KpATCC43816 Protein target profile

ribosomal protein L24

Accession: VK055_3766

Gene: rplX AIK82321.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GU18
Length 104
Pocket druggability (FPocket · AlphaFold DB model) 0.788
Direct ligand evidence 0 54 total records
Functional annotation 0 EC 7 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on 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 Target 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.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
13.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
100.0 Higher values support similarity to known essential genes.
DEG E-value
3.71e-70 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
89.44 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank)
Structure A0A0H3GU18
Pocket No pockets
Druggability (FPocket) 0.788
Structure A0A0H3GU18
Pocket Pocket 2
ColabFold model
FPocket 0.241 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 618 / 4744 genomes with a hit
Prevalence 13.0%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETIK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

7
  • GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.
  • GO:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
  • GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:1990904 A macromolecular complex that contains both RNA and protein molecules.
  • GO:0019843 Binding to a ribosomal RNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
3 103 NCBIfam TIGR01079 50S ribosomal protein L24
3 103 InterPro IPR003256 Ribosomal protein L24
8 72 CDD cd06089 KOW_RPL26
8 72 InterPro IPR041988 Ribosomal protein L26/L24, KOW domain
2 104 Gene3D G3DSA:2.30.30.30 -
2 104 InterPro IPR014722 Ribosomal protein L2, domain 2
39 103 Pfam PF17136 Ribosomal proteins 50S L24/mitochondrial 39S L24
39 103 InterPro IPR003256 Ribosomal protein L24
8 36 Pfam PF00467 KOW motif
8 36 InterPro IPR005824 KOW
4 100 SUPERFAMILY SSF50104 Translation proteins SH3-like domain
4 100 InterPro IPR008991 Translation protein SH3-like domain superfamily
3 97 Hamap MF_01326_B 50S ribosomal protein L24 [rplX].
3 97 InterPro IPR003256 Ribosomal protein L24
2 102 FunFam G3DSA:2.30.30.30:FF:000004 50S ribosomal protein L24
3 103 PANTHER PTHR12903 MITOCHONDRIAL RIBOSOMAL PROTEIN L24
8 25 ProSitePatterns PS01108 Ribosomal protein L24 signature.
8 25 InterPro IPR005825 Ribosomal protein L24/L26, conserved site
4 31 SMART SM00739 kow_9
4 31 InterPro IPR005824 KOW

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.

Download VMD script Full viewer

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

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

Pocket 1 FPocket #2
0.788
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

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 AF_A0A0H3GU18
AlphaFold DB full sequence Viewing
ColabFold VK055_3766
ColabFold full sequence Loaded

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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
NMY PDB via homolog 614.7 Da · LogP -8.90 · TPSA 353.1 Open detail RCSB PDB
PAR PDB via homolog Detail RCSB PDB
PEV PDB via homolog Detail RCSB PDB
PGV PDB via homolog Detail RCSB PDB
ZINC102190506 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
NMY RCSB PDB P60624 614.7 Da LogP -8.90 TPSA 353.1 3 viol. ✓ Clean C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…
PAR RCSB PDB P60624 615.6 Da LogP -8.86 TPSA 347.3 3 viol. ✓ Clean C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…
PEV RCSB PDB P60624 720.0 Da LogP 11.28 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)O[C@@H](COC(=O)CCCCCCCCCC…
PGV RCSB PDB P60624 749.0 Da LogP 10.45 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OC[C@H…

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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.