Protein target profile

PA1303

signal peptidase

Genome: NC_002516.2

Gene: PA1303 3D evidence: AlphaFold DB model UniProt Q9I441
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Length 179
Pocket druggability 0.721
Ligand records 80
EC / GO 1 / 12
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

4 signals

Strengths

Strong predicted binding pocket FPocket selected-pocket score 0.72. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model Ligand evidence via structure/bioactivity 2 structural and 28 bioactivity records.

Risks / watch

Human similarity Top human hit identity: 28.671%.

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
PA1303
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA1303
Status
annotated
Amino acids
179
3D evidence
AlphaFold DB model
EC
3.4.21.89
GO
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0008233 Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. GO:0004252 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). GO:0009003 An endopeptidase that cleaves a hydrophobic, N-terminal signal or leader sequences from mitochondrial, secreted and periplasmic proteins. GO:0051055 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids. GO:0045861 Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.

Target profile

Computed evidence for target prioritization.

Human off-target
Hit
Human identity (%)
28.671
Human E-value
2.02e-12
Gut microbiome off-target
Hit
Essential (DEG)
Y
Localization
CytoplasmicMembrane

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 0.721
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MGLLAAIMLAVYLANPFGTASLDPRARLLGVALYKIPSRSMEPTLQQGDFILANAARYAFADPQVGDLVVFRFPPQRSIAYVKRIAGIPGDRVRIDGGRLYVNERPVTEPYLAQQALRQPESLRMAERTVPAGQYFMLGDNRDNSNDSRYWGYVPRADLVGRVFAVWYAEDTRRIGSVR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 12 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

12
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0008233 Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
  • GO:0004252 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
  • GO:0009003 An endopeptidase that cleaves a hydrophobic, N-terminal signal or leader sequences from mitochondrial, secreted and periplasmic proteins.
  • GO:0051055 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.
  • GO:0045861 Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
  • GO:2000145 Any process that modulates the frequency, rate or extent of cell motility.
  • GO:1900376 Any process that modulates the frequency, rate or extent of secondary metabolite biosynthetic process.
  • GO:0006465 OBSOLETE. The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
  • GO:0008236 Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region
31 169 PANTHER PTHR43390 SIGNAL PEPTIDASE I
31 169 InterPro IPR000223 Peptidase S26A, signal peptidase I
30 170 SUPERFAMILY SSF51306 LexA/Signal peptidase
30 170 InterPro IPR036286 LexA/Signal peptidase-like superfamily
23 179 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
29 168 Pfam PF10502 Signal peptidase, peptidase S26
29 168 InterPro IPR019533 Peptidase S26
33 163 CDD cd06530 S26_SPase_I
33 163 InterPro IPR019533 Peptidase S26
15 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
83 95 ProSitePatterns PS00760 Signal peptidases I lysine active site.
83 95 InterPro IPR019757 Peptidase S26A, signal peptidase I, lysine active site
135 148 ProSitePatterns PS00761 Signal peptidases I signature 3.
135 148 InterPro IPR019758 Peptidase S26A, signal peptidase I, conserved site
1 20 SignalP_EUK SignalP-noTM SignalP-noTM
3 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
26 169 NCBIfam TIGR02227 signal peptidase I
26 169 InterPro IPR000223 Peptidase S26A, signal peptidase I
81 93 PRINTS PR00727 Bacterial leader peptidase 1 (S26A) family signature
81 93 InterPro IPR000223 Peptidase S26A, signal peptidase I
29 45 PRINTS PR00727 Bacterial leader peptidase 1 (S26A) family signature
29 45 InterPro IPR000223 Peptidase S26A, signal peptidase I
130 149 PRINTS PR00727 Bacterial leader peptidase 1 (S26A) family signature
130 149 InterPro IPR000223 Peptidase S26A, signal peptidase I
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
38 171 Gene3D G3DSA:2.10.109.10 Umud Fragment, subunit A

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 PA1303
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 #1
0.721
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.

80 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 80 via homologs
Structural ligands 2 0 loaded crystals
Bioactive compounds 28 50 ZINC proposed compounds
Drug-like & clean 53 0 PAINS alerts
Best available ligand signal
CZD PDB via homolog 892.1 Da · LogP 2.05 · TPSA 282.9 Open detail RCSB PDB
Detail RCSB PDB CZD PDB via homolog
Detail RCSB PDB PTY PDB via homolog
Detail ChEMBL CHEMBL5410707 ChEMBL via homolog · pchembl 9.36
Detail ChEMBL CHEMBL3947604 ChEMBL via homolog · pchembl 8.22

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
CZD RCSB PDB
6B88
P00803 892.1 Da LogP 2.05 TPSA 282.9 3 viol. ✓ Clean [H]/N=C\CNC(=O)[C@@H]1Cc2ccc(c(c2)-c3cc(ccc3OCC…
PTY RCSB PDB
4N31
R9TES9 734.1 Da LogP 11.67 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC…

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.