Research workbench

Human PDE9 in complex with selective inhibitor

Analyse Human PDE9 in complex with selective inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JSW
Type: protein
Length: 656 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A
EC: 3.1.4.35
UniProt: O76083
Ligands: JAR, ZN, MG
Pockets: 5 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	High affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35)	protein	328	71% helix, 0% strand	O76083

Ligands and binding sites

JAR · 6-[(3S,4S)-1-benzyl-4-methylpyrrolidin-3-yl]-1-(1-methylethyl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	365	0.74	0.85	42	MG, JAR
2	384	0.73	0.83	42	MG, JAR
3	84	0.46	0.81	18	empty
4	129	0.40	0.74	25	empty
5	82	0.39	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 833 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3JSW · Human PDE9 in complex with selective inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
O76083 · AlphaFold monomer V2.0 prediction for high affinity cgmp-specific 3',5'-cyclic… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O76083
Elsewhere: RCSB PDB 3JSW · PDBe 3JSW · UniProt O76083

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.