MolNFT v1 · #123558 · protein

PDE5A for NAV1.7

5JO3 · Cgmp-specific 3',5'-cyclic phosphodiesterase: “PDE5A for NAV1.7”. X-ray diffraction, 2 ligands (6LK, ZN), 3 pockets (best druggability 0.74). MolNFT v1 #123558 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JO3
Type: protein
Length: 323 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cgmp-specific 3',5'-cyclic phosphodiesterase
EC: 3.1.4.35
UniProt: O76074
Ligands: 6LK, ZN
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Cgmp-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35)	protein	323	70% helix, 0% strand	O76074

Ligands and binding sites

6LK · 1-(5-chloro-6-methoxypyridin-3-yl)-3-methyl-N-(methylsulfonyl)-1H-indazole-5-carboxamide · ligand · chains B
ZN · Zinc ion · metal · 2 copies · chains B

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

Pockets

3 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	446	0.74	0.83	41	ZN, 6LK
2	57	0.50	0.87	18	empty
3	61	0.28	0.74	15	empty

Compared structures

5JO3 · PDE5A for NaV1.7 · the same entry in another collection · chain B against B, TM-score 1.00
O76074 · AlphaFold monomer V2.0 prediction for cgmp-specific 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 O76074
Elsewhere: RCSB PDB 5JO3 · PDBe 5JO3 · UniProt O76074

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