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[1,2,4]TRIAZOLO[1,5-A]PYRIMIDINE phosphodiesterase 2 inhibitors

Analyse [1,2,4]TRIAZOLO[1,5-A]PYRIMIDINE phosphodiesterase 2 inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZQZ
Type: protein
Length: 1,339 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: QOQ, MG, ZN
Pockets: 13 · best druggability 0.75

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	339	69% helix, 0% strand	O00408
B	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	337	69% helix, 0% strand	O00408
C	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	327	70% helix, 0% strand	O00408
D	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	336	69% helix, 0% strand	O00408

Ligands and binding sites

QOQ · 5-[bis(fluoranyl)methyl]-7-[(3~{S})-1-[(2-chloranyl-6-methyl-pyridin-4-yl)methyl]piperidin-3-yl]-[1,2, 4]triazolo[1,5-a]pyrimidine · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	413	0.75	0.84	44	MG, QOQ
2	389	0.73	0.84	38	MG, QOQ
3	596	0.72	0.80	61	empty
4	396	0.72	0.83	40	MG, QOQ
5	368	0.72	0.83	38	MG, QOQ

Interfaces

6 interfaces between chains.

A–B · 662 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 399 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 391 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 206 Å² buried · 1 hydrogen bond · protein-protein
B–D · 97 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6ZQZ · [1,2,4]Triazolo[1,5-a]pyrimidine Phosphodiesterase 2 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 6ZQZ · PDBe 6ZQZ · UniProt O00408

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