Protein target profile

VK055_3046

chorismate lyase

Genome: KpATCC43816 Gene: ubiC AIK81631.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GGV2

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Length 165

Pocket druggability 0.91

Metabolic reactions 1

Chokepoint No

Direct ligand evidence 0 52 total records

Functional annotation 1 EC 5 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: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.91, P2Rank 0.67). Use the 3D pocket comparison to verify whether they identify the same site. Central metabolic position More central than 98.3% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. 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: 2.4% 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.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 92.42 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.91

Structure A0A0H3GGV2

Pocket Pocket 1

P2Rank 0.667

Structure A0A0H3GGV2

Pocket Pocket 1

ColabFold model

FPocket 0.931 · Pocket 1

P2Rank 0.544 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 112 / 4744 genomes with a hit

Prevalence 2.4%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GGV2

Pathways

KEGG R01302 BioCyc CHORPYRLY-RXN

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: more central than 98.3% of genes in this genome, no human homolog detected.

Relative network centrality 98.3% more central than 98.3% of genes in this genome

Chokepoint Not a chokepoint

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSHPALTRLRALRYFAVMPSLPPPLSDWLLLEDSMTQRFEQQGKQVTVTLVNEGYIGRDALTDEAALLPDEPRYWLREIILNADGEPWLAGRTVAPESTLCGPELALQQLGQTPLGRYLFTSSTLTRDFIEIGRDAALWGRRSRLRLSGKPLLLTELFLPASPLY

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

4.1.3.40

Gene Ontology (GO)

GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
GO:0008813 Catalysis of the reaction: chorismate = 4-hydroxybenzoate + pyruvate.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0042866 The chemical reactions and pathways resulting in the formation of pyruvate, 2-oxopropanoate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records

Show feature table

Start	End	DB	Term	Name
2	165	Gene3D	G3DSA:3.40.1410.10	-
2	165	InterPro	IPR028978	Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily
1	165	PANTHER	PTHR38683	CHORISMATE PYRUVATE-LYASE
1	165	InterPro	IPR007440	Chorismate--pyruvate lyase
8	165	SUPERFAMILY	SSF64288	Chorismate lyase-like
8	165	InterPro	IPR028978	Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily
12	165	Hamap	MF_01632	Chorismate pyruvate-lyase [ubiC].
12	165	InterPro	IPR007440	Chorismate--pyruvate lyase
2	165	FunFam	G3DSA:3.40.1410.10:FF:000002	Chorismate pyruvate-lyase
18	165	Pfam	PF04345	Chorismate lyase
18	165	InterPro	IPR007440	Chorismate--pyruvate lyase

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 · FPocket

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

Site 1 FPocket #1

0.91

Likely same site as P2Rank 1 0.5 Å 21 shared residues 95% of smaller site

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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.667

Likely same site as FPocket 1 0.5 Å 21 shared residues 95% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.008

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Surrounding area

Residue sets

UniProt: Binding site:115-115

UniProt: Binding site:156-156

UniProt: Binding site:35-35

UniProt: Binding site:77-77

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_A0A0H3GGV2	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_3046	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

PHB PDB via homolog 138.1 Da · LogP 1.09 · TPSA 57.5 Open detail RCSB PDB

VNL PDB via homolog Detail RCSB PDB

ZINC389804 ZINC proposed compound · Tanimoto 0.842 Detail ZINC

ZINC1747299 ZINC proposed compound · Tanimoto 0.750 Detail ZINC

ZINC33246180 ZINC proposed compound · Tanimoto 0.727 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
PHB RCSB PDB	1FW9	P26602	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)O)O`
VNL RCSB PDB	1XLR	P26602	167.1 Da LogP -0.24 TPSA 69.6	✓ Ro5	✓ Clean	`COc1cc(ccc1O)C(=O)[O-]`

