MolNFT v1 · #68728 · protein

The structure of the catalytic domain of human PDE4D with 4- (3-butoxy-4-METHOXYPHENYL)METHYL-2-imidazolidone

3K4S · Camp-specific 3',5'-cyclic phosphodiesterase 4D: “The structure of the catalytic domain of human PDE4D with 4- (3-butoxy-4-METHOXYPHENYL)METHYL-2-imidazolidone”. X-ray diffraction, 3 ligands (0MO, ZN, MG), 1 pocket (best…

PDB: 3K4S
Type: protein
Length: 329 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Camp-specific 3',5'-cyclic phosphodiesterase 4D
EC: 3.1.4.17
UniProt: Q08499
Ligands: 0MO, ZN, MG
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 64% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17)	protein	329	64% helix, 1% strand	Q08499

Ligands and binding sites

0MO · (4R)-4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-one · ligand · chains A
ZN · Zinc ion · metal · chains A
MG · Magnesium ion · metal · 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	449	0.72	0.82	40	0MO, MG

Compared structures

3K4S · The structure of the catalytic domain of human PDE4d with… · 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 Q08499
Elsewhere: RCSB PDB 3K4S · PDBe 3K4S · UniProt Q08499

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