KpATCC43816 Protein target profile
exonuclease I, 3' -- 5' specific deoxyribophosphodiesterase
Accession: VK055_5051
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
- 3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- Y
- DEG identity (%)
- 83.898 Higher values support similarity to known essential genes.
- DEG E-value
- 0.0 Smaller values mean stronger essential-gene similarity.
Structure confidence
- ColabFold pLDDT
- 95.87 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.
MQDSVNQPGFLFHDYETFGTSPSLDRPAQFAAIRTDAELNVLGEPEVFYCKPADDYLPQPQAVMITGITPQEALAKGDNEATFARRIHDLFTVPQTCIVGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGIAWPENDEGLPSFRLEHLTVANGIEHQNAHDAMADVYATIAMAKLVKTRQPRLFDYLYSHRNKRKLATLIDVPQMKPLVHVSGMFGAARGNTSLVAPLAWHPENRNAVIMVDLAGDMAPLLELDADALRERLYTPRAELGDLPAASIKLVHLNKCPVLAQANTLRPQDADRLGISIQRCLENAQLLRANPQVREKVVAVYAEAEPFVPSENVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFADQRIERLLFNYRARNFPGTLDEHEQQRWLEHRRQVFTPAFLQAYADELQMLYQQYADDKEKLAQLKALWQYAQDIV
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Cytoplasmic
Enzyme Commission (EC)
1Gene Ontology (GO)
7- GO:0003676 Binding to a nucleic acid.
- GO:0004529 Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of a DNA molecule.
- GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
- 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:0008310 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a single-stranded DNA molecule.
- GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
- GO:0046872 Binding to a metal ion.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 12 | 189 | Pfam | PF00929 | Exonuclease |
| 12 | 189 | InterPro | IPR013520 | Exonuclease, RNase T/DNA polymerase III |
| 358 | 474 | ProSiteProfiles | PS51785 | Exonuclease I (ExoI) C-terminal domain profile. |
| 358 | 474 | InterPro | IPR034748 | Exonuclease I, C-terminal alpha-helical domain |
| 439 | 466 | Coils | Coil | Coil |
| 213 | 352 | Gene3D | G3DSA:3.30.1520.20 | Exonuclease ExoI, domain 2 |
| 213 | 352 | InterPro | IPR038649 | Exonuclease I, SH3-like domain superfamily |
| 13 | 431 | PANTHER | PTHR11046 | OLIGORIBONUCLEASE, MITOCHONDRIAL |
| 13 | 431 | InterPro | IPR022894 | Oligoribonuclease |
| 358 | 419 | Gene3D | G3DSA:1.20.1280.70 | Exonuclease ExoI, domain 3 |
| 421 | 474 | Gene3D | G3DSA:1.10.287.1240 | - |
| 201 | 354 | ProSiteProfiles | PS51784 | Exonuclease I (ExoI) SH3-like domain profile. |
| 201 | 354 | InterPro | IPR034747 | Exonuclease I, SH3-like domain |
