Protein target profile

VK055_4849

NADH:ubiquinone oxidoreductase, membrane subunitN

Genome: KpATCC43816 Gene: nuoN AIK83376.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 3 reactions UniProt A0A0H3GWA2
Length 485
Pocket druggability 0.953
Metabolic reactions 3
Chokepoint No
Direct ligand evidence 0 71 total records
Functional annotation 1 EC 6 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.

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 (%)
21.866 Lower values reduce human off-target concern.
Human E-value
7.77e-12
Gut microbiome similarity
2.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
49.672 Higher values support similarity to known essential genes.
DEG E-value
4.63e-141 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
95.49 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.953
Structure A0A0H3GWA2
Pocket Pocket 1
P2Rank 0.221
Structure A0A0H3GWA2
Pocket Pocket 1
ColabFold model
FPocket 0.782 · Pocket 9
P2Rank 0.226 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 126 / 4744 genomes with a hit
Prevalence 2.7%

Cross-references

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

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network
Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

3 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MTITPQQLIALLPLLIVGLTVVVVMLSIAWRRNHFLNATLSVLGLNAALVSLWFVGQNGAMDVTPLIRVDGYAMLYTGLVLLASLATCTFAYPWLEGYKDNKEEFYLLVLIAALGGILLAGANHLAALFLGIELISLPLFGLVGYAFRQKRSLEASIKYTILSAAASSFLLFGMALVYANSGNLSFLALGKSLADNMLHEPLLLAGLGLMIVGLGFKLSLVPFHLWTPDVYQGAPAPVSTFLATASKIAIFGVVMRLFLYMPVGNSEAVRVVLGLIAFASIIFGNLMALSQTNIKRLLGYSSISHLGYLLVALIALQSGEMSMEAVGVYLAGYLFSSLGAFGVVSLMSSPYRGPDADSLFSYRGLFWHRPILSAVMTVMMLSLAGIPMTLGFIGKFYVLAVGVHAHLWWLVAAVVVGSAIGLYYYLRVAVSLYLSAPEQLNRDAPSNWQYSAGGIVVLISALLVLVLGIWPQPLISIVQLATPLM

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0042773 The transfer of electrons through a series of electron donors and acceptors, generating energy that is ultimately used for synthesis of ATP.
  • GO:0008137 Catalysis of the reaction: NADH + ubiquinone + 5 H+(in) = NAD+ + ubiquinol + 4 H+(out).
  • 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:0050136 Catalysis of the reaction: NADH + H+ + a quinone = NAD+ + a quinol.
  • GO:0048038 Binding to a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

50 records
Show feature table
Start End DB Term Name
450 472 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
72 94 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
35 55 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
125 147 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
395 405 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
21 479 PANTHER PTHR22773 NADH DEHYDROGENASE
260 270 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
128 147 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
105 122 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
75 93 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
328 351 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
291 296 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
427 446 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
408 430 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
227 237 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
317 327 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
159 181 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
371 394 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
29 34 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
56 74 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
406 426 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
201 226 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
447 470 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
6 475 Hamap MF_00445 NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic [ndhB].
6 475 InterPro IPR010096 NAD(P)H-quinone oxidoreductase, subunit N/subunit 2
297 319 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
329 351 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
201 223 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
238 259 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
182 200 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
6 28 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
122 420 Pfam PF00361 Proton-conducting membrane transporter
122 420 InterPro IPR001750 NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit
106 121 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
371 393 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
271 290 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
123 127 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
236 258 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
268 290 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
94 104 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
6 28 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
159 181 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
9 475 NCBIfam TIGR01770 NADH-quinone oxidoreductase subunit NuoN
9 475 InterPro IPR010096 NAD(P)H-quinone oxidoreductase, subunit N/subunit 2
148 158 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
471 485 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
352 370 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
35 57 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
297 316 Phobius TRANSMEMBRANE 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 · FPocket

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

Site 1 FPocket #1
0.953
Unusual size
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Surrounding area
Site 2 FPocket #30
0.377
Likely same site as P2Rank 3 1.6 Å 7 shared residues 88% of smaller site
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Surrounding area
Site 3 FPocket #12
0.265
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.221
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.161
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.139
Likely same site as FPocket 30 1.6 Å 7 shared residues 88% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.07
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Surrounding area
Site 5 P2Rank #5
0.066
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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_A0A0H3GWA2
AlphaFold DB full sequence Viewing
ColabFold VK055_4849
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.

