Protein profile

PA2990

phosphodiesterase

Genome: NC_002516.2

Gene: PA2990 Structure source: AlphaFold UniProt Q9HZL4
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Amino acids 240
Annotations 5
Features 10
PDB binders 2
Druggability 0.728

Overview

Basic information about this protein and its source genome.

Accession
PA2990
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA2990
Status
annotated
Amino acids
240
Structure source
AlphaFold
GO
GO:0047389 Catalysis of the reaction: H2O + L-1-glycero-3-phosphocholine = glycerol-3-phosphate + choline. GO:0008889 Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate. GO:0047395 Catalysis of the reaction: 1-(sn-glycero-3-phospho)-1D-myo-inositol + H2O = sn-glycerol 3-phosphate + myo-inositol + H+. GO:0006629 The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. GO:0008081 Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
45.455
Human E-value
3.01e-06
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.728
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MTLIYGHRGAKGEAPENTLASFQRCLEHGVNRCELDLHLSRDGELMVIHDPTLKRTTGRRGKVAEHDAATLATYDARKGGPGWVRPTPIPRLEELFEKCPFEHWQLEVKSASRERAARTVTRIRELTERFGNRDKVTVTSGSRTVLKALNELTPELSRGLVAEYAWLDPLKVAQHYGCALLALNWTLCTPERLLKAQRQGLHVSVWTVNEPALMRRLADFGVDSLITDFPGLASATLGNR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0047389 Catalysis of the reaction: H2O + L-1-glycero-3-phosphocholine = glycerol-3-phosphate + choline.
  • GO:0008889 Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.
  • GO:0047395 Catalysis of the reaction: 1-(sn-glycero-3-phospho)-1D-myo-inositol + H2O = sn-glycerol 3-phosphate + myo-inositol + H+.
  • GO:0006629 The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
  • GO:0008081 Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
1 237 SUPERFAMILY SSF51695 PLC-like phosphodiesterases
1 237 InterPro IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily
4 229 CDD cd08556 GDPD
2 237 ProSiteProfiles PS51704 GP-PDE domain profile.
2 237 InterPro IPR030395 Glycerophosphodiester phosphodiesterase domain
1 239 Gene3D G3DSA:3.20.20.190 Phosphatidylinositol (PI) phosphodiesterase
1 239 InterPro IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily
7 231 Pfam PF03009 Glycerophosphoryl diester phosphodiesterase family
7 231 InterPro IPR030395 Glycerophosphodiester phosphodiesterase domain
2 238 PANTHER PTHR46211 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA2990
AlphaFold — — full sequence — Viewing
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.728
2 0.216

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

52 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
G3P
5T9B
P37965 172.1 Da LogP -1.55 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@H](COP(=O)(O)O)O)O
PE4
3MZ2
A6LIT8 354.4 Da LogP 0.11 TPSA 84.8 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCO

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.