KpKP13 Protein target profile

50S ribosomal protein L23

Accession: KP13_00751

Gene: rplW AHE42368.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H3W7
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Length 100
Pocket druggability (P2Rank · AlphaFold DB model) 0.032
Functional annotation 0 EC 4 GO
Target summary

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

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

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Structure available AlphaFold DB model + ColabFold model

Risks to review

Human similarity Top human hit identity: 35.897%. Microbiome similarity 233 of 4744 screened genomes (4.9%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.40. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.03.

Evidence gaps

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.
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
Hit
Human identity (%)
35.897 Lower values reduce human off-target concern.
Human E-value
4.6e-06
Gut microbiome similarity
4.9% 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
3.1099999999999997e-68 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
89.69 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) 0.032
Structure A0A0H3H3W7
Pocket Pocket 1
Druggability (FPocket) 0.398
Structure A0A0H3H3W7
Pocket Pocket 2
ColabFold model
P2Rank 0.021 · Pocket 1
FPocket 0.367 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 233 / 4744 genomes with a hit
Prevalence 4.9%

Cross-references

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

Sequence

UniProt A0A0H3H3W7

Sequence

Primary amino-acid sequence viewer.

MIREERLLKVLRAPHVSEKASTAMEKTNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNLDFVGGAE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

4
  • GO:0019843 Binding to a ribosomal RNA.
  • 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:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
9 95 Pfam PF00276 Ribosomal protein L23
9 95 InterPro IPR013025 Ribosomal protein L25/L23
7 95 PANTHER PTHR11620 60S RIBOSOMAL PROTEIN L23A
7 95 InterPro IPR013025 Ribosomal protein L25/L23
8 98 Hamap MF_01369_B 50S ribosomal protein L23 [rplW].
8 98 InterPro IPR013025 Ribosomal protein L25/L23
1 100 FunFam G3DSA:3.30.70.330:FF:000001 50S ribosomal protein L23
6 97 SUPERFAMILY SSF54189 Ribosomal proteins S24e, L23 and L15e
6 97 InterPro IPR012678 Ribosomal protein L23/L15e core domain superfamily
81 96 ProSitePatterns PS00050 Ribosomal protein L23 signature.
81 96 InterPro IPR001014 Ribosomal protein L23/L25, conserved site
1 100 Gene3D G3DSA:3.30.70.330 -
1 100 InterPro IPR012677 Nucleotide-binding alpha-beta plait domain superfamily

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.

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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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.032
Likely same site as FPocket 2 0.9 Å 11 shared residues 100% of smaller site
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2
0.398
Likely same site as P2Rank 1 0.9 Å 11 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #3
0.205
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_A0A0H3H3W7
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_00751
ColabFold — — full sequence — Loaded