71 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 21 records from similar proteins
Structural ligands 21 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3PE PDB via homolog 748.1 Da · LogP 12.06 · TPSA 134.4 Open detail RCSB PDB
970 PDB via homolog Detail RCSB PDB
AYA PDB via homolog Detail RCSB PDB
BCR PDB via homolog Detail RCSB PDB
CDL 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
3PE RCSB PDB O78748 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
970 RCSB PDB O78748 394.4 Da LogP 3.70 TPSA 63.2 ✓ Ro5 ✓ Clean CC(=C)[C@H]1Cc2c(ccc3c2O[C@@H]4COc5cc(c(cc5[C@@…
AYA RCSB PDB O78748 131.1 Da LogP -0.40 TPSA 66.4 ✓ Ro5 ✓ Clean C[C@@H](C(=O)O)NC(=O)C
BCR RCSB PDB Q8DKX9 536.9 Da LogP 12.61 TPSA 0.0 2 viol. ✓ Clean CC1=C(C(CCC1)(C)C)\C=C\C(=C\C=C\C(=C\C=C\C=C(/C…
CDL RCSB PDB O78748 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
DCQ RCSB PDB O78748 322.4 Da LogP 4.49 TPSA 52.6 ✓ Ro5 Alert CCCCCCCCCCC1=C(C(=O)C(=C(C1=O)OC)OC)C
DGD RCSB PDB Q8DKX9 949.3 Da LogP 7.61 TPSA 231.1 4 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[C@H]1[C@@H]([C…
FES RCSB PDB Q8DKX9 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FME RCSB PDB O78748 177.2 Da LogP -0.06 TPSA 66.4 ✓ Ro5 ✓ Clean CSCC[C@@H](C(=O)O)NC=O
LHG RCSB PDB Q8DKX9 723.0 Da LogP 9.89 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@…
LMG RCSB PDB Q8DKX9 787.2 Da LogP 9.78 TPSA 152.0 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[C@H]1[C@@H]([C…
MYR RCSB PDB O78748 228.4 Da LogP 4.77 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCCCC(=O)O
PC1 RCSB PDB P03892 790.2 Da LogP 12.17 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])…
PGT RCSB PDB Q8DMR6 751.0 Da LogP 10.67 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)O[C@@H](COC(=O)CCCCCCCCCC…
PL9 RCSB PDB Q8DKX9 749.2 Da LogP 16.57 TPSA 34.1 2 viol. Alert CC1=C(C(=O)C(=CC1=O)CC=C(C)CCC=C(C)CCC=C(C)CCC=…
PNS RCSB PDB O78748 358.4 Da LogP -0.96 TPSA 145.2 1 viol. ✓ Clean CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
PQN RCSB PDB Q8DKX9 450.7 Da LogP 9.16 TPSA 34.1 1 viol. Alert CC1=C(C(=O)c2ccccc2C1=O)C\C=C(/C)\CCC[C@H](C)CC…
SQD RCSB PDB Q8DKX9 795.1 Da LogP 8.12 TPSA 186.1 3 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](COC1[C@@H]([C@H]([C…
UMQ RCSB PDB Q56229 496.6 Da LogP -0.84 TPSA 178.5 2 viol. ✓ Clean CCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)…
UQ2 RCSB PDB P03892 318.4 Da LogP 4.04 TPSA 52.6 ✓ Ro5 Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CCC=C(C)C
ZMP RCSB PDB O78748 568.7 Da LogP 4.07 TPSA 162.3 1 viol. ✓ Clean CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(C…

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.