Protein target profile

PA4742

tRNA pseudouridine synthase B

Genome: NC_002516.2

Gene: orp truB PA4742 3D evidence: AlphaFold DB model UniProt P72154
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Length 304
Pocket druggability 0.716
EC / GO 1 / 9
Target summary

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

3 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

Risks / watch

Human similarity Top human hit identity: 42.593%.

Missing evidence

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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
PA4742
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
orp truB PA4742
Status
annotated
Amino acids
304
3D evidence
AlphaFold DB model
EC
5.4.99.25
GO
GO:0009982 Catalysis of the reaction: a uridine in RNA = a pseudouridine in RNA. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0160148 Catalysis of the reaction: uridine(55) in tRNA = pseudouridine(55) in tRNA. GO:1990481 The intramolecular conversion of uridine to pseudouridine in an mRNA molecule. GO:0006400 The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically. GO:0031119 The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.

Target profile

Computed evidence for target prioritization.

Human off-target
Hit
Human identity (%)
42.593
Human E-value
9.25e-08
Gut microbiome off-target
Hit
Essential (DEG)
Y
Localization
Cytoplasmic

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 0.716
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MAQVKRIRRSISGILVLDKPRGMSSNQALQKVRWLLNAEKAGHTGSLDPLATGVLPLCFGEATKFSQYLLDADKGYETVMRMGITTTTGDAEGELLAERDVTVGRDDLEQALPRFRGDIEQVPPMYSALKKDGQPLYKLARAGEVVEREARSVTITRLDLLSFEPPCATLAVSCSKGTYVRTLVEDLGQVLGCGAHVAALRRTQAGPFALAQAITLETLERVHAEGGPEALDQFLMPEDSGLLHWPVLQLSEHSAYYWLHGQPVRAPEAPKFGWLRVQDHTGRFIGIGEVTDDGRIAPRRLIRS

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0009982 Catalysis of the reaction: a uridine in RNA = a pseudouridine in RNA. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0160148 Catalysis of the reaction: uridine(55) in tRNA = pseudouridine(55) in tRNA.
  • GO:1990481 The intramolecular conversion of uridine to pseudouridine in an mRNA molecule.
  • GO:0006400 The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
  • GO:0031119 The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.
  • GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
  • GO:0001522 The intramolecular conversion of uridine to pseudouridine within an RNA molecule.
  • GO:0009451 The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
246 302 Pfam PF09157 Pseudouridine synthase II TruB, C-terminal
246 302 InterPro IPR015240 tRNA pseudouridine synthase II, TruB, subfamily 1, C-terminal
11 241 SUPERFAMILY SSF55120 Pseudouridine synthase
11 241 InterPro IPR020103 Pseudouridine synthase, catalytic domain superfamily
1 243 FunFam G3DSA:3.30.2350.10:FF:000003 tRNA pseudouridine synthase B
8 226 PANTHER PTHR13767 TRNA-PSEUDOURIDINE SYNTHASE
8 226 InterPro IPR014780 tRNA pseudouridine synthase II, TruB
244 304 Gene3D G3DSA:2.30.130.10 PUA domain
244 304 InterPro IPR036974 PUA domain superfamily
244 304 FunFam G3DSA:2.30.130.10:FF:000012 tRNA pseudouridine synthase B
243 302 CDD cd21152 PUA_TruB_bacterial
2 242 Gene3D G3DSA:3.30.2350.10 Pseudouridine synthase
13 220 CDD cd02573 PseudoU_synth_EcTruB
13 220 InterPro IPR014780 tRNA pseudouridine synthase II, TruB
181 242 Pfam PF16198 tRNA pseudouridylate synthase B C-terminal domain
181 242 InterPro IPR032819 tRNA pseudouridylate synthase B, C-terminal
12 219 NCBIfam TIGR00431 tRNA pseudouridine(55) synthase TruB
12 219 InterPro IPR014780 tRNA pseudouridine synthase II, TruB
245 303 SUPERFAMILY SSF88697 PUA domain-like
245 303 InterPro IPR015947 PUA-like superfamily
11 302 Hamap MF_01080 tRNA pseudouridine synthase B [truB].
11 302 InterPro IPR014780 tRNA pseudouridine synthase II, TruB
33 180 Pfam PF01509 TruB family pseudouridylate synthase (N terminal domain)
33 180 InterPro IPR002501 Pseudouridine synthase II, N-terminal

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 PA4742
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
0.716
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Site 2 FPocket #2
0.4
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Site 3 FPocket #4
0.205
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