| 9 | 473 | SUPERFAMILY | SSF53098 | Ribonuclease H-like |
| 9 | 473 | InterPro | IPR012337 | Ribonuclease H-like superfamily |
| 9 | 200 | Gene3D | G3DSA:3.30.420.10 | - |
| 9 | 200 | InterPro | IPR036397 | Ribonuclease H superfamily |
| 9 | 202 | SMART | SM00479 | exoiiiendus |
| 9 | 202 | InterPro | IPR013520 | Exonuclease, RNase T/DNA polymerase III |
| 2 | 474 | PIRSF | PIRSF000977 | Exodeoxyribonuclease_I |
| 2 | 474 | InterPro | IPR023607 | Exodeoxyribonuclease I |
| 213 | 351 | FunFam | G3DSA:3.30.1520.20:FF:000001 | Exodeoxyribonuclease I |
| 11 | 194 | CDD | cd06138 | ExoI_N |
| 8 | 200 | FunFam | G3DSA:3.30.420.10:FF:000033 | Exodeoxyribonuclease I |
| 359 | 419 | FunFam | G3DSA:1.20.1280.70:FF:000001 | Exodeoxyribonuclease I |
| 211 | 471 | Pfam | PF08411 | Exonuclease C-terminal |
| 211 | 471 | InterPro | IPR013620 | Exodeoxyribonuclease I, C-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_A0A0H3GSG0
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_5051
|
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 |
|---|---|---|---|---|---|
| ZINC5283936 ZINC | 0.702 | 273.4 Da LogP 3.44 TPSA 45.6 | ✓ Ro5 | ✓ Clean |
CC(C)(C)C1=NN(c2nc3ccccc3s2)C(=O)C1
|
| ZINC1579743 ZINC | 0.660 | 315.7 Da LogP 4.80 TPSA 49.3 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1Nc1cc(C(F)(F)F)ccc1Cl
|
| ZINC4099443 ZINC | 0.660 | 277.7 Da LogP 3.79 TPSA 58.6 | ✓ Ro5 | Alert |
COc1ccc(Nc2ccccc2Cl)c(C(=O)O)c1
|
| ZINC101566 ZINC | 0.600 | 329.7 Da LogP 4.62 TPSA 38.3 | ✓ Ro5 | ✓ Clean |
COc1ccc(C(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1
|
| ZINC1729836 ZINC | 0.587 | 273.3 Da LogP 3.15 TPSA 67.8 | ✓ Ro5 | Alert |
COc1ccc(Nc2ccc(OC)cc2C(=O)O)cc1
|
| ZINC272451 ZINC | 0.566 | 343.7 Da LogP 4.55 TPSA 38.3 | ✓ Ro5 | ✓ Clean |
COc1ccc(CC(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1
|
| ZINC58157306 ZINC | 0.561 | 423.8 Da LogP 3.95 TPSA 81.7 | ✓ Ro5 | ✓ Clean |
COC(=O)c1cc(OC)ccc1NS(=O)(=O)c1cc(C(F)(F)F)ccc1…
|
| ZINC437703 ZINC | 0.556 | 329.7 Da LogP 4.62 TPSA 38.3 | ✓ Ro5 | ✓ Clean |
COc1cccc(C(=O)Nc2cc(C(F)(F)F)ccc2Cl)c1
|
| ZINC6936383 ZINC | 0.556 | 369.3 Da LogP 3.67 TPSA 84.9 | ✓ Ro5 | ✓ Clean |
COc1ccc(C(=O)Nc2cc(C(F)(F)F)ccc2C(=O)O)c(OC)c1
|
| ZINC2848323 ZINC | 0.545 | 373.8 Da LogP 4.77 TPSA 47.6 | ✓ Ro5 | ✓ Clean |
COc1ccc(O[C@@H](C)C(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1
|
| ZINC2848324 ZINC | 0.545 | 373.8 Da LogP 4.77 TPSA 47.6 | ✓ Ro5 | ✓ Clean |
