Promising target candidate with multiple supporting evidence streams.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Risks to review
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 (%)
- 35.484 Lower values reduce human off-target concern.
- Human E-value
- 4.82e-16
- Gut microbiome similarity
- 7.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- Y
- DEG identity (%)
- 83.254 Higher values support similarity to known essential genes.
- DEG E-value
- 1.21e-130 Smaller values mean stronger essential-gene similarity.
Structure confidence
- ColabFold pLDDT
- 97.48 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelP2Rank'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.
Sequence
Primary amino-acid sequence viewer.
MNKAKRLAILTRLRENDPHPTTELHFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLALGVDGVKSYIKTIGLFNSKAENVIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPGKNVEQVEEKLLKVVPAEFKVDCHHWLILHGRYTCIARKPRCGSCLIEDLCEYKDKVYA
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Cytoplasmic
Enzyme Commission (EC)
1Gene Ontology (GO)
10- GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
- GO:0003906 Catalysis of the cleavage of the C-O-P bond in the AP site created when DNA glycosylase removes a damaged base, involved in the DNA base excision repair pathway (BER).
- GO:0006284 In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
- GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
- GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
- GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
- GO:0140078 Catalysis of the cleavage of an AP site 3' of the baseless site by a beta-lyase mechanism, leaving an unsaturated aldehyde, termed a 3'-(4-hydroxy-5-phospho-2-pentenal) residue, and a 5'-phosphate.
- GO:0019104 Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.
- GO:0046872 Binding to a metal ion.
- GO:0006285 The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 21 | 132 | FunFam | G3DSA:1.10.340.30:FF:000001 | Endonuclease III |
| 187 | 203 | Pfam | PF10576 | Iron-sulfur binding domain of endonuclease III |
| 187 | 203 | InterPro | IPR003651 | Endonuclease III-like, iron-sulphur cluster loop motif |
| 12 | 205 | Gene3D | G3DSA:1.10.1670.10 | - |
| 12 | 205 | InterPro | IPR023170 | Helix-hairpin-helix, base-excision DNA repair, C-terminal |
| 186 | 206 | SMART | SM00525 | ccc3 |
| 186 | 206 | InterPro | IPR003651 | Endonuclease III-like, iron-sulphur cluster loop motif |
| 2 | 208 | PANTHER | PTHR10359 | A/G-SPECIFIC ADENINE GLYCOSYLASE/ENDONUCLEASE III |
| 21 | 132 | Gene3D | G3DSA:1.10.340.30 | Hypothetical protein; domain 2 |
| 1 | 209 | Hamap | MF_00942 | Endonuclease III [nth]. |
| 1 | 209 | InterPro | IPR005759 | Endonuclease III |
| 30 | 183 | CDD | cd00056 | ENDO3c |
| 30 | 183 | InterPro | IPR003265 | HhH-GPD domain |
| 100 | 127 | Pfam | PF00633 | Helix-hairpin-helix motif |
| 100 | 127 | InterPro | IPR000445 | Helix-hairpin-helix motif |
| 34 | 168 | Pfam | PF00730 | HhH-GPD superfamily base excision DNA repair protein |
| 34 | 168 | InterPro | IPR003265 | HhH-GPD domain |
| 3 | 207 | SUPERFAMILY | SSF48150 | DNA-glycosylase |
| 3 | 207 | InterPro | IPR011257 | DNA glycosylase |
| 38 | 185 | SMART | SM00478 | endo3end |
| 38 | 185 | InterPro | IPR003265 | HhH-GPD domain |
| 1 | 210 | PIRSF | PIRSF001435 | Nth |
| 187 | 203 | ProSitePatterns | PS00764 | Endonuclease III iron-sulfur binding region signature. |
| 187 | 203 | InterPro | IPR004035 | Endonuclease III, iron-sulphur binding site |
| 127 | 205 | FunFam | G3DSA:1.10.1670.10:FF:000001 | Endonuclease III |
| 4 | 194 | NCBIfam | TIGR01083 | endonuclease III |
| 4 | 194 | InterPro | IPR005759 | Endonuclease III |
| 102 | 131 | ProSitePatterns | PS01155 | Endonuclease III family signature. |
| 102 | 131 | InterPro | IPR004036 | Endonuclease III-like, conserved site-2 |
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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Residue sets
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
All structural evidence
Structural evidence
0 + 2Experimental 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_A0A0H3GTN3
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_05170
|
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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC43463386 ZINC | 0.533 | 261.0 Da LogP 0.54 TPSA 80.5 | ✓ Ro5 | ✓ Clean |
Nc1nc(I)nc2[nH]cnc12
|
| ZINC4552271 ZINC | 0.533 | 237.5 Da LogP 2.18 TPSA 54.5 | ✓ Ro5 | ✓ Clean |
ClC(Cl)(Cl)c1ncnc2[nH]cnc12
|
| ZINC4707072 ZINC | 0.533 | 214.0 Da LogP 0.70 TPSA 80.5 | ✓ Ro5 | ✓ Clean |
Nc1nc(Br)nc2[nH]cnc12
|
| ZINC5543260 ZINC | 0.500 | 200.2 Da LogP -0.40 TPSA 108.8 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)c1ncnc2[nH]cnc12
|
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.