KpATCC43816 Protein target profile

NADH dehydrogenase II

Accession: VK055_1359

Gene: AIK79982.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GMU6
Length 434
Pocket druggability (P2Rank · AlphaFold DB model) 0.944
Direct ligand evidence 0 61 total records
Functional annotation 0 EC 3 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
No hit
Gut microbiome similarity
3.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
87.21 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) 0.944
Structure A0A0H3GMU6
Pocket Pocket 1
Druggability (FPocket) 0.818
Structure A0A0H3GMU6
Pocket Pocket 26
ColabFold model
P2Rank 0.983 · Pocket 1
FPocket 0.861 · Pocket 28
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 155 / 4744 genomes with a hit
Prevalence 3.3%

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.

MTTPLKKIVIVGGGAGGLELATQLGRKLGRHKKAKITLVDRNHSHLWKPLLHEVATGSLDEGVDALSYLAHARNHGFQFQLGSVVDINREGKTITLGELRNEKGELLVAERKLPYDTLVMALGSTSNDFNIPGVKENCIFLDNPHQARRFHQEMLNLFLKYSANLGANGKVNIAIVGGGATGVELSAELHNAVKQLHSYGYKGLTNEALNVTLVEAGERILPALPPRISGAAHNELTKLGVRVLTQTMVTSADAGGLHTKDGEYIEADLMVWAAGIKAPDFMKEIGGLETNRINQLVVEPTLQTTRDADIFAIGDCASCARPEGGFVPPRAQAAHQMATCALNNILAQMKGKPLKAYTYKDHGSLVSLSNYSTVGSLMGNLMRGSMMVEGRIARFVYISLYRMHQIALHGYFKTGLMMLVGRINRIIRPRLKLH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

3
  • 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:0003955 Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a quinol.
  • GO:0019646 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to oxygen to generate a transmembrane electrochemical gradient.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
6 403 PANTHER PTHR42913 APOPTOSIS-INDUCING FACTOR 1
6 338 Pfam PF07992 Pyridine nucleotide-disulphide oxidoreductase
6 338 InterPro IPR023753 FAD/NAD(P)-binding domain
5 413 FunFam G3DSA:3.50.50.100:FF:000001 NADH dehydrogenase
172 197 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
310 317 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
7 29 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
115 133 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
8 27 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
172 190 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
295 317 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
5 413 Gene3D G3DSA:3.50.50.100 -
6 342 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
6 342 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily

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

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.944
Likely same site as FPocket 26 6.4 Å 35 shared residues 74% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.882
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.457
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.332
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.006
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #26
0.818 Unusual size
Likely same site as P2Rank 1 6.4 Å 35 shared residues 74% 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_A0A0H3GMU6
AlphaFold DB full sequence Viewing
ColabFold VK055_1359
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.

61 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 11 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 6 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
4W0 PDB via homolog 427.4 Da · LogP 6.13 · TPSA 42.1 Open detail RCSB PDB
CXS PDB via homolog Detail RCSB PDB
HQO PDB via homolog Detail RCSB PDB
MLI PDB via homolog Detail RCSB PDB
TRT 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
4W0 RCSB PDB Q8I302 427.4 Da LogP 6.13 TPSA 42.1 1 viol. ✓ Clean CC1=C(Nc2cccc(c2C1=O)F)c3ccc(cc3)Cc4ccc(cc4)OC(…
CXS RCSB PDB Q8I302 221.3 Da LogP 1.19 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCCS(=O)(=O)O
HQO RCSB PDB F5L3B8 259.3 Da LogP 3.69 TPSA 47.2 ✓ Ro5 Alert CCCCCCCc1cc(c2ccccc2[n+]1[O-])O
MLI RCSB PDB Q2FZV7 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
TRT RCSB PDB Q8I302 352.5 Da LogP 4.46 TPSA 36.9 ✓ Ro5 ✓ Clean CC(C)(C)CC(C)(C)c1ccc(cc1)OCCOCCOCCOC

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.