Genome KpKP13

Protein target profile

Na(+)-translocating NADH-quinone reductase subunit D

Accession: KP13_02922

Gene: nqrD AHE46198.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GN35
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Length 212
Pocket druggability (P2Rank · AlphaFold DB model) 0.026
Functional annotation 1 EC 5 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.

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. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.81. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 614 of 4744 screened genomes (12.9%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.81) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.03.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. 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
12.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
74.519 Higher values support similarity to known essential genes.
DEG E-value
2.9599999999999997e-115 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
84.38 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) 0.026
Structure A0A0H3GN35
Pocket Pocket 1
Druggability (FPocket) 0.807
Structure A0A0H3GN35
Pocket Pocket 5
ColabFold model
P2Rank 0.019 · Pocket 1
FPocket 0.771 · Pocket 4
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 614 / 4744 genomes with a hit
Prevalence 12.9%

Cross-references

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

Sequence

UniProt A0A0H3GN35

Sequence

Primary amino-acid sequence viewer.

MAEQSDMKEVKRVLVGPLIANNPIALQVLGVCSALAVTTKLETAFVMTIAVTLVTAFSSMFISMIRHHIPNSVRIIVQMAIIASLVIVVDQLLRAFAYETSKQLSVFVGLIITNCIVMGRAEAYAMKSPPLASFMDGIGNGLGYGAILIIVGFLRELIGSGKLFGITVLETVQNGGWYQPNGLFLLAPSAFFIIGLLIWALRSWKPEQQEKE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • 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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0012505 A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • 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.

28 records
Show feature table
Start End DB Term Name
44 65 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
182 201 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
64 74 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
75 97 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
12 37 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
8 210 NCBIfam TIGR01939 NADH:ubiquinone reductase (Na(+)-transporting) subunit D
8 210 InterPro IPR011292 Na(+)-translocating NADH-quinone reductase subunit D
6 212 PIRSF PIRSF006102 NQR_DE
6 212 InterPro IPR003667 NqrDE/RnfAE
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
5 210 Hamap MF_00428 Na(+)-translocating NADH-quinone reductase subunit D [nqrD].
5 210 InterPro IPR011292 Na(+)-translocating NADH-quinone reductase subunit D
182 201 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
133 154 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
12 198 Pfam PF02508 Rnf-Nqr subunit, membrane protein
12 198 InterPro IPR003667 NqrDE/RnfAE
15 37 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
38 42 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
43 63 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
75 97 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
98 102 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
7 211 PANTHER PTHR30586 ELECTRON TRANSPORT COMPLEX PROTEIN RNFE
131 153 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
103 121 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
122 132 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
155 181 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
202 212 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
104 121 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.

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
0.026
Likely same site as FPocket 2 2.2 Å 6 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.025
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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 #5
0.807
Likely same site as P2Rank 1 5.1 Å 4 shared residues 67% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #2
0.294
Likely same site as P2Rank 1 2.2 Å 6 shared residues 100% of smaller site
Show in viewer
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_A0A0H3GN35
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_02922
ColabFold — — full sequence — Loaded