COc1ccc(O[C@H](C)C(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1
|
| ZINC2172100 ZINC | 0.542 | 253.6 Da LogP 3.54 TPSA 38.3 | ✓ Ro5 | ✓ Clean |
COC(=O)Nc1cc(C(F)(F)F)ccc1Cl
|
| ZINC94596758 ZINC | 0.542 | 281.2 Da LogP 4.15 TPSA 49.3 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cc(C(F)(F)F)ccc1Nc1ccccc1
|
| ZINC22151790 ZINC | 0.537 | 316.7 Da LogP 4.20 TPSA 62.2 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cccnc1Nc1cc(C(F)(F)F)ccc1Cl
|
| ZINC481307 ZINC | 0.537 | 310.3 Da LogP 3.56 TPSA 64.3 | ✓ Ro5 | ✓ Clean |
COc1ccc(Nc2cccc(C(F)(F)F)c2)c(C(N)=O)c1
|
| ZINC1140239 ZINC | 0.536 | 357.8 Da LogP 4.94 TPSA 38.3 | ✓ Ro5 | ✓ Clean |
COc1ccc(CCC(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1
|
| ZINC13320435 ZINC | 0.536 | 358.7 Da LogP 4.69 TPSA 50.4 | ✓ Ro5 | ✓ Clean |
COc1ccc(CNC(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1
|
| ZINC753310 ZINC | 0.528 | 365.8 Da LogP 4.17 TPSA 55.4 | ✓ Ro5 | ✓ Clean |
COc1ccc(S(=O)(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1
|
| ZINC4922336 ZINC | 0.526 | 358.7 Da LogP 4.91 TPSA 53.8 | ✓ Ro5 | Alert |
COc1ccc(/C(C)=N/Nc2cc(C(F)(F)F)ccc2Cl)c(O)c1
|
| ZINC13320494 ZINC | 0.525 | 413.8 Da LogP 4.72 TPSA 44.8 | ✓ Ro5 | Alert |
COc1ccc(N2CCN(C(=O)Nc3cc(C(F)(F)F)ccc3Cl)CC2)cc1
|
| ZINC56838 ZINC | 0.523 | 224.6 Da LogP 3.06 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cc(C(F)(F)F)ccc1Cl
|
| ZINC164757 ZINC | 0.520 | 250.2 Da LogP 2.33 TPSA 55.8 | ✓ Ro5 | ✓ Clean |
COc1ccc(OCC(F)(F)F)c(C(=O)O)c1
|
| ZINC2814773 ZINC | 0.519 | 343.7 Da LogP 4.31 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccccc1C(=O)Nc1cc(C(F)(F)F)ccc1Cl
|
| ZINC683171 ZINC | 0.519 | 389.8 Da LogP 4.64 TPSA 56.8 | ✓ Ro5 | ✓ Clean |
COc1cc(OC)c(C(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1OC
|
| ZINC13320421 ZINC | 0.517 | 372.8 Da LogP 4.73 TPSA 50.4 | ✓ Ro5 | ✓ Clean |
COc1ccc(CCNC(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1
|
| ZINC20739021 ZINC | 0.517 | 382.8 Da LogP 4.96 TPSA 43.3 | ✓ Ro5 | ✓ Clean |
COc1ccc2c(ccn2CC(=O)Nc2cc(C(F)(F)F)ccc2Cl)c1
|
| ZINC13320508 ZINC | 0.516 | 457.9 Da LogP 4.73 TPSA 54.0 | ✓ Ro5 | ✓ Clean |
COc1ccc(OC)c(CN2CCN(C(=O)Nc3cc(C(F)(F)F)ccc3Cl)…
|
| ZINC12956694 ZINC | 0.511 | 220.1 Da LogP 2.41 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
COc1ccc(C(F)(F)F)cc1C(=O)O
|
| ZINC134025 ZINC | 0.511 | 209.2 Da LogP 1.35 TPSA 75.6 | ✓ Ro5 | ✓ Clean |
COc1ccc(NC(C)=O)c(C(=O)O)c1
|
| ZINC20220689 ZINC | 0.511 | 238.6 Da LogP 3.15 TPSA 26.3 | ✓ Ro5 | ✓ Clean |
