KpATCC43816 Protein target profile

exodeoxyribonuclease III

Accession: VK055_1238

Gene: xth AIK79861.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A235PVE3
Length 268
Pocket druggability (P2Rank · AlphaFold DB model) 0.736
Direct ligand evidence 0 151 total records
Functional annotation 1 EC 7 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.

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 (%)
30.172 Lower values reduce human off-target concern.
Human E-value
6.47e-11
Gut microbiome similarity
3.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
72.285 Higher values support similarity to known essential genes.
DEG E-value
1.04e-148 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.02 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) 0.736
Structure A0A235PVE3
Pocket Pocket 1
Druggability (FPocket) 0.186
Structure A0A235PVE3
Pocket Pocket 1
ColabFold model
P2Rank 0.824 · Pocket 1
FPocket 0.599 · Pocket 10
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 151 / 4744 genomes with a hit
Prevalence 3.2%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MKFVSFNINGLRARPHQLAAIVEKHQPDVIGLQETKVHDDMFPLEEVARLGYNVFYHGQKGHYGVALLTKETPIAVRRGFPDDGEEAQRRIIMAEIPSPFGNVTVINGYFPQGESRDHETKFPAKAAFYQNLQNYLETELNKENPVLIMGDMNISPTDLDIGIGEENRKRWLRTGKCSFLPEEREWMDRLLGWGLVDTWRQANPDNHEHFSWFDYRSKGFDDNRGLRIDLLLASQPLAQRCVETGIDYEIRGMEKPSDHAPVWATFRP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • 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:0008311 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA 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:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0004518 Catalysis of the cleavage of ester linkages within nucleic acids.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
1 268 ProSiteProfiles PS51435 AP endonucleases family 1 profile.
1 268 InterPro IPR004808 AP endonuclease 1
1 266 NCBIfam TIGR00195 exodeoxyribonuclease III
1 268 FunFam G3DSA:3.60.10.10:FF:000006 Exodeoxyribonuclease III
1 267 SUPERFAMILY SSF56219 DNase I-like
1 267 InterPro IPR036691 Endonuclease/exonuclease/phosphatase superfamily
1 266 CDD cd09086 ExoIII-like_AP-endo
1 266 InterPro IPR037493 Exodeoxyribonuclease III-like
223 234 ProSitePatterns PS00728 AP endonucleases family 1 signature 3.
223 234 InterPro IPR020848 AP endonuclease 1, conserved site
1 268 Gene3D G3DSA:3.60.10.10 Endonuclease/exonuclease/phosphatase
1 268 InterPro IPR036691 Endonuclease/exonuclease/phosphatase superfamily
1 267 PANTHER PTHR43250 -
1 267 InterPro IPR037493 Exodeoxyribonuclease III-like
4 259 Pfam PF03372 Endonuclease/Exonuclease/phosphatase family
4 259 InterPro IPR005135 Endonuclease/exonuclease/phosphatase
27 36 ProSitePatterns PS00726 AP endonucleases family 1 signature 1.
27 36 InterPro IPR020847 AP endonuclease 1, binding site
1 266 NCBIfam TIGR00633 exodeoxyribonuclease III
1 266 InterPro IPR004808 AP endonuclease 1

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
0.736
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.029
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.02
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.017
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_A0A235PVE3
AlphaFold DB full sequence Viewing
ColabFold VK055_1238
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.

151 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 101 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
PGA PDB via homolog 156.0 Da · LogP -0.82 · TPSA 104.1 Open detail RCSB PDB
CHEMBL187266 ChEMBL via homolog · pchembl 9.06 (~0.9 nM) Detail ChEMBL
CHEMBL1323786 ChEMBL via homolog · pchembl 8.96 (~1.1 nM) Detail ChEMBL
CHEMBL1305422 ChEMBL via homolog · pchembl 8.89 (~1.3 nM) Detail ChEMBL
CHEMBL1566820 ChEMBL via homolog · pchembl 8.89 (~1.3 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
PGA RCSB PDB P27695 156.0 Da LogP -0.82 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)O)OP(=O)(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.

