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Crystal structure of human KDM4D in complex with 2-1H- pyrazol-4-yloxy-3H,4H-pyrido-3,4-D-pyrimidin-4-one

Analyse Crystal structure of human KDM4D in complex with 2-1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FPB
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: HA6, ZN, CO, SO4
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 4D (EC 1.14.11.-)	protein	330	32% helix, 25% strand	Q6B0I6

Ligands and binding sites

HA6 · 2-(1H-pyrazol-4-yloxy)-3H-pyrido[3,4-d]pyrimidin-4-one · ligand · chains A
ZN · Zinc ion · metal · chains A
CO · Cobalt (II) ion · metal · chains A
SO4 · Sulfate ion · ion · 7 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	545	0.77	0.84	66	CO, HA6, SO4
2	82	0.36	0.76	23	empty

Compared structures

5FPB · Crystal structure of human KDM4D in complex with 2-1H-pyrazol-4-yloxy… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q6B0I6
Elsewhere: RCSB PDB 5FPB · PDBe 5FPB · UniProt Q6B0I6

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