MolNFT v1 · #135469 · protein

Crystal structure of human phosphodiesterase 2A in complex with 1-[(3- bromo-4-FLUOROPHENYL)CARBONYL]-3,3-difluoro-5-{5-methyl-[1,2, 4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL}PIPERIDINE

5TZZ · Cgmp-dependent 3',5'-cyclic phosphodiesterase: “Crystal structure of human phosphodiesterase 2A in complex with 1-[(3…”. X-ray diffraction, 3 ligands (7OJ, ZN, MG), 13 pockets (best druggability 0.83). MolNFT v1 #135469 on…

PDB: 5TZZ
Type: protein
Length: 1,340 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: 7OJ, ZN, MG
Pockets: 13 · best druggability 0.83

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	342	70% helix, 0% strand	O00408
B	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	339	69% helix, 0% strand	O00408
C	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	327	69% helix, 0% strand	O00408
D	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	332	69% helix, 0% strand	O00408

Ligands and binding sites

7OJ · (3-bromo-4-fluorophenyl)[(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl]methanone · 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

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

Pockets

13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	856	0.83	0.85	69	7OJ, MG
2	409	0.74	0.84	41	7OJ, MG
3	787	0.73	0.78	68	empty
4	384	0.73	0.84	41	7OJ, MG
5	361	0.72	0.84	39	7OJ, MG

Interfaces

5 interfaces between chains.

C–D · 894 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 853 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 822 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 484 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 145 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5TZZ · CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX 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 O00408
Elsewhere: RCSB PDB 5TZZ · PDBe 5TZZ · UniProt O00408

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