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PDE2 in complex with molecule 5

Analyse PDE2 in complex with molecule 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6EZF
Type: protein
Length: 342 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cgmp-dependent 3',5'-cyclic phosphodiesterase
EC: 3.1.4.17
UniProt: O00408
Ligands: C6Z, MG, ZN, NA, SO4
Pockets: 1 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 67% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	342	67% helix, 1% strand	O00408

Ligands and binding sites

C6Z · 6-[(2,4-dichlorophenyl)methyl]pyridazine-3-thiol · ligand · chains A
MG · Magnesium ion · metal · chains A
ZN · Zinc ion · metal · chains A
NA · Sodium ion · metal · chains A
SO4 · Sulfate ion · ion · chains A
GOL · Glycerol · additive · 2 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	364	0.85	0.94	45	MG, C6Z, NA

Compared structures

6EZF · PDE2 in complex with molecule 5 · 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 O00408
Elsewhere: RCSB PDB 6EZF · PDBe 6EZF · UniProt O00408

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