KpATCC43816 Protein target profile
5'-3' exonuclease, C-terminal SAM fold family protein
Accession: VK055_4362
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
Evidence coverage
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
- 2.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 34.286 Higher values support similarity to known essential genes.
Structure confidence
- ColabFold pLDDT
- 95.71 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.
MAVHLLIVDALNLIRRIHAVQGSPCVDTCLHALEQLIVHSQPTHAVAVFDDEDRAHGWRHQRLPEYKAGRAPMPETLVAEMPALRAAFEQRGIRCWASPGSEADDLAATLAVKVAQAGHQATIVSTDKGYCQLLSPTIRIRDYFQKRWLDAPFIASEFGVTPEQLADYWGLAGISSSKVPGVAGIGPKSAAQLLNEFQDLEGLYARLAEVPEKWRKKLAAHQEMAFTCREVARLQTDLQLDGNLQQLRLTR
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Cytoplasmic
Enzyme Commission (EC)
1Gene Ontology (GO)
8- GO:0017108 Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis.
- 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:0033567 The DNA metabolic process, occurring during lagging strand synthesis, by which RNA primers are removed from Okazaki fragments, the resulting gaps filled by DNA polymerization, and the ends ligated to form a continuous strand.
- GO:0048256 Catalysis of the cleavage of a flap structure in DNA, but not other DNA structures; processes the ends of Okazaki fragments in lagging strand DNA synthesis.
- GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
- GO:0008409 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end.
- GO:0000287 Binding to a magnesium (Mg) ion.
- GO:0030955 Binding to a potassium ion (K+).
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 190 | 210 | Coils | Coil | Coil |
| 162 | 251 | FunFam | G3DSA:1.10.150.20:FF:000003 | DNA polymerase I |
| 162 | 234 | CDD | cd09898 | H3TH_53EXO |
| 162 | 234 | InterPro | IPR020045 | DNA polymerase I-like, H3TH domain |
| 4 | 240 | PANTHER | PTHR42646 | FLAP ENDONUCLEASE XNI |
| 4 | 240 | InterPro | IPR038969 | Flap endonuclease |
| 1 | 19 | SignalP_EUK | SignalP-noTM | SignalP-noTM |
| 160 | 250 | Pfam | PF01367 | 5'-3' exonuclease, C-terminal SAM fold |
| 160 | 250 | InterPro | IPR020045 | DNA polymerase I-like, H3TH domain |
| 2 | 251 | Hamap | MF_01192 | Flap endonuclease Xni [xni]. |
| 2 | 251 | InterPro | IPR022895 | Flap endonuclease Xni |
| 1 | 161 | Gene3D | G3DSA:3.40.50.1010 | - |
| 162 | 197 | SMART | SM00279 | HhH_4 |
| 162 | 197 | InterPro | IPR008918 | Helix-hairpin-helix motif, class 2 |
| 162 | 251 | Gene3D | G3DSA:1.10.150.20 | - |
| 160 | 243 | SUPERFAMILY | SSF47807 | 5' to 3' exonuclease, C-terminal subdomain |
| 160 | 243 | InterPro | IPR036279 | 5'-3' exonuclease, C-terminal domain superfamily |
| 4 | 159 | SUPERFAMILY | SSF88723 | PIN domain-like |
| 4 | 159 | InterPro | IPR029060 | PIN-like domain superfamily |
| 7 | 154 | CDD | cd09859 | PIN_53EXO |
| 1 | 161 | FunFam | G3DSA:3.40.50.1010:FF:000011 | Flap endonuclease Xni |
| 3 | 250 | SMART | SM00475 | 53exo3 |
| 3 | 250 | InterPro | IPR002421 | 5'-3' exonuclease |
| 5 | 151 | Pfam | PF02739 | 5'-3' exonuclease, N-terminal resolvase-like domain |
| 5 | 151 | InterPro | IPR020046 | 5'-3' exonuclease, alpha-helical arch, N-terminal |
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
Residue sets
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_A0A0H3GWW8
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_4362
|
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 |
|---|---|---|---|---|---|
| ZINC4521259 ZINC | 1.000 | 282.3 Da LogP -4.01 TPSA 145.4 | 1 viol. | ✓ Clean |
OCC(CO)(CO)NCCCNC(CO)(CO)CO
|
| ZINC115591405 ZINC | 0.636 | 373.6 Da LogP 4.55 TPSA 72.7 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCCCCCCNC(CO)(CO)CO
|
| ZINC115591837 ZINC | 0.636 | 317.5 Da LogP 2.99 TPSA 72.7 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCCNC(CO)(CO)CO
|
| ZINC143575268 ZINC | 0.636 | 289.5 Da LogP 2.21 TPSA 72.7 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCNC(CO)(CO)CO
|
| ZINC2322313 ZINC | 0.636 | 233.4 Da LogP 0.65 TPSA 72.7 | ✓ Ro5 | ✓ Clean |
CCCCCCCCNC(CO)(CO)CO
|
| ZINC97996983 ZINC | 0.636 | 345.6 Da LogP 3.77 TPSA 72.7 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCCCCNC(CO)(CO)CO
|
| ZINC1611594 ZINC | 0.583 | 243.3 Da LogP -2.43 TPSA 127.1 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCCNC(CO)(CO)CO
|
| ZINC5273895 ZINC | 0.583 | 257.3 Da LogP -2.04 TPSA 127.1 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCCCNC(CO)(CO)CO
|
| ZINC114433005 ZINC | 0.571 | 231.9 Da LogP 1.58 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CC(Br)(Br)C(=O)O
|
| ZINC98087485 ZINC | 0.533 | 228.3 Da LogP 2.54 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
CC(C)(C)/C(C(=O)O)=C(\C(=O)O)C(C)(C)C
|
| ZINC104203687 ZINC | 0.500 | 202.2 Da LogP 1.17 TPSA 99.3 | ✓ Ro5 | Alert |
CC(C)(/N=N\C(C)(C)C(=O)O)C(=O)O
|
| ZINC104203691 ZINC | 0.500 | 202.2 Da LogP 1.17 TPSA 99.3 | ✓ Ro5 | Alert |
CC(C)(/N=N/C(C)(C)C(=O)O)C(=O)O
|
| ZINC1530141 ZINC | 0.500 | 229.3 Da LogP -2.82 TPSA 127.1 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCNC(CO)(CO)CO
|
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.