Protein target profile

PA3866

pyocin protein

Genome: NC_002516.2

Gene: PA3866 3D evidence: AlphaFold DB model UniProt Q9HXE0
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Length 764
Pocket druggability 0.712
Ligand records 52
EC / GO 0 / 7
Target summary

Promising target candidate with multiple supporting evidence streams.

5 signals

Strengths

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Strong predicted binding pocket FPocket selected-pocket score 0.71. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model Ligand evidence via structure/bioactivity 2 structural and 0 bioactivity records.

Risks / watch

No major risk signal surfaced in the loaded evidence.

Missing evidence

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
How to read this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal TPW pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Overview

Basic information about this protein and its source genome.

Accession
PA3866
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3866
Status
annotated
Amino acids
764
3D evidence
AlphaFold DB model
GO
GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks. GO:0004540 Catalysis of the cleavage of phosphodiester bonds in chains of RNA. GO:0005102 Binding to one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. GO:0019835 The rupture of cell membranes and the loss of cytoplasm. GO:0042742 Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. GO:0031640 Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
Hit
Essential (DEG)
N
Localization
Extracellular

Selected pocket evidence

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.712
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MTNNSAPPLVVTRGNDNGYEPGSMVITHVQASGLDIIQYIPGRSSYGTPPFVPPGPSPYVGPGMQEYRRLRDTLDKSNSELKKNLKNKTLKEVDELKSEAGLPVKAVSANDIRDEKSIVDALMDAKAKSLKAIEDRPANLYTASDFPQKSEAMYQNQLLASRKFYGEFLDRHMSELAKAYSADIYKAQIAILKQTSQELESKARSMEAQAQQVTQQLGADFNAITTPTATKVQQRVKAVDASLSQVSTQVSGAVASATQAVQVKTAQAQQQANSQISSSQNLISAAFRNQIALAAQASGEAQVTAFNTQVKQIVNEATAFSTARKQALAQFAANAAAEVETEVNRLTAQVKASPTKAASQAAQATLRQFTESTYAKVNTYAQQTEAELQAKAKEVSAAVAEAQRAATNDLQKTADVVPGQIIQAANTLAMPATSTPLVSVAGFGSAAVETARLAASLTNAVNRLVQIAGSGPGAYVATFAVLSLYSDQAGKDSDKVPAGVRNALALEASALGLPGTADLQSVAKAGGTVDMPVRLTSAAQESPSGKSQIAAMLTNGATVPKGVPVRAATLNAATGRYEVTVPAKSTVPNTPPLILTWTPATPPGSQNPSSTTPVVPQPVPVYEGATITPVQAEPESYPGVPLDLDDLIVIFPVGSGVKPIYIMFNHNPHDVVIDDKIREQIPIRGWTEVEVRDVIGKGATGSSSDKRRPNKTIDGLGRNDSATVYGSPPNGYIVVNDRTGEIIQIADRNDSAWAVDGRIIWRNK

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks.
  • GO:0004540 Catalysis of the cleavage of phosphodiester bonds in chains of RNA.
  • GO:0005102 Binding to one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
  • GO:0019835 The rupture of cell membranes and the loss of cytoplasm.
  • GO:0042742 Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
  • GO:0031640 Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
  • GO:0009617 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
519 663 Pfam PF06958 S-type Pyocin
519 663 InterPro IPR016128 Pyosin/cloacin translocation domain
697 720 MobiDBLite mobidb-lite consensus disorder prediction
669 757 Pfam PF12106 Colicin E5 ribonuclease domain
669 757 InterPro IPR021964 Colicin E5 ribonuclease domain
329 349 Coils Coil Coil
182 216 Coils Coil Coil
381 405 Coils Coil Coil
671 763 SUPERFAMILY SSF102824 Colicin D/E5 nuclease domain
671 763 InterPro IPR038233 Colicin D/E5 nuclease domain superfamily
64 87 Coils Coil Coil
663 764 Gene3D G3DSA:3.30.2310.30 -
663 764 InterPro IPR038234 Colicin E5 ribonuclease domain superfamily
457 692 SUPERFAMILY SSF69369 Cloacin translocation domain
457 692 InterPro IPR036302 Pyosin/cloacin translocation domain superfamily
420 441 PRINTS PR01300 Pyocin S killer protein signature
420 441 InterPro IPR003060 Pyocin S killer protein
466 484 PRINTS PR01300 Pyocin S killer protein signature
466 484 InterPro IPR003060 Pyocin S killer protein
501 524 PRINTS PR01300 Pyocin S killer protein signature
501 524 InterPro IPR003060 Pyocin S killer protein

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

3D visualization script Full viewer

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Structural evidence

0 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB PA3866
AlphaFold DB — — full sequence — Viewing
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #3
0.712
Show in viewer
Site 2 FPocket #13
0.474
Show in viewer
Site 3 FPocket #21
0.381
Show in viewer

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
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 52 via homologs
Structural ligands 2 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 43 1 PAINS alerts
Best available ligand signal
3PD PDB via homolog 347.2 Da · LogP -1.54 · TPSA 185.8 Open detail RCSB PDB
Detail RCSB PDB 3PD PDB via homolog
Detail RCSB PDB UM3 PDB via homolog
Detail ZINC ZINC14963236 ZINC proposed compound · Tanimoto 1.000
Detail ZINC ZINC14963244 ZINC proposed compound · Tanimoto 1.000

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
3PD RCSB PDB
2DJH
P18000 347.2 Da LogP -1.54 TPSA 185.8 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO)OP(=O)(O)O)N…
UM3 RCSB PDB
2DJH
P18000 308.2 Da LogP -1.71 TPSA 151.1 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO)OP(=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.