KpKP13 Protein target profile

Exodeoxyribonuclease V alpha chain

Accession: KP13_02294

Gene: AHE42865.1 recD 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H2A9
Length 614
Pocket druggability (P2Rank · AlphaFold DB model) 0.754
Direct ligand evidence 0 51 total records
Functional annotation 1 EC 11 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
72.533 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
89.21 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) 0.754
Structure A0A0H3H2A9
Pocket Pocket 1
Druggability (FPocket) 0.712
Structure A0A0H3H2A9
Pocket Pocket 42
ColabFold model
P2Rank 0.798 · Pocket 1
FPocket 0.173 · Pocket 16
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 114 / 4744 genomes with a hit
Prevalence 2.4%

Sequence

Primary amino-acid sequence viewer.

MTFEQLLLAAVEQRLLRPLDVQFALMVAQNDPPAVKLAAALLSRDAGEGHVCLPLSRLSGDEALSGKAGEIRDRLLAEAGAPEDWPALLLASSAVSCGDAPAPMILCGDRLYLNRMWRNELTVARFFNEANRVLEMDEARLASTLNALFPATSETDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQIEDSPRCRIRLAAPTGKAAARLTESLGAALRKLPLTDAQKALIPTEASTLHRLLGAQPGSQRMRYHAGNPLHLDVLVVDEASMIDLPMMSRLIDALPAHGRVIFLGDRDQLASVEAGAVLGDICAWASSGYTAARAQELTRLTGSPVPAGEGAIAGALRDSLCLLQKSYRFGSHSGIGSLARAVNAGARAEVKATLRQPFDDIALHPLSTTEEYEAMLGAAQQGYERYLQLRRERAEPQAMLAAFSEFQLLCALREGPYGVSGVNERLEQRLNRQRAIALPRHSRWYDGRPIMISRNDSALGLFNGDIGIALERNGELRVWFLMPDGAIKSVQPSRLPEHDTAWAMTVHKSQGSEFEHAALILPARSVPLVTRELVYTAITRAKRRLSLYADEQVLSQAIVTRTERRSGLAEIFAGRETP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0006302 The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
  • GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
  • GO:0008854 Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides.
  • GO:0009338 An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA.
  • GO:0043139 Unwinding a DNA helix in the 5' to 3' direction, driven by ATP hydrolysis.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0017116 Catalysis of the reaction: ATP + H2O = ADP + phosphate, in the presence of single-stranded DNA; drives the unwinding of a DNA helix.
  • GO:0000724 The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
1 114 Gene3D G3DSA:1.10.10.1020 -
1 114 InterPro IPR041851 RecBCD enzyme subunit RecD, N-terminal domain
115 359 FunFam G3DSA:3.40.50.300:FF:000912 RecBCD enzyme subunit RecD
537 583 Pfam PF13538 UvrD-like helicase C-terminal domain
537 583 InterPro IPR027785 UvrD-like helicase C-terminal domain
9 606 NCBIfam TIGR01447 exodeoxyribonuclease V subunit alpha
9 606 InterPro IPR006344 RecBCD enzyme subunit RecD
537 585 CDD cd18809 SF1_C_RecD
157 319 CDD cd17933 DEXSc_RecD-like
159 336 Pfam PF13604 AAA domain
144 591 PANTHER PTHR43788 DNA2/NAM7 HELICASE FAMILY MEMBER
167 337 SMART SM00382 AAA_5
167 337 InterPro IPR003593 AAA+ ATPase domain
16 606 Hamap MF_01487 RecBCD enzyme subunit RecD [recD].
16 606 InterPro IPR006344 RecBCD enzyme subunit RecD
369 479 Gene3D G3DSA:3.40.50.300 -
369 479 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
480 597 Gene3D G3DSA:3.40.50.300 -
480 597 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
285 608 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
285 608 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
115 359 Gene3D G3DSA:3.40.50.300 -
115 359 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
480 597 FunFam G3DSA:3.40.50.300:FF:000965 RecBCD enzyme subunit RecD
7 364 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
7 364 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase

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
0.754
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Surrounding area
Pocket 2 P2Rank #2
0.517
Likely same site as FPocket 5 3.1 Å 16 shared residues 94% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.244
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Surrounding area
Pocket 4 P2Rank #4
0.186
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Surrounding area
Pocket 5 P2Rank #5
0.128
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #42
0.712 Unusual size
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Surrounding area
Pocket 2 FPocket #17
0.227
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Surrounding area
Pocket 3 FPocket #5
0.226
Likely same site as P2Rank 2 3.1 Å 16 shared residues 94% of smaller site
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Surrounding area
Residue sets
UniProt: Binding site:175-182
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_A0A0H3H2A9
AlphaFold DB full sequence Viewing
ColabFold KP13_02294
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.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ANP PDB via homolog 506.2 Da · LogP -2.06 · TPSA 281.9 Open detail RCSB PDB
ZINC12360002 ZINC proposed compound · Tanimoto 0.810 Detail ZINC
ZINC12360703 ZINC proposed compound · Tanimoto 0.810 Detail ZINC
ZINC12503599 ZINC proposed compound · Tanimoto 0.810 Detail ZINC
ZINC16546165 ZINC proposed compound · Tanimoto 0.810 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
ANP RCSB PDB Q9RT63 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.