Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: PA2352
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA2352
Status: annotated
Amino acids: 375
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 (%): 48.315
Human E-value: 2.97e-17
Gut microbiome off-target: hit
Essential (DEG): N
Localization: Periplasmic

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 0.746

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MRQRFWQGTFKTLGFLGLTAGLAAQAAEPSGKALSAAAGVPWPAVIAHRGASYDAPEETAAAYLLARDLGADYLEADVQRSRDGVLVALHDDTLERTTDVAEVFPERAKDPVSSFTLAELKRLDAGSWFNRAFPQRARPGFVGLRILTLDEMLDIAEGGANKPGLYLETKVPAQFPGIEDDLRKLLERRGWLQPRERAAAGHVDVAHGNGRVILQTFEKSSLELLQESMPQVPKILLLWLGDGYLEARSPVTFKESGETDKAAFYARQEVKSEAEFGAWLDWAKAHGALGTGPSATLSERGEQSYADLVKPWMNRMTHARGLFIHAYSVDSAEDFKALGAAGVDGFFTNRTSELLKFQGRPAAQDMDALLRRHGY

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.

18 records

Show feature table

Start	End	DB	Term	Name
43	358	CDD	cd08601	GDPD_SaGlpQ_like
41	358	Gene3D	G3DSA:3.20.20.190	Phosphatidylinositol (PI) phosphodiesterase
41	358	InterPro	IPR017946	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily
12	22	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
27	375	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	24	SignalP_EUK	SignalP-noTM	SignalP-noTM
20	360	PANTHER	PTHR46211	GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
1	26	Phobius	SIGNAL_PEPTIDE	Signal peptide region
23	26	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
43	358	ProSiteProfiles	PS51704	GP-PDE domain profile.
43	358	InterPro	IPR030395	Glycerophosphodiester phosphodiesterase domain
1	11	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	26	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
1	26	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
41	357	SUPERFAMILY	SSF51695	PLC-like phosphodiesterases
41	357	InterPro	IPR017946	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily
48	351	Pfam	PF03009	Glycerophosphoryl diester phosphodiesterase family
48	351	InterPro	IPR030395	Glycerophosphodiester phosphodiesterase domain

3D Structure

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

Loading 3D structure...

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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 PA2352	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				0.746

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.

19 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

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`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1529618	0.739	246.2 Da LogP -2.17 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(OC[C@@H](O)CO)OC[C@H](O)CO`
ZINC1529620	0.739	246.2 Da LogP -2.17 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(OC[C@@H](O)CO)OC[C@@H](O)CO`
ZINC5975509	0.640	202.1 Da LogP -2.19 TPSA 127.5	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)CO`
ZINC2516111	0.593	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC2522704	0.593	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC3869812	0.593	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC4095590	0.567	215.1 Da LogP -1.57 TPSA 122.2	✓ Ro5	✓ Clean	`NCCO[P@@](=O)(O)OC[C@H](O)CO`
ZINC4095591	0.567	215.1 Da LogP -1.57 TPSA 122.2	✓ Ro5	✓ Clean	`NCCO[P@@](=O)(O)OC[C@@H](O)CO`
ZINC1680142	0.533	212.1 Da LogP -0.34 TPSA 96.2	✓ Ro5	✓ Clean	`C=CCOC[C@@H](O)COP(=O)(O)O`
ZINC5426687	0.533	212.1 Da LogP -0.34 TPSA 96.2	✓ Ro5	✓ Clean	`C=CCOC[C@H](O)COP(=O)(O)O`
ZINC100067589	0.531	334.2 Da LogP -4.34 TPSA 197.4	1 viol.	✓ Clean	`O=[P@@](O)(OC[C@H](O)CO)O[C@H]1[C@H](O)[C@@H](O…`
ZINC100620818	0.531	334.2 Da LogP -4.34 TPSA 197.4	1 viol.	✓ Clean	`O=[P@@](O)(OC[C@H](O)CO)O[C@H]1[C@@H](O)[C@@H](…`
ZINC1532714	0.515	258.2 Da LogP -0.82 TPSA 96.2	✓ Ro5	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)OC[C@H](O)CO`
ZINC1842903	0.515	258.2 Da LogP -0.82 TPSA 96.2	✓ Ro5	✓ Clean	`C[N+](C)(C)CCO[P@](=O)(O)OC[C@@H](O)CO`
ZINC1529626	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532567	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532851	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC30320708	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`

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.

PA2352