DYQ · UniProt Q6B0I6

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