KpATCC43816 Protein target profile

rnfC Barrel sandwich hybrid domain protein

Accession: VK055_4307

Gene: AIK82852.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3H299
Length 408
Pocket druggability (P2Rank · AlphaFold DB model) 0.821
Direct ligand evidence 0 52 total records
Functional annotation 0 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.

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
1.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
95.72 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) 0.821
Structure A0A0H3H299
Pocket Pocket 1
Druggability (FPocket) 0.719
Structure A0A0H3H299
Pocket Pocket 8
ColabFold model
P2Rank 0.661 · Pocket 1
FPocket 0.428 · Pocket 24
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 47 / 4744 genomes with a hit
Prevalence 1.0%

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.

MDTVLVNAAECEPMLKVDQQLMAQQADRLIRGLGYAMTATGAREGIIALKAKYAPAIAALTPRLPEWARLHILPDVYPAGDEVLTIWLATGRRVPPAALPVSVGVVVNNVQTVLNIARAVEQGYPVTRRTLTVNGAVARPLTLAVPLGISLREVLDLAGGATVDDPGFINGGPMMGSLITSLETPVTKTTGGLLVLPGNHPLIQRRRQDERTLLAIARTVCEQCRLCTDLCPRHLIGHELSPHLLVRAVNYRQAATPSLLLSALTCSECNVCESVACPVGISPMRINRLLKRELRAKNLRYDGPLRPADEMAKHRLVPVKRLISKLGLDPWYQEAPLTAVEPEVACVTLPLRQHIGISAVPCVAPGERVTRGQLLADIPADALGAPVHASIDGQVSAITEQAITLVRG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

5
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
221 281 Pfam PF13534 4Fe-4S dicluster domain
2 135 SUPERFAMILY SSF142019 Nqo1 FMN-binding domain-like
2 135 InterPro IPR037225 NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily
212 241 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
212 241 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
1 407 PIRSF PIRSF036408 PduS
1 407 InterPro IPR017054 Cobalamin reductase PduS
132 176 Pfam PF10531 SLBB domain
132 176 InterPro IPR019554 Soluble ligand binding domain
126 193 Gene3D G3DSA:3.10.20.600 -
198 302 Gene3D G3DSA:1.10.1060.10 -
198 302 InterPro IPR009051 Alpha-helical ferredoxin
2 117 Pfam PF01512 Respiratory-chain NADH dehydrogenase 51 Kd subunit
2 117 InterPro IPR011538 NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain
171 298 SUPERFAMILY SSF46548 alpha-helical ferredoxin
336 400 PANTHER PTHR43034 ION-TRANSLOCATING OXIDOREDUCTASE COMPLEX SUBUNIT C
336 400 InterPro IPR010208 Ion-translocating oxidoreductase complex, subunit RnfC/RsxC
129 197 SUPERFAMILY SSF142984 Nqo1 middle domain-like
1 125 Gene3D G3DSA:3.40.50.11540 -
1 125 InterPro IPR037225 NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily
346 404 Pfam PF13375 RnfC Barrel sandwich hybrid domain
346 404 InterPro IPR026902 RnfC Barrel sandwich hybrid domain

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
0.821
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Surrounding area
Pocket 2 P2Rank #2
0.408
Likely same site as FPocket 8 3.5 Å 12 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.27
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Surrounding area
Pocket 4 P2Rank #4
0.102
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Surrounding area
Pocket 5 P2Rank #5
0.049
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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 #8
0.719
Likely same site as P2Rank 2 3.5 Å 12 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_A0A0H3H299
AlphaFold DB full sequence Viewing
ColabFold VK055_4307
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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
FES PDB via homolog 175.8 Da · LogP 1.29 · TPSA 0.0 Open detail RCSB PDB
L3W PDB via homolog Detail RCSB PDB
ZINC12360002 ZINC proposed compound · Tanimoto 0.635 Detail ZINC
ZINC12360703 ZINC proposed compound · Tanimoto 0.635 Detail ZINC
ZINC12503599 ZINC proposed compound · Tanimoto 0.635 Detail ZINC

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
FES RCSB PDB O66841 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
L3W RCSB PDB O66841 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)…

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.