Protein target profile

PA3680

ribosomal RNA small subunit methyltransferase J

Genome: NC_002516.2

Gene: rsmJ PA3680 3D evidence: AlphaFold DB model UniProt Q9HXW0
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Length 261
Pocket druggability 0.716
EC / GO 1 / 5
Target summary

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

4 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 0.72. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model

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. 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
PA3680
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
rsmJ PA3680
Status
annotated
Amino acids
261
3D evidence
AlphaFold DB model
EC
2.1.1.242
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0036308 Catalysis of the reaction: guanosine(1516) in 16S rRNA + S-adenosyl-L-methionine = N(2)-methylguanosine(1516) in 16S rRNA + S-adenosyl-L-homocysteine + H+. GO:0070475 The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule. GO:0008990 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine. GO:0031167 The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
Hit
Essential (DEG)
Y
Localization
Unknown

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.

MTDSAAPRLHVQALSADCAEAARRWAERLGLPLAADDEAEFAVQVGEQGLQVLQLGADSPGPVRVDFVEGASAHRRKFGGGSGQMIAKAVGVQPGIRPRVLDATAGLGRDGFVLASLGCEVTLVERQPLIAALLEDGLERARRDPDVAPIAARMRLLGGNSADLMRAWDGEAPQVVYLDPMFPHRDKSALVKKEMRLFRPLVGDDLDAPALLQAALALASHRVVVKRPRKAPIIEGPKPGYSLEGKSSRYDIYPKKALGKG

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0036308 Catalysis of the reaction: guanosine(1516) in 16S rRNA + S-adenosyl-L-methionine = N(2)-methylguanosine(1516) in 16S rRNA + S-adenosyl-L-homocysteine + H+.
  • GO:0070475 The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.
  • GO:0008990 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine.
  • GO:0031167 The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
9 256 InterPro IPR007536 Ribosomal RNA small subunit methyltransferase J
9 256 Hamap MF_01523 Ribosomal RNA small subunit methyltransferase J [rsmJ].
65 260 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
65 260 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
27 254 Pfam PF04445 Putative SAM-dependent methyltransferase
27 254 InterPro IPR007536 Ribosomal RNA small subunit methyltransferase J
7 257 PANTHER PTHR36112 RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE J
7 257 InterPro IPR007536 Ribosomal RNA small subunit methyltransferase J
14 256 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
14 256 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
99 184 CDD cd02440 AdoMet_MTases

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 PA3680
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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