COC(=O)c1cc(C(F)(F)F)ccc1Cl
|
| ZINC308840216 ZINC | 0.511 | 299.5 Da LogP 3.52 TPSA 26.3 | ✓ Ro5 | ✓ Clean |
COc1ccc(Cl)c(C(=O)C(F)(F)Br)c1
|
| ZINC351305 ZINC | 0.511 | 237.6 Da LogP 3.32 TPSA 29.1 | ✓ Ro5 | ✓ Clean |
CC(=O)Nc1cc(C(F)(F)F)ccc1Cl
|
| ZINC389373086 ZINC | 0.511 | 238.6 Da LogP 3.09 TPSA 26.3 | ✓ Ro5 | ✓ Clean |
COc1ccc(Cl)c(C(=O)C(F)(F)F)c1
|
| ZINC54527155 ZINC | 0.511 | 219.2 Da LogP 2.45 TPSA 49.3 | ✓ Ro5 | ✓ Clean |
CNc1ccc(C(F)(F)F)cc1C(=O)O
|
| ZINC72338570 ZINC | 0.511 | 220.1 Da LogP 2.41 TPSA 46.5 | ✓ Ro5 | ✓ Clean |
COc1ccc(C(F)(F)F)c(C(=O)O)c1
|
| ZINC18044165 ZINC | 0.510 | 319.6 Da LogP 4.79 TPSA 32.7 | ✓ Ro5 | ✓ Clean |
CC(C)(C)C1=NN(c2c(Cl)cc(Cl)cc2Cl)C(=O)C1
|
| ZINC102646525 ZINC | 0.509 | 327.8 Da LogP 4.09 TPSA 45.6 | ✓ Ro5 | ✓ Clean |
O=C1CC(c2ccc(Cl)cc2)=NN1c1nc2ccccc2s1
|
| ZINC438360 ZINC | 0.509 | 329.7 Da LogP 4.62 TPSA 38.3 | ✓ Ro5 | ✓ Clean |
COc1ccccc1C(=O)Nc1cc(C(F)(F)F)ccc1Cl
|
| ZINC712722 ZINC | 0.509 | 359.7 Da LogP 4.63 TPSA 47.6 | ✓ Ro5 | ✓ Clean |
COc1ccc(C(=O)Nc2cc(C(F)(F)F)ccc2Cl)cc1OC
|
| ZINC7791601 ZINC | 0.509 | 343.7 Da LogP 4.55 TPSA 38.3 | ✓ Ro5 | ✓ Clean |
COc1ccc(CC(=O)Nc2ccc(C(F)(F)F)cc2Cl)cc1
|
| ZINC1182672 ZINC | 0.509 | 418.8 Da LogP 4.50 TPSA 59.6 | ✓ Ro5 | ✓ Clean |
COc1cc(OC)cc(C(=O)NC(=S)Nc2cc(C(F)(F)F)ccc2Cl)c1
|
| ZINC4922856 ZINC | 0.509 | 358.7 Da LogP 4.82 TPSA 42.9 | ✓ Ro5 | ✓ Clean |
COc1ccc(OC)c(/C=N/Nc2cc(C(F)(F)F)ccc2Cl)c1
|
| ZINC12697899 ZINC | 0.508 | 429.8 Da LogP 3.88 TPSA 70.7 | ✓ Ro5 | ✓ Clean |
COc1ccc(NC(=O)CN(C)CC(=O)Nc2cc(C(F)(F)F)ccc2Cl)…
|
| ZINC1148669 ZINC | 0.508 | 436.8 Da LogP 3.63 TPSA 75.7 | ✓ Ro5 | ✓ Clean |
COc1ccc(S(=O)(=O)N(C)CC(=O)Nc2cc(C(F)(F)F)ccc2C…
|
| ZINC3052213 ZINC | 0.500 | 422.8 Da LogP 3.80 TPSA 75.7 | ✓ Ro5 | ✓ Clean |
CN(C)S(=O)(=O)Oc1ccc(C(=O)Nc2cc(C(F)(F)F)ccc2Cl…
|
| ZINC308807291 ZINC | 0.500 | 255.0 Da LogP 3.36 TPSA 26.3 | ✓ Ro5 | ✓ Clean |
COc1ccc(Cl)c(C(=O)C(F)(F)Cl)c1
|
| ZINC346997 ZINC | 0.500 | 279.8 Da LogP 4.31 TPSA 28.5 | ✓ Ro5 | ✓ Clean |
CC1=NN(c2nc3ccc(Cl)cc3s2)C(C)(C)C1
|
| ZINC4842878 ZINC | 0.500 | 359.7 Da LogP 4.63 TPSA 47.6 | ✓ Ro5 | ✓ Clean |
COc1cc(OC)cc(C(=O)Nc2ccc(C(F)(F)F)cc2Cl)c1
|
| ZINC6145620 ZINC | 0.500 | 344.7 Da LogP 4.52 TPSA 53.9 | ✓ Ro5 | Alert |
COc1ccc(O)c(/C=N/Nc2cc(C(F)(F)F)ccc2Cl)c1
|
| ZINC753351 ZINC | 0.500 | 359.7 Da LogP 4.63 TPSA 47.6 | ✓ Ro5 | ✓ Clean |
COc1cccc(OC)c1C(=O)Nc1cc(C(F)(F)F)ccc1Cl
|
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.