KpKP13 Protein target profile

Type IV restriction endonuclease family protein

Accession: KP13_01408

Gene: AHE47422.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0U3AUH3
Export view
Length 195
Pocket druggability (P2Rank · AlphaFold DB model) 0.111
Functional annotation 0 EC 5 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

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 6 of 4744 screened genomes (0.1%) have a significant similarity hit. Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.10. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.11.

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
No hit
Gut microbiome similarity
0.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
91.34 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) 0.111
Structure A0A0U3AUH3
Pocket Pocket 1
Druggability (FPocket) 0.1
Structure A0A0U3AUH3
Pocket Pocket 4
ColabFold model
FPocket 0.534 · Pocket 10
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 6 / 4744 genomes with a hit
Prevalence 0.1%

Sequence

Primary amino-acid sequence viewer.

MNESIHVVGSFILAGILLYGLWLGTRRRRRRHERKQASAVRVIDKINTFPHFGQKIAYLRKIDPFVFEELLLEGFERRGFEVIRNRRYTGDGGIDGRVKIDGQTWLIQAKRYTSYIAVGHVRDFSDLLNATGARGFFCHTGKTREGTKSLIRGDSRMILVSGQKLLDLIATDAPFIPYPGYRPPAEMVQPEQETT

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

5
  • GO:0003676 Binding to a nucleic acid.
  • GO:0009307 A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks.
  • GO:0015666 Catalysis of endonucleolytic cleavage of DNA in a site-specific manner, resulting in double-strand breaks.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
5 24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
33 173 Gene3D G3DSA:3.40.1350.10 -
33 173 InterPro IPR011856 tRNA endonuclease-like domain superfamily
63 171 SUPERFAMILY SSF52980 Restriction endonuclease-like
63 171 InterPro IPR011335 Restriction endonuclease type II-like
26 195 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
6 25 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
16 171 PANTHER PTHR30015 MRR RESTRICTION SYSTEM PROTEIN
59 169 Pfam PF04471 Restriction endonuclease
59 169 InterPro IPR007560 Restriction endonuclease type IV, Mrr

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

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.111
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_A0A0U3AUH3
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_01408
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0U3AUH3