KpATCC43816 Protein target profile

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

Accession: VK055_2322

Gene: AIK80926.1 nqrF 3D evidence: Experimental + ColabFold model Metabolism Not in network UniProt A6T526
Length 407
Pocket druggability (P2Rank · Experimental) 0.576
Direct ligand evidence 0 57 total records
Functional annotation 0 EC 6 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
Hit
Human identity (%)
26.531 Lower values reduce human off-target concern.
Human E-value
2.27e-08
Gut microbiome similarity
8.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
28.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
93.52 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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) 0.576
Structure 7QU0
Pocket Pocket 1
Druggability (FPocket) 0.966
Structure 7QTY
Pocket Pocket 1
ColabFold model
P2Rank 0.576 · Pocket 1
FPocket 0.817 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 417 / 4744 genomes with a hit
Prevalence 8.8%

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.

MEIILGVVMFTLIVLVLSGLILAARSKLVNAGDVVIEINNEADKQIRTPAGDKLLNTLSSNGIFVSSACGGGGSCGQCRVTVKEGGGDILPTELSHITKRDAKAGCRLACQVAVKQNMKIELPEEIFGVKKWECEVISNDNKATFIKELKLRIPEGEVVPFRAGGYIQIECPPHKVAYADFDVPDEYRSDWDKFNLFRYVSEVKEPTLRAYSMANYPEEKGIIMLNVRIATPPPKVPDAPPGIMSSYIWSLKPGDKVTISGPFGEFFAKETDAEMVFIGGGAGMAPMRSHIFDQLKRLHSTRKISFWYGARSLREMFYDEEFEQLARDNPNFTFHVALSDPLPEDNWTGHTGFIHNVLYENYLRDHPAPEDCEFYMCGPPVMNAAVIKMLKDLGVEDENILLDDFGG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

6
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • 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.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

47 records
Show feature table
Start End DB Term Name
123 405 CDD cd06188 NADH_quinone_reductase
275 393 Gene3D G3DSA:3.40.50.80 -
275 393 InterPro IPR039261 Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
373 381 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
373 381 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
242 251 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
242 251 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
209 216 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
209 216 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
276 295 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
276 295 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
314 325 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
314 325 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
32 126 ProSiteProfiles PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
32 126 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain
37 124 SUPERFAMILY SSF54292 2Fe-2S ferredoxin-like
37 124 InterPro IPR036010 2Fe-2S ferredoxin-like superfamily
126 264 FunFam G3DSA:2.40.30.10:FF:000064 Na(+)-translocating NADH-quinone reductase subunit F
34 125 Gene3D G3DSA:3.10.20.30 -
34 125 InterPro IPR012675 Beta-grasp domain superfamily
24 31 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
43 115 Pfam PF00111 2Fe-2S iron-sulfur cluster binding domain
43 115 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain
2 24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
255 402 SUPERFAMILY SSF52343 Ferredoxin reductase-like, C-terminal NADP-linked domain
255 402 InterPro IPR039261 Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
4 23 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 23 SignalP_EUK SignalP-TM SignalP-TM
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 31 Phobius SIGNAL_PEPTIDE Signal peptide region
1 407 PIRSF PIRSF000044 Cis_Diol_DH_RD
1 407 InterPro IPR010205 Na(+)-translocating NADH-quinone reductase subunit F
3 407 NCBIfam TIGR01941 NADH:ubiquinone reductase (Na(+)-transporting) subunit F
3 407 InterPro IPR010205 Na(+)-translocating NADH-quinone reductase subunit F
204 266 Pfam PF00970 Oxidoreductase FAD-binding domain
204 266 InterPro IPR008333 Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain
126 264 Gene3D G3DSA:2.40.30.10 Translation factors
129 269 ProSiteProfiles PS51384 Ferredoxin reductase-type FAD binding domain profile.
129 269 InterPro IPR017927 FAD-binding domain, ferredoxin reductase-type
23 407 PANTHER PTHR43644 NA(+)-TRANSLOCATING NADH-QUINONE REDUCTASE SUBUNIT
275 393 FunFam G3DSA:3.40.50.80:FF:000014 Na(+)-translocating NADH-quinone reductase subunit F
1 407 Hamap MF_00430 Na(+)-translocating NADH-quinone reductase subunit F [nqrF].
105 272 SUPERFAMILY SSF63380 Riboflavin synthase domain-like
105 272 InterPro IPR017938 Riboflavin synthase-like beta-barrel
277 386 Pfam PF00175 Oxidoreductase NAD-binding domain
277 386 InterPro IPR001433 Oxidoreductase FAD/NAD(P)-binding
32 407 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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 · FPocket

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

Pocket 1 FPocket #1
0.966
Show in viewer
Surrounding area
All structural evidence 2 experimental · 1 predicted

Structural evidence

2 + 1

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
PDB 7QTY
X-ray A Viewing
PDB 7QU0
X-ray A Loaded
ColabFold VK055_2322
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
BTB PDB via homolog 209.2 Da · LogP -3.01 · TPSA 104.4 Open detail RCSB PDB
DGG PDB via homolog Detail RCSB PDB
ECN PDB via homolog Detail RCSB PDB
FDA PDB via homolog Detail RCSB PDB
FES PDB via homolog Detail RCSB PDB

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
BTB RCSB PDB Q03304 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
DGG RCSB PDB P39662 735.0 Da LogP 9.75 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@…
ECN RCSB PDB P39662 381.7 Da LogP 5.80 TPSA 27.1 1 viol. ✓ Clean c1cc(ccc1COC(Cn2ccnc2)c3ccc(cc3Cl)Cl)Cl
FDA RCSB PDB P22868 787.6 Da LogP -1.75 TPSA 363.3 3 viol. ✓ Clean Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…
FES RCSB PDB A0A076MZ01 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
KKK RCSB PDB P39662 531.4 Da LogP 4.21 TPSA 69.1 1 viol. Alert CC(=O)N1CCN(CC1)c2ccc(cc2)OC[C@H]3CO[C@](O3)(Cn…
X89 RCSB PDB P39662 416.1 Da LogP 6.45 TPSA 27.1 1 viol. ✓ Clean c1cc(c(cc1Cl)Cl)CO[C@@H](Cn2ccnc2)c3ccc(cc3Cl)Cl

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.