KpATCC43816 Protein target profile

ATP-dependent DNA helicase Rep

Accession: VK055_3199

Gene: rep AIK81767.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GKB6
Length 673
Pocket druggability (P2Rank · AlphaFold DB model) 0.82
Direct ligand evidence 0 52 total records
Functional annotation 1 EC 13 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
3.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
88.23 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) 0.82
Structure A0A0H3GKB6
Pocket Pocket 1
Druggability (FPocket) 0.51
Structure A0A0H3GKB6
Pocket Pocket 38
ColabFold model
P2Rank 0.963 · Pocket 1
FPocket 0.448 · Pocket 47
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 158 / 4744 genomes with a hit
Prevalence 3.3%

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.

MRLNPGQQQAVEFVTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGRKEARGLMISTFHTLGLDIIKREYAALGMKSNFSLFDDTDQVALLKELTEGLIEDDKVVLQQLISTISNWKNDLKTPAQAAAGAKGERDRIFAHCYGLYDAHMKACNVLDFDDLILLPTLLLQRNEEVRERWQNKIRYLLVDEYQDTNTSQYELVKLLVGQRARFTVVGDDDQSIYSWRGARPQNLVLLSQDFPALQVIKLEQNYRSSGRILKAANILIANNPHVFEKRLFSELGYGAELKVLSANNEDHEAERVAGELIAHHFINKTNYKDYAILYRGNHQSRVFEKMLMQNRIPYKISGGTSFFSRPEIKDLLAYLRVLTNPDDDSAFLRIVNTPKREIGPATLQKLGEWAMGRNKGLFTASFDMGLSQTLTGRGYESLTRFTHWLREIQQLAEREPVNAVRDLIRGIDYESWLYETSPSPKAAEMRMKNVNQLFTWMTEMLEGSEIDEPMTLTQVVTRFTLRDMMERGESDEELDQVQLMTLHASKGLEFPYVYLVGMEEGLLPHQSSIDEDNVDEERRLAYVGITRAQKELSFTLCKERRQYGELVRPEPSRFLLELPQDDLIWEQARKTITPEERMQKGQANVANIRAMLAKAKKA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 13 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

13
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0006268 OBSOLETE. The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
  • GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0032991 A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
  • GO:0043138 Unwinding a DNA helix in the direction 5' to 3', driven by ATP hydrolysis.
  • 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:0003697 Binding to single-stranded DNA.
  • GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
  • GO:0000725 A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous DNA region.
  • GO:0009314 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
279 610 CDD cd18807 SF1_C_UvrD
108 181 FunFam G3DSA:1.10.10.160:FF:000001 ATP-dependent DNA helicase
3 265 Pfam PF00580 UvrD/REP helicase N-terminal domain
3 265 InterPro IPR014016 UvrD-like helicase, ATP-binding domain
108 181 Gene3D G3DSA:1.10.10.160 -
108 181 InterPro IPR013986 DExx box DNA helicase domain superfamily
274 631 Gene3D G3DSA:3.40.50.300 -
274 631 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
4 266 Gene3D G3DSA:3.40.50.300 -
4 266 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
271 613 Pfam PF13361 UvrD-like helicase C-terminal domain
271 613 InterPro IPR014017 UvrD-like DNA helicase, C-terminal
281 562 ProSiteProfiles PS51217 UvrD-like DNA helicase C-terminal domain profile.
281 562 InterPro IPR014017 UvrD-like DNA helicase, C-terminal
2 636 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
2 636 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
2 667 NCBIfam TIGR01074 DNA helicase Rep
2 667 InterPro IPR005752 ATP-dependent DNA helicase Rep
377 544 Gene3D G3DSA:1.10.486.10 PCRA; domain 4
1 280 ProSiteProfiles PS51198 UvrD-like DNA helicase ATP-binding domain profile.
1 280 InterPro IPR014016 UvrD-like helicase, ATP-binding domain
2 648 PANTHER PTHR11070 UVRD / RECB / PCRA DNA HELICASE FAMILY MEMBER
2 648 InterPro IPR000212 DNA helicase, UvrD/REP type
377 544 FunFam G3DSA:1.10.486.10:FF:000002 ATP-dependent DNA helicase Rep
4 277 CDD cd17932 DEXQc_UvrD
1 668 Hamap MF_01920 ATP-dependent DNA helicase Rep [rep].
1 668 InterPro IPR005752 ATP-dependent DNA helicase Rep

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
0.82
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Surrounding area
Pocket 2 P2Rank #2
0.748
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Surrounding area
Pocket 3 P2Rank #3
0.276
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Surrounding area
Pocket 4 P2Rank #4
0.243
Likely same site as FPocket 39 3.9 Å 15 shared residues 100% of smaller site
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Surrounding area
Pocket 5 P2Rank #5
0.078
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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 #38
0.51
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Surrounding area
Pocket 2 FPocket #39
0.493 Unusual size
Likely same site as P2Rank 4 3.9 Å 15 shared residues 100% of smaller site
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Surrounding area
Pocket 3 FPocket #33
0.466
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Surrounding area
Residue sets
UniProt: Binding site:22-29
UniProt: Binding site:278-278
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_A0A0H3GKB6
AlphaFold DB full sequence Viewing
ColabFold VK055_3199
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
ANP PDB via homolog 506.2 Da · LogP -2.06 · TPSA 281.9 Open detail RCSB PDB
MGF PDB via homolog 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

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.

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Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
ANP RCSB PDB A0QTR9 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)…
MGF RCSB PDB P03018 81.3 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean F[Mg-](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.