KpKP13 Protein target profile

50S ribosomal protein L13

Accession: KP13_03996

Gene: rplM AHE42452.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GW96
Length 142
Pocket druggability (P2Rank · AlphaFold DB model) 0.055
Direct ligand evidence 0 55 total records
Functional annotation 0 EC 6 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.

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 (%)
37.0 Lower values reduce human off-target concern.
Human E-value
1.84e-19
Gut microbiome similarity
63.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
96.479 Higher values support similarity to known essential genes.
DEG E-value
4.06e-101 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
95.29 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) 0.055
Structure A0A0H3GW96
Pocket Pocket 1
Druggability (FPocket) 0.338
Structure A0A0H3GW96
Pocket Pocket 4
ColabFold model
P2Rank 0.021 · Pocket 1
FPocket 0.5 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3000 / 4744 genomes with a hit
Prevalence 63.2%

Sequence

Primary amino-acid sequence viewer.

MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAEKVAVTGNKREDKMYYHHTGHIGGIKEATFEEMIARRPERVIEIAVKGMLPKGPLGRAMYRKLKVYAGNEHNHAAQQPQVLDI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

6
  • GO:0003735 The action of a molecule that contributes to the structural integrity of 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: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:0022625 The large subunit of a ribosome located in the cytosol.
  • GO:0003729 Binding to messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
  • GO:0017148 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
1 142 PIRSF PIRSF002181 RPL13p_RPL13Aa_RPL16e_RPL13o
1 142 InterPro IPR005822 Ribosomal protein L13
4 142 NCBIfam TIGR01066 50S ribosomal protein L13
4 142 InterPro IPR005823 Ribosomal protein L13, bacterial-type
15 128 CDD cd00392 Ribosomal_L13
15 128 InterPro IPR005822 Ribosomal protein L13
105 127 ProSitePatterns PS00783 Ribosomal protein L13 signature.
105 127 InterPro IPR023563 Ribosomal protein L13, conserved site
1 141 PANTHER PTHR11545 RIBOSOMAL PROTEIN L13
1 141 InterPro IPR005822 Ribosomal protein L13
13 131 Pfam PF00572 Ribosomal protein L13
13 131 InterPro IPR005822 Ribosomal protein L13
1 142 FunFam G3DSA:3.90.1180.10:FF:000001 50S ribosomal protein L13
1 142 Gene3D G3DSA:3.90.1180.10 Ribosomal protein L13
1 142 InterPro IPR036899 Ribosomal protein L13 superfamily
1 140 SUPERFAMILY SSF52161 Ribosomal protein L13
1 140 InterPro IPR036899 Ribosomal protein L13 superfamily
15 141 Hamap MF_01366 50S ribosomal protein L13 [rplM].
15 141 InterPro IPR005822 Ribosomal protein L13

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
0.055
Likely same site as FPocket 4 1.5 Å 10 shared residues 91% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #4
0.338
Likely same site as P2Rank 1 1.5 Å 10 shared residues 91% of smaller site
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_A0A0H3GW96
AlphaFold DB full sequence Viewing
ColabFold KP13_03996
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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 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
OHX PDB via homolog Detail RCSB PDB
PAR PDB via homolog Detail RCSB PDB
SPD PDB via homolog Detail RCSB PDB
YMZ PDB via homolog Detail RCSB PDB

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 P0AA10 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@…
OHX RCSB PDB P60488 286.4 Da LogP -3.55 TPSA 156.1 1 viol. ✓ Clean N[Os](N)(N)(N)(N)N
PAR RCSB PDB P0AA10 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@…
SPD RCSB PDB Q9RXY1 145.2 Da LogP -0.34 TPSA 64.1 ✓ Ro5 ✓ Clean C(CCNCCCN)CN
YMZ RCSB PDB Q8IJZ7 378.3 Da LogP 4.45 TPSA 45.2 ✓ Ro5 ✓ Clean c1cc2c(cc(nc2c(c1)C(F)(F)F)C(F)(F)F)[C@H]([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.