KpATCC43816 Protein target profile

nuoE

Accession: VK055_4840

Gene: AIK83367.1 nuoE 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GR55
Length 166
Pocket druggability (FPocket · AlphaFold DB model) 0.506
Direct ligand evidence 0 72 total records
Functional annotation 0 EC 5 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 (%)
35.032 Lower values reduce human off-target concern.
Human E-value
6.270000000000001e-27
Gut microbiome similarity
2.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
90.89 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
Structure A0A0H3GR55
Pocket
Druggability (FPocket) 0.506
Structure A0A0H3GR55
Pocket Pocket 3
ColabFold model
P2Rank 0.023 · Pocket 1
FPocket 0.053 · Pocket 11
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 137 / 4744 genomes with a hit
Prevalence 2.9%

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.

MHENQQPQTEAFELSAAEREAIEHEKHHYEDPRAASIEALKIVQKQRGWVPDGAIYAIADVLGIPASDVEGVATFYSQIFRQPVGRHVIRYCDSVVCHITGYQGIQAAIEKKLNIKPGQTTFDGRFTLLPTCCLGNCDKGPTMMIDEDTHSHLTPEAIPDLLEQYK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

5
  • 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: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:0046872 Binding to a metal ion.
  • GO:0003954 Catalysis of the reaction: NADH + H+ + acceptor = NAD+ + reduced acceptor.
  • 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.

17 records
Show feature table
Start End DB Term Name
83 165 FunFam G3DSA:3.40.30.10:FF:000015 NADH-quinone oxidoreductase subunit E
12 83 FunFam G3DSA:1.10.10.1590:FF:000001 NADH-quinone oxidoreductase subunit E
24 166 Pfam PF01257 Thioredoxin-like [2Fe-2S] ferredoxin
5 166 PANTHER PTHR10371 NADH DEHYDROGENASE UBIQUINONE FLAVOPROTEIN 2, MITOCHONDRIAL
123 141 ProSitePatterns PS01099 Respiratory-chain NADH dehydrogenase 24 Kd subunit signature.
123 141 InterPro IPR002023 NADH-quinone oxidoreductase subunit E-like
86 165 CDD cd03064 TRX_Fd_NuoE
86 165 InterPro IPR042128 NuoE domain
83 165 Gene3D G3DSA:3.40.30.10 Glutaredoxin
16 165 SUPERFAMILY SSF52833 Thioredoxin-like
16 165 InterPro IPR036249 Thioredoxin-like superfamily
1 166 PIRSF PIRSF000216 NDH-1_E
1 166 InterPro IPR002023 NADH-quinone oxidoreductase subunit E-like
13 82 Gene3D G3DSA:1.10.10.1590 -
13 82 InterPro IPR041921 NADH-quinone oxidoreductase subunit E, N-terminal
22 166 NCBIfam TIGR01958 NADH-quinone oxidoreductase subunit NuoE
22 166 InterPro IPR002023 NADH-quinone oxidoreductase subunit E-like

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.

Download VMD script Full viewer

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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
0.0
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #3
0.506 Unusual size
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:133-133
UniProt: Binding site:137-137
UniProt: Binding site:92-92
UniProt: Binding site:97-97
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_A0A0H3GR55
AlphaFold DB full sequence Viewing
ColabFold VK055_4840
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.

72 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 22 records from similar proteins
Structural ligands 22 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
CDL PDB via homolog Detail RCSB PDB
CPL 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 Q9UUT9 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 W5NRY1 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 W5NRY1 131.1 Da LogP -0.40 TPSA 66.4 ✓ Ro5 ✓ Clean C[C@@H](C(=O)O)NC(=O)C
CDL RCSB PDB F1SM98 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
CPL RCSB PDB F2Z6C0 758.1 Da LogP 10.94 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])OC…
DCQ RCSB PDB W5NRY1 322.4 Da LogP 4.49 TPSA 52.6 ✓ Ro5 Alert CCCCCCCCCCC1=C(C(=O)C(=C(C1=O)OC)OC)C
EHZ RCSB PDB F2Z6C0 584.7 Da LogP 3.04 TPSA 182.5 2 viol. ✓ Clean CCCCCCCCCCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H]…
FES RCSB PDB Q9UUT9 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FME RCSB PDB W5NRY1 177.2 Da LogP -0.06 TPSA 66.4 ✓ Ro5 ✓ Clean CSCC[C@@H](C(=O)O)NC=O
L3W RCSB PDB O66842 697.4 Da LogP -3.38 TPSA 354.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
LMN RCSB PDB F2Z6C0 1005.2 Da LogP -1.68 TPSA 357.1 3 viol. ✓ Clean CCCCCCCCCCC(CCCCCCCCCC)(CO[C@@H]1[C@@H]([C@@H](…
LMT RCSB PDB F2Z6C0 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…
MYR RCSB PDB W5NRY1 228.4 Da LogP 4.77 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCCCC(=O)O
PC1 RCSB PDB W5NRY1 790.2 Da LogP 12.17 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])…
PEE RCSB PDB F1SM98 744.0 Da LogP 11.61 TPSA 134.4 2 viol. ✓ Clean CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN…
PLC RCSB PDB F2Z6C0 622.8 Da LogP 8.12 TPSA 108.4 2 viol. ✓ Clean CCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)…
PLX RCSB PDB F1SM98 767.1 Da LogP 11.61 TPSA 114.7 2 viol. ✓ Clean CCCCCCCCCCCCCCCCC[C@@H](O)O[C@H](CO[C@@H](CCCCC…
PNS RCSB PDB W5NRY1 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
PSC RCSB PDB F2Z6C0 759.1 Da LogP 11.58 TPSA 108.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC[N…
T7X RCSB PDB F2Z6C0 887.1 Da LogP 9.17 TPSA 209.5 4 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OC1[C@@…
UQ9 RCSB PDB F2Z6C0 795.2 Da LogP 16.13 TPSA 52.6 2 viol. Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CC\C=C(/C)…
ZMP RCSB PDB Q9UUT9 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.

Cross-references

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