KpATCC43816 Protein target profile

phenylacetic acid catabolic family protein

Accession: VK055_1041

Gene: AIK79664.1 3D evidence: Experimental + AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A6T8I0

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Length 309

Pocket druggability (P2Rank · AlphaFold DB model) 0.953

Direct ligand evidence 1 7 total records

Functional annotation 0 EC 2 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 0.95, FPocket 0.82). 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. Direct ligand evidence 1 direct ligand records. Strong known ligand: co-crystal structure 1 PDB record(s) show a ligand actually co-crystallized with this exact protein - real experimental evidence, not a computational prediction. 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: 1.5% 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: 97.95 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) 0.953

Structure A6T8I0

Pocket Pocket 1

Druggability (FPocket) 0.818

Structure A6T8I0

Pocket Pocket 1

ColabFold model

P2Rank 0.945 · Pocket 1

FPocket 0.43 · Pocket 2

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 70 / 4744 genomes with a hit

Prevalence 1.5%

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.

MTEEQRFDQRIAQETAIEPQDWMPDAYRKTLIRQIGQHAHSEIVGMLPEGNWITRAPTLRRKAILLAKVQDEAGHGLYLYSAAETLGCAREDLYQKMLDGQMKYSSIFNYPTLSWADIGVIGWLVDGAAIVNQVALCRTSYGPYARAMVKICKEESFHQRQGFEACMALAQGNDAQRQMLQDAINRFWWPALMMFGPNDDNSPNSARSMAWKIKLHSNDELRQRFVDNTVPQVEILGMTVPDPDLQFDEASGHYRFGEIDWQEFNEVISGRGICNHERLAAKRKAWEEGEWVREAALAHAQKQQARSAA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0010124 The chemical reactions and pathways resulting in the breakdown of phenylacetate.
GO:0097266 Catalysis of the reaction: phenylacetyl-CoA + H+ + NADPH + O2 = 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + H2O + NADP+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

10 records

Show feature table

Start	End	DB	Term	Name
1	309	FunFam	G3DSA:1.20.1260.10:FF:000010	1,2-phenylacetyl-CoA epoxidase subunit A
1	309	Gene3D	G3DSA:1.20.1260.10	-
1	309	InterPro	IPR012347	Ferritin-like
7	295	NCBIfam	TIGR02156	1,2-phenylacetyl-CoA epoxidase subunit A
7	295	InterPro	IPR011881	1,2-phenylacetyl-CoA epoxidase, subunit A
17	291	Pfam	PF05138	Phenylacetic acid catabolic protein
17	291	InterPro	IPR007814	1,2-phenylacetyl-CoA epoxidase, subunit A/C
3	291	PANTHER	PTHR30458	PHENYLACETIC ACID DEGRADATION PROTEIN PAA
27	269	SUPERFAMILY	SSF47240	Ferritin-like
27	269	InterPro	IPR009078	Ferritin-like 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.

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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

0.893

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Surrounding area

Pocket 2 P2Rank #2

0.306

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Surrounding area

Pocket 3 P2Rank #3

0.17

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Surrounding area

Pocket 4 P2Rank #4

0.079

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Surrounding area

Pocket 5 P2Rank #6

0.027

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Surrounding area

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.953

Likely same site as FPocket 1 4.0 Å 24 shared residues 86% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.159

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Surrounding area

Pocket 3 P2Rank #3

0.078

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Surrounding area

Pocket 4 P2Rank #4

0.057

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Surrounding area

Pocket 5 P2Rank #5

0.033

Likely same site as FPocket 2 1.0 Å 13 shared residues 100% of smaller site

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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

0.818

Likely same site as P2Rank 1 4.0 Å 24 shared residues 86% of smaller site

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Surrounding area

Pocket 2 FPocket #2

0.364

Likely same site as P2Rank 5 1.0 Å 13 shared residues 100% of smaller site

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Surrounding area

All structural evidence 1 experimental · 2 predicted

Structural evidence

1 + 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
PDB 4IIT	X-ray	—	A	—	PDBe RCSB PDBj File	Viewing
AlphaFold DB AF_A6T8I0	AlphaFold DB	—	—	full sequence	—	Loaded
ColabFold VK055_1041	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.

7 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 1 same-protein records

Transferred evidence 2 records from similar proteins

Structural ligands 3 1 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 4 similarity-based ZINC candidates

Best available ligand signal

FAQ PDB co-crystal 885.7 Da · LogP -0.09 · TPSA 363.6 Open detail RCSB PDB

3HC PDB via homolog Detail RCSB PDB

BYC PDB via homolog Detail RCSB PDB

ZINC12501123 ZINC proposed compound · Tanimoto 0.528 Detail ZINC

ZINC79671662 ZINC proposed compound · Tanimoto 0.528 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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
FAQ RCSB PDB	4IIT Open crystal	885.7 Da LogP -0.09 TPSA 363.6	3 viol.	✓ Clean	`CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H](…`

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
3HC RCSB PDB	3PVT	P76077	853.6 Da LogP -1.56 TPSA 383.9	3 viol.	✓ Clean	`CC(CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](…`
BYC RCSB PDB	3PVR	P76077	871.6 Da LogP -0.02 TPSA 363.6	3 viol.	✓ Clean	`CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H](…`

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
ZINC12501123 ZINC	0.528	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC79671662 ZINC	0.528	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC79671663 ZINC	0.528	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC4228234 ZINC	0.511	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`

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 A6T8I0

Structure

PDB 4IIT