Cross-references

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

Chemistry

ChEMBL CHEMBL187266 ChEMBL CHEMBL1323786 ChEMBL CHEMBL1305422 ChEMBL CHEMBL1566820 ChEMBL CHEMBL1432717 ChEMBL CHEMBL3210521 ChEMBL CHEMBL578390 ChEMBL CHEMBL1410367 ChEMBL CHEMBL3197141 ChEMBL CHEMBL1391063 ChEMBL CHEMBL1971760 ChEMBL CHEMBL1465659 ChEMBL CHEMBL1611306 ChEMBL CHEMBL1321148 ChEMBL CHEMBL1409844 ChEMBL CHEMBL1451059 ChEMBL CHEMBL1994685 ChEMBL CHEMBL1441170 ChEMBL CHEMBL1500249 ChEMBL CHEMBL3145010 ChEMBL CHEMBL1538023 ChEMBL CHEMBL1610567 ChEMBL QHM ChEMBL REF ChEMBL CHEMBL1576814 ChEMBL CHEMBL1404357 ChEMBL CHEMBL3196993 ChEMBL CHEMBL1257131 ChEMBL CHEMBL1358777 ChEMBL CHEMBL1331939 ChEMBL CHEMBL1425538 ChEMBL CHEMBL4210534 ChEMBL QU4 ChEMBL CHEMBL4205402 ChEMBL CHEMBL1307297 ChEMBL CHEMBL1322274 ChEMBL DWT ChEMBL CHEMBL279014 ChEMBL CHEMBL311663 ChEMBL CHEMBL3191714 ChEMBL CHEMBL109037 ChEMBL CHEMBL4216250 ChEMBL CHEMBL1601846 ChEMBL CHEMBL1419637 ChEMBL FIC ChEMBL CHEMBL351042 ChEMBL CHEMBL1325390 ChEMBL CHEMBL1525544 ChEMBL CHEMBL4205877 ChEMBL CHEMBL563444 ChEMBL CHEMBL4217125 ChEMBL CHEMBL56393 ChEMBL CHEMBL404600 ChEMBL CHEMBL1160025 ChEMBL CHEMBL1365553 ChEMBL CHEMBL4205950 ChEMBL CHEMBL1553873 ChEMBL CHEMBL1323312 ChEMBL CHEMBL1394337 ChEMBL CHEMBL1554829 ChEMBL CHEMBL59451 ChEMBL MYC ChEMBL CHEMBL1509377 ChEMBL CHEMBL1305518 ChEMBL CHEMBL1346456 ChEMBL CHEMBL1438439 ChEMBL CHEMBL1560245 ChEMBL CHEMBL3189657 ChEMBL CHEMBL1376492 ChEMBL CHEMBL487203 ChEMBL TIY ChEMBL CHEMBL234338 ChEMBL CHEMBL253570 ChEMBL CHEMBL3191528 ChEMBL CHEMBL33864 ChEMBL PQR ChEMBL CHEMBL1524942 ChEMBL CHEMBL337702 ChEMBL CHEMBL718 ChEMBL 3WL ChEMBL ROA ChEMBL CHEMBL5917464 ChEMBL CHEMBL5969187 ChEMBL CHEMBL1314924 ChEMBL CHEMBL1386676 ChEMBL CHEMBL1560136 ChEMBL CHEMBL1224512 ChEMBL CHEMBL1495997 ChEMBL CHEMBL4211672 ChEMBL LNR ChEMBL CHEMBL1353644 ChEMBL CHEMBL1385364 ChEMBL CHEMBL1414095 ChEMBL CHEMBL1416177 ChEMBL CHEMBL255881 ChEMBL CHEMBL4203747 ChEMBL FSE ChEMBL CHEMBL1357760 ChEMBL CHEMBL1526624 ChEMBL CHEMBL1706858