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
ZINC389804 ZINC	0.842	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(O)cc2)cc1`
ZINC1747299 ZINC	0.750	302.3 Da LogP 2.18 TPSA 93.1	✓ Ro5	Alert	`COc1cc(C(=O)C(=O)c2ccc(O)c(OC)c2)ccc1O`
ZINC33246180 ZINC	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccc(O)cc2)cc1`
ZINC3896282 ZINC	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccc(O)cc2)cc1`
ZINC392302 ZINC	0.727	230.2 Da LogP 2.88 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(O)cc2)cc1`
ZINC289893 ZINC	0.696	278.3 Da LogP 1.92 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(S(=O)(=O)c2ccc(O)cc2)cc1`
ZINC1595860 ZINC	0.677	316.3 Da LogP 2.48 TPSA 82.1	✓ Ro5	Alert	`COc1cc(C(=O)C(=O)c2ccc(OC)c(OC)c2)ccc1O`
ZINC114185151 ZINC	0.667	298.2 Da LogP 2.15 TPSA 108.7	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC2924369 ZINC	0.667	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccc(O)cc1`
ZINC103291148 ZINC	0.656	356.4 Da LogP 3.52 TPSA 93.1	✓ Ro5	✓ Clean	`COc1cc(C(=O)/C(C)=C(/C)C(=O)c2ccc(O)c(OC)c2)ccc…`
ZINC3156317 ZINC	0.640	258.2 Da LogP 2.31 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(=O)c2ccc(O)cc2)cc1`
ZINC4903179 ZINC	0.640	257.2 Da LogP 2.34 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2ccc(O)cc2)cc1`
ZINC134079 ZINC	0.632	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1640789 ZINC	0.632	374.3 Da LogP 3.55 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)c3ccc(C(=O)O)cc3)cc…`
ZINC2146859 ZINC	0.632	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC28449 ZINC	0.632	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(O)cc1`
ZINC3147211 ZINC	0.632	318.3 Da LogP 4.42 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC332365 ZINC	0.632	318.3 Da LogP 3.56 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(C(=O)c2ccc(O)cc2)cc1`
ZINC1705144 ZINC	0.619	226.2 Da LogP 2.46 TPSA 54.4	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccccc1`
ZINC1747330 ZINC	0.618	362.3 Da LogP 2.13 TPSA 111.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)OCCOC(=O)c2ccc(O)c(OC)c2)ccc1O`
ZINC38237511 ZINC	0.618	242.3 Da LogP 2.94 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)c2ccc(C)cc2)ccc1O`
ZINC49181262 ZINC	0.600	372.4 Da LogP 2.73 TPSA 105.6	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@@]2(C)O[C@@]2(C)C(=O)c2ccc(O)c(O…`
ZINC49181265 ZINC	0.600	372.4 Da LogP 2.73 TPSA 105.6	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@@]2(C)O[C@]2(C)C(=O)c2ccc(O)c(OC…`
ZINC49181268 ZINC	0.600	372.4 Da LogP 2.73 TPSA 105.6	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@]2(C)O[C@@]2(C)C(=O)c2ccc(O)c(OC…`
ZINC6338454 ZINC	0.593	268.3 Da LogP 2.99 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/C(=O)c2ccc(O)cc2)cc1`
ZINC1747304 ZINC	0.583	288.3 Da LogP 2.54 TPSA 76.0	✓ Ro5	✓ Clean	`COc1cc(CC(=O)c2ccc(O)c(OC)c2)ccc1O`
ZINC266 ZINC	0.583	223.3 Da LogP 1.88 TPSA 49.8	✓ Ro5	✓ Clean	`CCN(CC)C(=O)c1ccc(O)c(OC)c1`
ZINC36108805 ZINC	0.583	224.2 Da LogP 1.45 TPSA 83.8	✓ Ro5	✓ Clean	`COc1cc(C(=O)CCC(=O)O)ccc1O`
ZINC65340137 ZINC	0.583	258.2 Da LogP 2.46 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)cc(-c2ccc(O)cc2)c1`
ZINC167246 ZINC	0.571	248.0 Da LogP 1.99 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)cc1`
ZINC3269660 ZINC	0.571	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC34573580 ZINC	0.571	496.5 Da LogP 4.86 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(c2ccc(C(=O)O)cc2)(c2ccc(C(=O)O)cc…`
ZINC388063 ZINC	0.571	201.0 Da LogP 2.15 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Br)cc1`
ZINC65342513 ZINC	0.571	244.2 Da LogP 2.77 TPSA 66.8	✓ Ro5	✓ Clean	`COc1cc(-c2ccc(C(=O)O)cc2)ccc1O`
ZINC13340359 ZINC	0.568	212.2 Da LogP -0.06 TPSA 87.0	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@H](O)CO)ccc1O`
ZINC13340360 ZINC	0.568	212.2 Da LogP -0.06 TPSA 87.0	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@@H](O)CO)ccc1O`
ZINC1668317 ZINC	0.568	210.2 Da LogP 1.97 TPSA 55.8	✓ Ro5	✓ Clean	`CCCOC(=O)c1ccc(O)c(OC)c1`
ZINC1747307 ZINC	0.568	304.3 Da LogP 2.03 TPSA 96.2	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@H](O)c2ccc(O)c(OC)c2)ccc1O`
ZINC2042188 ZINC	0.568	304.3 Da LogP 2.03 TPSA 96.2	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@@H](O)c2ccc(O)c(OC)c2)ccc1O`
ZINC75616154 ZINC	0.568	208.3 Da LogP 2.77 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCC(=O)c1ccc(O)c(OC)c1`
ZINC82722760 ZINC	0.568	238.2 Da LogP 1.54 TPSA 72.8	✓ Ro5	✓ Clean	`COC(=O)CCC(=O)c1ccc(O)c(OC)c1`
ZINC1747263 ZINC	0.553	224.3 Da LogP 2.21 TPSA 55.8	✓ Ro5	✓ Clean	`COc1cc(C(=O)OCC(C)C)ccc1O`
ZINC34133836 ZINC	0.553	211.2 Da LogP 0.12 TPSA 78.8	✓ Ro5	✓ Clean	`COc1cc(C(=O)NCCO)ccc1O`
ZINC4792435 ZINC	0.553	223.3 Da LogP 1.54 TPSA 49.8	✓ Ro5	✓ Clean	`COc1cc(C(=O)CCN(C)C)ccc1O`
ZINC5234593 ZINC	0.552	293.3 Da LogP 1.89 TPSA 103.7	✓ Ro5	Alert	`O=C(O)c1ccc(S(=O)(=O)Nc2ccc(O)cc2)cc1`
ZINC156520 ZINC	0.545	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/c2ccc(C(=O)O)cc2)cc1`
ZINC241160 ZINC	0.545	258.2 Da LogP 2.88 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(C(=O)O)cc2)cc1`
ZINC2504355 ZINC	0.545	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC4792283 ZINC	0.545	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C\c2ccc(C(=O)O)cc2)cc1`
ZINC8418684 ZINC	0.545	257.2 Da LogP 2.83 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Nc2ccc(C(=O)O)cc2)cc1`

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.