KpATCC43816 Protein target profile

rieske [2Fe-2S] domain protein

Accession: VK055_0826

Gene: AIK79449.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GPR1
Length 345
Pocket druggability (P2Rank · AlphaFold DB model) 0.954
Direct ligand evidence 0 58 total records
Functional annotation 0 EC 3 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
0.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
93.76 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) 0.954
Structure A0A0H3GPR1
Pocket Pocket 1
Druggability (FPocket) 0.92
Structure A0A0H3GPR1
Pocket Pocket 4
ColabFold model
P2Rank 0.947 · Pocket 1
FPocket 0.972 · Pocket 21
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 34 / 4744 genomes with a hit
Prevalence 0.7%

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.

MKTTTPTPPAHCTFDPEDWLRLARCWHPVARACDIAGAPVKATLLDEQLVIYRIKGQVVVARDVCPHRGVPLTLGFHEEEGIVCPYHGLRFGEDGRCNRIPSSPGQPIPAKLHLTSFAVEERYGLIWTCLACDPDNPPPLPTMPHWDDAGFQQINCPAFEVKGFAGRQVEGFLDVAHFAWIHTDTFADPDNQQVPDYTPQETPFGFVADYWSSVGNYPASSDFRAPEGFQWLRHFEMHLPFTATLTIHFPADARLVIMNAASPVSSRVTRMFAPIARNFDLHVPVEDVHAFNLRVFEEDRLMVETQRPERLPLDLTLEAHIPADRSSIAYRRGLKKMGFGDFFLV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

3
  • 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:0005506 Binding to an iron (Fe) ion.
  • 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.

16 records
Show feature table
Start End DB Term Name
170 337 Pfam PF19112 Vanillate O-demethylase oxygenase C-terminal domain
170 337 InterPro IPR044043 Vanillate O-demethylase oxygenase-like, C-terminal catalytic domain
26 135 CDD cd03469 Rieske_RO_Alpha_N
65 87 ProSitePatterns PS00570 Bacterial ring hydroxylating dioxygenases alpha-subunit signature.
65 87 InterPro IPR015881 Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site
152 338 Gene3D G3DSA:3.90.380.10 -
19 336 PANTHER PTHR21266 IRON-SULFUR DOMAIN CONTAINING PROTEIN
133 338 SUPERFAMILY SSF55961 Bet v1-like
14 134 SUPERFAMILY SSF50022 ISP domain
14 134 InterPro IPR036922 Rieske [2Fe-2S] iron-sulphur domain superfamily
20 146 Gene3D G3DSA:2.102.10.10 -
20 146 InterPro IPR036922 Rieske [2Fe-2S] iron-sulphur domain superfamily
26 128 ProSiteProfiles PS51296 Rieske [2Fe-2S] iron-sulfur domain profile.
26 128 InterPro IPR017941 Rieske [2Fe-2S] iron-sulphur domain
26 104 Pfam PF00355 Rieske [2Fe-2S] domain
26 104 InterPro IPR017941 Rieske [2Fe-2S] iron-sulphur 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
0.954
Likely same site as FPocket 4 3.6 Å 17 shared residues 89% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.606
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Surrounding area
Pocket 3 P2Rank #3
0.197
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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 #4
0.92
Likely same site as P2Rank 1 3.6 Å 17 shared residues 89% of smaller site
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Surrounding area
Pocket 2 FPocket #13
0.331
Likely same site as P2Rank 1 6.7 Å 14 shared residues 93% of smaller site
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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_A0A0H3GPR1
AlphaFold DB full sequence Viewing
ColabFold VK055_0826
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.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
37T PDB via homolog 180.2 Da · LogP -1.04 · TPSA 72.7 Open detail RCSB PDB
CFF PDB via homolog Detail RCSB PDB
D3M PDB via homolog Detail RCSB PDB
FES PDB via homolog Detail RCSB PDB
HXX 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
37T RCSB PDB H9N289 180.2 Da LogP -1.04 TPSA 72.7 ✓ Ro5 ✓ Clean Cn1cnc2c1C(=O)NC(=O)N2C
CFF RCSB PDB H9N289 194.2 Da LogP -1.03 TPSA 61.8 ✓ Ro5 ✓ Clean Cn1cnc2c1C(=O)N(C(=O)N2C)C
D3M RCSB PDB Q5S3I3 221.0 Da LogP 2.70 TPSA 46.5 ✓ Ro5 ✓ Clean COc1c(ccc(c1C(=O)O)Cl)Cl
FES RCSB PDB C3RVP5 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
HXX RCSB PDB Q5S3I3 207.0 Da LogP 2.40 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(c(c(c1Cl)C(=O)O)O)Cl
OXY RCSB PDB Q5S3I3 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean O=O
TEP RCSB PDB H9N289 180.2 Da LogP -1.04 TPSA 72.7 ✓ Ro5 ✓ Clean CN1c2c([nH]cn2)C(=O)N(C1=O)C
U5A RCSB PDB C3RVP5 267.3 Da LogP -1.72 TPSA 139.4 1 viol. ✓ Clean [H]/N=C\1/N[C@H]2[C@@H](N/C(=N/[H])/N3[C@]2(N1)…

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.