MolNFT v1 · #135727 · protein

PDE2 catalytic domain complexed with inhibitors

5U7K · Cgmp-dependent 3',5'-cyclic phosphodiesterase: “PDE2 catalytic domain complexed with inhibitors”. X-ray diffraction, 4 ligands (7Y1, ZN, MG), 13 pockets (best druggability 0.84). MolNFT v1 #135727 on GenesisL1: 3D structure, binding…

PDB: 5U7K
Type: protein
Length: 1,349 residues
Chains: 4
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: 7Y1, ZN, MG, CL
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	340	69% helix, 0% strand	O00408
B	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	343	69% helix, 0% strand	O00408
C	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	339	67% helix, 0% strand	O00408
D	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	327	69% helix, 0% strand	O00408

Ligands and binding sites

7Y1 · 3-[5-(4-ethylphenyl)-1-methyl-1H-pyrazol-4-yl]-5-propoxy[1,2,4]triazolo[4,3-a]pyrazine · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
CL · Chloride ion · ion · chains C, D

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

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	945	0.84	0.85	69	MG, 7Y1
2	412	0.76	0.85	42	MG, 7Y1
3	429	0.76	0.85	42	MG, 7Y1
4	395	0.75	0.85	39	MG, 7Y1
5	1166	0.74	0.77	97	empty

Interfaces

5 interfaces between chains.

C–D · 864 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 864 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 854 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 474 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 125 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5U7K · PDE2 catalytic domain complexed with inhibitors · 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 5U7K · PDBe 5U7K · UniProt O00408

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