MolNFT v1 · #135439 · protein

Crystal structure of human phosphodiesterase 2A in complex with [1,2, 4]TRIAZOLO[1,5-A]PYRIMIDIN-7-yl}-N-(naphthalene-2-YL)PIPERIDINE-3- carboxamide

5TZ3 · Cgmp-dependent 3',5'-cyclic phosphodiesterase: “Crystal structure of human phosphodiesterase 2A in complex with [1,2…”. X-ray diffraction, 3 ligands (7OM, ZN, MG), 12 pockets (best druggability 0.85). MolNFT v1 #135439 on GenesisL1…

PDB: 5TZ3
Type: protein
Length: 1,342 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: 7OM, ZN, MG
Pockets: 12 · best druggability 0.85

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	341	69% helix, 0% strand	O00408
B	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	340	69% helix, 0% strand	O00408
C	Cgmp-dependent 3',5'-cyclic phosphodiesterase (EC 3.1.4.17)	protein	334	69% 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

7OM · (3~{R})-1-(5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-~{N}-naphthalen-2-yl-piperidine-3-carboxamide · 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

12 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	988	0.85	0.86	108	7OM, MG
2	713	0.75	0.80	90	empty
3	380	0.74	0.84	39	7OM, MG
4	424	0.74	0.83	42	7OM, MG
5	392	0.73	0.83	37	7OM, MG

Interfaces

5 interfaces between chains.

C–D · 846 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 833 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 744 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 460 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 116 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5TZ3 · 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 5TZ3 · PDBe 5TZ3 · UniProt O00408

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