KpATCC43816 Protein target profile

exonuclease I, 3' -- 5' specific deoxyribophosphodiesterase

Accession: VK055_5051

Gene: AIK83577.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GSG0
Length 474
Pocket druggability (P2Rank · AlphaFold DB model) 0.678
Direct ligand evidence 0 52 total records
Functional annotation 1 EC 7 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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
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 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) 0.678
Structure A0A0H3GSG0
Pocket Pocket 1
Druggability (FPocket) 0.468
Structure A0A0H3GSG0
Pocket Pocket 15
ColabFold model
P2Rank 0.678 · Pocket 1
FPocket 0.78 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 143 / 4744 genomes with a hit
Prevalence 3.0%

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.

MQDSVNQPGFLFHDYETFGTSPSLDRPAQFAAIRTDAELNVLGEPEVFYCKPADDYLPQPQAVMITGITPQEALAKGDNEATFARRIHDLFTVPQTCIVGYNNVRFDDEVTRNIFYRNFYDPYAWSWQHDNSRWDLLDVMRACYALRPEGIAWPENDEGLPSFRLEHLTVANGIEHQNAHDAMADVYATIAMAKLVKTRQPRLFDYLYSHRNKRKLATLIDVPQMKPLVHVSGMFGAARGNTSLVAPLAWHPENRNAVIMVDLAGDMAPLLELDADALRERLYTPRAELGDLPAASIKLVHLNKCPVLAQANTLRPQDADRLGISIQRCLENAQLLRANPQVREKVVAVYAEAEPFVPSENVDAQLYNGFFSDADRAAMKIVLETEPRNLPALDITFADQRIERLLFNYRARNFPGTLDEHEQQRWLEHRRQVFTPAFLQAYADELQMLYQQYADDKEKLAQLKALWQYAQDIV

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: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.

27 records
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.

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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
0.678
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.278
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.22
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.154
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.044
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #15
0.468
Show in viewer
Surrounding area
Pocket 2 FPocket #36
0.218
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:14-14
UniProt: Binding site:16-16
UniProt: Binding site:164-164
UniProt: Binding site:185-185
UniProt: Site:147-147 Important for interaction with ssb
UniProt: Site:180-180 Important for activity
UniProt: Site:206-206 Important for interaction with ssb
UniProt: Site:310-310 Important for interaction with ssb
UniProt: Site:337-337 Important for interaction with ssb
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_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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
BBP PDB via homolog 307.8 Da · LogP 4.09 · TPSA 45.6 Open detail RCSB PDB
CF1 PDB via homolog Detail RCSB PDB
ZINC5283936 ZINC proposed compound · Tanimoto 0.702 Detail ZINC
ZINC1579743 ZINC proposed compound · Tanimoto 0.660 Detail ZINC
ZINC4099443 ZINC proposed compound · Tanimoto 0.660 Detail ZINC

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
BBP RCSB PDB P04995 307.8 Da LogP 4.09 TPSA 45.6 ✓ Ro5 ✓ Clean CC(C)(C)C1=NN(C(=O)C1)c2nc3ccc(cc3s2)Cl
CF1 RCSB PDB P04995 345.7 Da LogP 4.81 TPSA 58.6 ✓ Ro5 Alert COc1ccc(c(c1)C(=O)O)Nc2cc(ccc2Cl)C(F)(F)F

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.