Protein target profile

PA1946

ribose ABC transporter substrate-binding protein

Genome: NC_002516.2

Gene: rbsB PA1946 3D evidence: AlphaFold DB model UniProt Q9I2F8
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Length 319
Pocket druggability 0.714
Ligand records 27
EC / GO 0 / 3
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
PA1946
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
rbsB PA1946
Status
annotated
Amino acids
319
3D evidence
AlphaFold DB model
GO
GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall. GO:0048029 Binding to a monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

Target profile

Computed evidence for target prioritization.

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

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 0.714
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MKRVASRRLLAAVVLTACSSFLPLSAVHAETPEKPRIALVMKSLANEFFLTMEDGAKAYQKEHADRFELVSNGIKDETDTSSQIRIVEQMIVSGVDALVIAPADSKALVPVVKKALDAGIVVVNIDNRFDPQVLQAKKIGVPFVGPDNRKGARLVGEYLAKRLKVGDEVGIIEGVSTTTNAQQRTAGFKDAMDAAGMKIVSLQSGNWEIEKGNAVASAMLNEHPDLKALLAGNDSMALGAVSAVRAAGRAGQVKVVGYDNIQAIKPMLKDGRVLATADQFAAKQAVFGIQTALKLLAGQTPEHEKDGVVETPVELVTAP

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • GO:0048029 Binding to a monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
36 315 CDD cd19970 PBP1_ABC_sugar_binding-like
1 29 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
9 24 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 29 SignalP_EUK SignalP-noTM SignalP-noTM
1 29 Phobius SIGNAL_PEPTIDE Signal peptide region
25 29 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 318 PANTHER PTHR46847 D-ALLOSE-BINDING PERIPLASMIC PROTEIN-RELATED
41 295 Gene3D G3DSA:3.40.50.2300 -
37 299 Pfam PF13407 Periplasmic binding protein domain
37 299 InterPro IPR025997 Periplasmic binding protein
145 281 Gene3D G3DSA:3.40.50.2300 -
24 318 SUPERFAMILY SSF53822 Periplasmic binding protein-like I
24 318 InterPro IPR028082 Periplasmic binding protein-like I
30 319 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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 PA1946
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 #2
0.714
Show in viewer
Site 2 FPocket #5
0.297
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.

27 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 27 via homologs
Structural ligands 2 0 loaded crystals
Bioactive compounds 0 25 ZINC proposed compounds
Drug-like & clean 2 0 PAINS alerts
Best available ligand signal
3VB PDB via homolog 122.1 Da · LogP -2.31 · TPSA 80.9 Open detail RCSB PDB
Detail RCSB PDB 3VB PDB via homolog
Detail RCSB PDB RIP PDB via homolog
Detail ZINC ZINC100055463 ZINC proposed compound · Tanimoto 0.615
Detail ZINC ZINC100064885 ZINC proposed compound · Tanimoto 0.615

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
3VB RCSB PDB
4RSM
A0QYB5 122.1 Da LogP -2.31 TPSA 80.9 ✓ Ro5 ✓ Clean C([C@H]([C@@H](CO)O)O)O
RIP RCSB PDB
4ZJP
A6VKT0 150.1 Da LogP -2.58 TPSA 90.2 ✓ Ro5 ✓ Clean C1[C@H]([C@H]([C@H]([C@@H](O1)O)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.