KpATCC43816 Protein target profile

free methionine-(R)-sulfoxide reductase

Accession: VK055_0101

Gene: AIK78729.1 yebR 3D evidence: Experimental + ColabFold model Metabolism Not in network UniProt A0A0H3GUR8

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Length 165

Pocket druggability (P2Rank · Experimental) 0.738

Direct ligand evidence 0 24 total records

Functional annotation 0 EC 4 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.

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.74, FPocket 0.89). Use the 3D pocket comparison to verify whether they identify the same site. Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Strong predicted binding pocket FPocket selected-pocket score 0.89. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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: 8.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 42.254 Higher values support similarity to known essential genes.
DEG E-value: 5.85e-35 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 94.58 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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) 0.738

Structure 8DGD

Pocket Pocket 1

Druggability (FPocket) 0.894

Structure 8DGD

Pocket Pocket 1

ColabFold model

P2Rank 0.662 · Pocket 1

FPocket 0.797 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 396 / 4744 genomes with a hit

Prevalence 8.3%

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.

MSKTEFYADLNRDFQALMASETSFLAMIANTSALLFERLSEVNWVGFYLLEGDTLVLGPFQGKLACVRIPVGRGVCGAAVAQAQVQRVEDVHAFDGHIACDAASNSEIVFPLRVNGQIIGVLDIDSPAYGRFTAEDEQGLRTLVEHLEKLIAATDYQKIFTRVVG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization: Unknown

Gene Ontology (GO)

GO:0005515 Binding to a protein.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0033745 Catalysis of the reaction: [thioredoxin]-disulfide + L-methionine + H2O = L-methionine (R)-S-oxide + [thioredoxin]-dithiol.
GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records

Show feature table

Start	End	DB	Term	Name
90	107	ProSitePatterns	PS01320	Uncharacterized protein family UPF0067 signature.
90	107	InterPro	IPR000614	Free Met sulfoxide reductase conserved site
28	162	PANTHER	PTHR21021	GAF/PUTATIVE CYTOSKELETAL PROTEIN
1	152	FunFam	G3DSA:3.30.450.40:FF:000008	GAF domain-containing proteins
9	161	SMART	SM00065	gaf_1
9	161	InterPro	IPR003018	GAF domain
1	152	Gene3D	G3DSA:3.30.450.40	-
1	152	InterPro	IPR029016	GAF-like domain superfamily
38	150	Pfam	PF13185	GAF domain
38	150	InterPro	IPR003018	GAF domain
2	147	SUPERFAMILY	SSF55781	GAF domain-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.

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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

0.738

Likely same site as FPocket 1 1.9 Å 18 shared residues 100% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.066

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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 #1

0.894

Likely same site as P2Rank 1 1.9 Å 18 shared residues 100% of smaller site

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1

0.797

Likely same site as P2Rank 1 0.9 Å 15 shared residues 100% of smaller site

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Surrounding area

Pocket 2 FPocket #4

0.235

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Surrounding area

All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 8DGD	X-ray	1.90 Å	A,B	100.0% 1-165	PDBe RCSB PDBj File	Viewing
ColabFold VK055_0101	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.

24 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 23 similarity-based ZINC candidates

Best available ligand signal

SME PDB via homolog 165.2 Da · LogP -0.83 · TPSA 80.4 Open detail RCSB PDB

ZINC308411996 ZINC proposed compound · Tanimoto 0.581 Detail ZINC

ZINC308411998 ZINC proposed compound · Tanimoto 0.581 Detail ZINC

ZINC5759012 ZINC proposed compound · Tanimoto 0.581 Detail ZINC

ZINC5759013 ZINC proposed compound · Tanimoto 0.581 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
SME RCSB PDB	3KO6	P36088	165.2 Da LogP -0.83 TPSA 80.4	✓ Ro5	✓ Clean	`C[S@@](=O)CC[C@@H](C(=O)O)N`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC308411996 ZINC	0.581	221.3 Da LogP 0.42 TPSA 69.4	✓ Ro5	✓ Clean	`C[S@@](=O)CC[C@H](N)C(=O)OC(C)(C)C`
ZINC308411998 ZINC	0.581	221.3 Da LogP 0.42 TPSA 69.4	✓ Ro5	✓ Clean	`C[S@](=O)CC[C@H](N)C(=O)OC(C)(C)C`
ZINC5759012 ZINC	0.581	207.3 Da LogP 0.34 TPSA 80.4	✓ Ro5	✓ Clean	`CCCC[S@@](=O)CC[C@H](N)C(=O)O`
ZINC5759013 ZINC	0.581	207.3 Da LogP 0.34 TPSA 80.4	✓ Ro5	✓ Clean	`CCCC[S@](=O)CC[C@H](N)C(=O)O`
ZINC5759014 ZINC	0.581	207.3 Da LogP 0.34 TPSA 80.4	✓ Ro5	✓ Clean	`CCCC[S@@](=O)CC[C@@H](N)C(=O)O`
ZINC5759015 ZINC	0.581	207.3 Da LogP 0.34 TPSA 80.4	✓ Ro5	✓ Clean	`CCCC[S@](=O)CC[C@@H](N)C(=O)O`
ZINC3055005 ZINC	0.520	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007 ZINC	0.520	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010 ZINC	0.520	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555366 ZINC	0.500	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1555367 ZINC	0.500	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555369 ZINC	0.500	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720127 ZINC	0.500	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1720128 ZINC	0.500	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720130 ZINC	0.500	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC4642766 ZINC	0.500	201.2 Da LogP -0.78 TPSA 100.6	✓ Ro5	✓ Clean	`C[S@@](=O)CC[C@@H](N)P(=O)(O)O`
ZINC4642767 ZINC	0.500	201.2 Da LogP -0.78 TPSA 100.6	✓ Ro5	✓ Clean	`C[S@](=O)CC[C@@H](N)P(=O)(O)O`
ZINC4899638 ZINC	0.500	207.3 Da LogP -0.66 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CC[S@](C)=O)C(=O)O`
ZINC4899639 ZINC	0.500	207.3 Da LogP -0.66 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CC[S@@](C)=O)C(=O)O`
ZINC5431484 ZINC	0.500	207.3 Da LogP -0.66 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CC[S@](C)=O)C(=O)O`
ZINC5431485 ZINC	0.500	207.3 Da LogP -0.66 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CC[S@@](C)=O)C(=O)O`
ZINC5519141 ZINC	0.500	201.2 Da LogP -0.78 TPSA 100.6	✓ Ro5	✓ Clean	`C[S@@](=O)CC[C@H](N)P(=O)(O)O`
ZINC5519143 ZINC	0.500	201.2 Da LogP -0.78 TPSA 100.6	✓ Ro5	✓ Clean	`C[S@](=O)CC[C@H](N)P(=O)(O)O`

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.

Sequence

UniProt A0A0H3GUR8

Structure

PDB 8DGD