Protein target profile

VK055_4454

NADH-Ubiquinone/plastoquinone (complex I), various chains family protein

Genome: KpATCC43816 Gene: AIK82997.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GX92
Length 602
Pocket druggability 0.971
Direct ligand evidence 0 60 total records
Functional annotation 0 EC 4 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
Hit
Human identity (%)
27.027 Lower values reduce human off-target concern.
Human E-value
2.35e-14
Gut microbiome similarity
1.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
93.73 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 0.971
Structure A0A0H3GX92
Pocket Pocket 15
P2Rank 0.707
Structure A0A0H3GX92
Pocket Pocket 1
ColabFold model
FPocket 0.797 · Pocket 9
P2Rank 0.625 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 55 / 4744 genomes with a hit
Prevalence 1.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MNQAVAWYAASAVLAFLFAMRKPLSGAIAGIGGAVASAMLVVAGGAALLMPERIHGGMLQFLHLMIRVGGVNALWLLAIGLSALPVSLFNISWHRHPQVKPNGPLVNLLLAAATCAVVVTNIGSLVVMAEIMALCAAFLTGCAASGKLWFALGRLGTLLMAWTCWLVWSTYGTLELAQINLQAVDMMQNPLLWLPGLVGFALLAGAIPLHGWAPQAHAGASAPAAALFSTVVMKVGLYGMLTVSLAGGVPPLWWGVMLLALGMITAFIGGLYALMEHNIQRLLAYHTLENIGIILLGLGAFVTGVATRNSTLMVLGFIGGMYHLINHSLFKTTLFLGAGAVWFRTGHRDIEKLGGIGKKMPLISLAMLVGLMAMAALPPLNGFAGEWVIYQSFFKMSTGDLFIGRLLGPLLAVGLAITGALAVMCMAKVYGVTFLGAPRTKEAENATCAPWLMTLSVVLAAVFCLVGGIAAPWLLPLVSGAFPVQAQVSSVVSQPMIALLLIACPLLPFLLMIFFKGDRLAARSRGAAWVCGYDHEQSMVITAHGFAMPVKEAFAPLLKLRHWLNPVRLVPGWQSASAPALLRGIALVELAVLVVIVISRGA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

55 records
Show feature table
Start End DB Term Name
368 394 PRINTS PR01437 NADH-ubiquinone oxidoreductase subunit 4 signature
368 394 InterPro IPR003918 NADH:ubiquinone oxidoreductase
218 242 PRINTS PR01437 NADH-ubiquinone oxidoreductase subunit 4 signature
218 242 InterPro IPR003918 NADH:ubiquinone oxidoreductase
391 409 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
495 515 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
253 275 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
455 477 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
192 214 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
305 323 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
451 475 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
4 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
282 304 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
516 579 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
3 600 PANTHER PTHR42682 HYDROGENASE-4 COMPONENT F
224 246 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
4 21 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
213 223 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
324 343 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
89 107 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
61 88 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
252 275 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
172 190 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
29 49 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
580 599 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
155 177 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
282 304 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
344 362 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
140 150 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
401 423 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
410 430 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
476 494 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
144 399 Pfam PF00361 Proton-conducting membrane transporter
144 399 InterPro IPR001750 NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit
247 251 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
15 19 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
191 212 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
50 60 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
363 390 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
108 139 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
319 341 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
151 171 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
28 50 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
105 127 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 19 Phobius SIGNAL_PEPTIDE Signal peptide region
492 514 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
431 450 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
362 381 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
227 249 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
600 602 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
70 92 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
276 281 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
131 153 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
20 28 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: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #15
0.971
Likely same site as P2Rank 3 2.2 Å 13 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #7
0.692
Likely same site as P2Rank 1 1.2 Å 14 shared residues 93% of smaller site
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Surrounding area
Site 3 FPocket #30
0.679
Unusual size
Show in viewer
Surrounding area
Site 4 FPocket #29
0.246
Likely same site as P2Rank 4 5.5 Å 13 shared residues 81% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.707
Likely same site as FPocket 7 1.2 Å 14 shared residues 93% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.569
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.546
Likely same site as FPocket 15 2.2 Å 13 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.33
Likely same site as FPocket 29 5.5 Å 13 shared residues 81% of smaller site
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.248
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_A0A0H3GX92
AlphaFold DB full sequence Viewing
ColabFold VK055_4454
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.

60 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 10 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
BCR PDB via homolog 536.9 Da · LogP 12.61 · TPSA 0.0 Open detail RCSB PDB
DGD PDB via homolog Detail RCSB PDB
FES PDB via homolog Detail RCSB PDB
LHG PDB via homolog Detail RCSB PDB
LMG 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
BCR RCSB PDB Q8DKY0 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…
DGD RCSB PDB Q8DKY0 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 Q8DKY0 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
LHG RCSB PDB Q8DKY0 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 Q8DKY0 787.2 Da LogP 9.78 TPSA 152.0 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[C@H]1[C@@H]([C…
LMT RCSB PDB A0A221C8X0 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…
PL9 RCSB PDB Q8DKY0 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=…
PQN RCSB PDB Q8DKY0 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…
PTY RCSB PDB B7GL84 734.1 Da LogP 11.67 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC…
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…

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.