Genome KpKP13

Protein target profile

Ribonuclease 3

Accession: KP13_00813

Gene: AHE43177.1 rnc 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWU8
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Length 226
Pocket druggability (P2Rank · AlphaFold DB model) 0.02
Direct ligand evidence 0 60 total records
Functional annotation 1 EC 12 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 Ligand evidence via structure/bioactivity 1 structural and 9 bioactivity records.

Risks to review

Human similarity Top human hit identity: 35.065%. Microbiome similarity 202 of 4744 screened genomes (4.3%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.37. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.02.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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 (%)
35.065 Lower values reduce human off-target concern.
Human E-value
9.48e-07
Gut microbiome similarity
4.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
96.903 Higher values support similarity to known essential genes.
DEG E-value
8.29e-165 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.93 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) 0.02
Structure A0A0H3GWU8
Pocket Pocket 1
Druggability (FPocket) 0.374
Structure A0A0H3GWU8
Pocket Pocket 2
ColabFold model
P2Rank 0.043 · Pocket 1
FPocket 0.358 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 202 / 4744 genomes with a hit
Prevalence 4.3%

Cross-references

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

Sequence

UniProt A0A0H3GWU8

Chemistry

ChEMBL CHEMBL5170759 ChEMBL CHEMBL5180444 ChEMBL CHEMBL826 ChEMBL CHEMBL5178502 ChEMBL CHEMBL5175086 ChEMBL CHEMBL5201452 ChEMBL CHEMBL463499 ChEMBL CHEMBL5092946 ChEMBL CHEMBL5093445

Sequence

Primary amino-acid sequence viewer.

MNPIVINRLQRKLGYTFHHQELLQQALTHRSASSKHNERLEFLGDSILSFVIANALYHRFPRVDEGDMSRMRATLVRGNTLAEIAREFELGECLRLGPGELKSGGFRRESILADTVEALIGGVFLDSDIQNVERLILSWYQTRLDEISPGDKQKDPKTRLQEYLQGRHLPLPSYLVVQVRGEAHDQEFTIHCQVSGLSEPVVGTGSSRRKAEQAAAEQALKKLELE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 12 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

12
  • GO:0004525 Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt.
  • GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
  • GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0003725 Binding to double-stranded RNA.
  • GO:0042802 Binding to an identical protein or proteins.
  • GO:0046872 Binding to a metal ion.
  • GO:0019843 Binding to a ribosomal RNA.
  • GO:0006397 Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
  • GO:0010468 Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).
  • GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
9 223 PANTHER PTHR11207 RIBONUCLEASE III
9 223 InterPro IPR011907 Ribonuclease III
5 159 SUPERFAMILY SSF69065 RNase III domain-like
5 159 InterPro IPR036389 Ribonuclease III, endonuclease domain superfamily
4 147 Gene3D G3DSA:1.10.1520.10 Ribonuclease III domain
4 147 InterPro IPR036389 Ribonuclease III, endonuclease domain superfamily
4 147 FunFam G3DSA:1.10.1520.10:FF:000001 Ribonuclease 3
6 128 ProSiteProfiles PS50142 Ribonuclease III family domain profile.
6 128 InterPro IPR000999 Ribonuclease III domain
109 223 SUPERFAMILY SSF54768 dsRNA-binding domain-like
38 46 ProSitePatterns PS00517 Ribonuclease III family signature.
38 46 InterPro IPR000999 Ribonuclease III domain
156 223 Pfam PF00035 Double-stranded RNA binding motif
156 223 InterPro IPR014720 Double-stranded RNA-binding domain
9 220 Hamap MF_00104 Ribonuclease 3 [rnc].
9 220 InterPro IPR011907 Ribonuclease III
208 226 Coils Coil Coil
154 224 Gene3D G3DSA:3.30.160.20 -
21 149 SMART SM00535 riboneu5
21 149 InterPro IPR000999 Ribonuclease III domain
20 141 Pfam PF14622 Ribonuclease-III-like
20 141 InterPro IPR000999 Ribonuclease III domain
9 223 NCBIfam TIGR02191 ribonuclease III
155 225 ProSiteProfiles PS50137 Double stranded RNA-binding domain (dsRBD) profile.
155 225 InterPro IPR014720 Double-stranded RNA-binding domain
156 224 SMART SM00358 DRBM_3
156 224 InterPro IPR014720 Double-stranded RNA-binding domain
21 149 CDD cd00593 RIBOc
154 225 FunFam G3DSA:3.30.160.20:FF:000003 Ribonuclease 3
154 210 CDD cd10845 DSRM_RNAse_III_family

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
0.02
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.005
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2
0.374
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:23-23
UniProt: Active site:95-95
UniProt: Binding site:19-19
UniProt: Binding site:92-92
UniProt: Binding site:95-95
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_A0A0H3GWU8
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_00813
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.

60 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 9 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
MLI PDB via homolog 102.0 Da · LogP -3.12 · TPSA 80.3 Open detail RCSB PDB
CHEMBL5170759 ChEMBL via homolog · pchembl 7.98 (~10.5 nM) Detail ChEMBL
CHEMBL5180444 ChEMBL via homolog · pchembl 7.72 (~19.1 nM) Detail ChEMBL
CHEMBL826 ChEMBL via homolog · pchembl 7.03 (~93.3 nM) Detail ChEMBL
CHEMBL5178502 ChEMBL via homolog · pchembl 6.90 (~125.9 nM) Detail ChEMBL

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
MLI RCSB PDB
3LLH
Q15633-2 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]

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.