KpATCC43816 Protein target profile

ubiquinone oxidoreductase, Na(+)-translocating, A subunit

Accession: VK055_2327

Gene: nqrA AIK80931.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GJV1
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Length 447
Pocket druggability (P2Rank · AlphaFold DB model) 0.882
Functional annotation 1 EC 2 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.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Second pocket predictor agrees P2Rank predicted binding-site probability 0.88. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 115 of 4744 screened genomes (2.4%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.88) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant. Best pocket may be a modeling artifact FPocket selected-pocket score 0.49, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

Evidence gaps

No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
96.25 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) 0.882
Structure A0A0H3GJV1
Pocket Pocket 1
Druggability (FPocket) 0.487
Structure A0A0H3GJV1
Pocket Pocket 28
ColabFold model
P2Rank 0.88 · Pocket 1
FPocket 0.558 · Pocket 6
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 115 / 4744 genomes with a hit
Prevalence 2.4%

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.

MIKITKGLDLPIAGMPLQQISPAPAVKRVALLGEEYVGMRPAMAVKEGDRVKKGQILFEDKKIPGVCFTAPASGIVSAIHRGERRVLQSVVIDIEGNDAVAFTRYAADALAELPRDTVQQQLLASGQWTALRTRPFSKTPLPGSTPAAIFVNAMDTNPLAAEPQPIILAERAAFDAGLTVLTRLTDGKVHVCQPSGGKLGGHPLGQVCFNQFSGPHPAGLPGTHIHFLEPVSLNKQVWHLNYQDAIAIGKLFLDGELYCERVIALGGPQVTSPRLVKTTLGASLEDLLAGELQEGENRVISGSVLSGARAHGPHAFLGRFHLQVSVVKEGREKELFGWVMPGKEKFSITRTTLGHFFKRKRFHFSTDTNGGERAMVPIGNYERVMPLDILPTILLRDLLAGDTDSAQALGCLELDEEDLALCTYVCPGKYEYGPALRSVLTRIEQEG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

2
  • GO:0016655 Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
  • GO:0006814 The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
1 447 PANTHER PTHR37839 NA(+)-TRANSLOCATING NADH-QUINONE REDUCTASE SUBUNIT A
1 447 InterPro IPR008703 Na(+)-translocating NADH-quinone reductase subunit A
262 311 Pfam PF11973 NQRA C-terminal domain
262 311 InterPro IPR022615 Na(+)-translocating NADH-quinone reductase subunit A, C-terminal domain
42 90 Gene3D G3DSA:2.40.50.100 -
1 447 Hamap MF_00425 Na(+)-translocating NADH-quinone reductase subunit A [nqrA].
1 257 Pfam PF05896 Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
1 257 InterPro IPR008703 Na(+)-translocating NADH-quinone reductase subunit A
2 447 NCBIfam TIGR01936 NADH:ubiquinone reductase (Na(+)-transporting) subunit A
2 447 InterPro IPR008703 Na(+)-translocating NADH-quinone reductase subunit A

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
0.882
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Surrounding area
Pocket 2 P2Rank #2
0.459
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Surrounding area
Pocket 3 P2Rank #3
0.071
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Surrounding area
Pocket 4 P2Rank #4
0.008
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Surrounding area
Pocket 5 P2Rank #5
0.004
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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 #28
0.487 Unusual size
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Surrounding area
Pocket 2 FPocket #3
0.426
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Surrounding area
Pocket 3 FPocket #10
0.221
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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_A0A0H3GJV1
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2327
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GJV1