Protein target profile

VK055_3045

4-hydroxybenzoate polyprenyl transferase

Genome: KpATCC43816 Gene: ubiA AIK81630.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 6 reactions UniProt A0A0H3GKX8
Length 288
Pocket druggability 0.994
Metabolic reactions 6
Chokepoint Yes
Direct ligand evidence 0 52 total records
Functional annotation 1 EC 6 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
Hit
Human identity (%)
39.583 Lower values reduce human off-target concern.
Human E-value
2.5e-25
Gut microbiome similarity
3.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
89.199 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
92.92 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 0.994
Structure A0A0H3GKX8
Pocket Pocket 1
P2Rank 0.989
Structure A0A0H3GKX8
Pocket Pocket 1
ColabFold model
FPocket 0.891 · Pocket 1
P2Rank 0.989 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 165 / 4744 genomes with a hit
Prevalence 3.5%

Cross-references

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

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing & consuming chokepoint reaction, no isoenzyme backup detected, more central than 91.5% of genes in this genome.

Relative network centrality 91.5% more central than 91.5% of genes in this genome
Chokepoint Chokepoint gene
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

6 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MEWSLSQNKLLAFHRLMRTDKPIGALLLLWPTLWALWVASPGVPPLWILAVFVAGVWLMRAAGCVVNDYADRKFDGHVKRTARRPLPSGDVTEKEARTLFIVLVLLSFLLVLTLNTMTILLSVAALALAWVYPFMKRYTHLPQVVLGAAFGWSIPMAFSAVSESLPLSCWLMFLANILWAVAYDTQYAMVDRDDDLKIGIKSTAILFGENDRLIIGILQVAVLALMGAVGWLNGLGWEYYWSLFVAAGLFGWQQKLIFNRDRDNCFKAFMNNNYVGLVLFLGLAMSYL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0004659 Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0008412 Catalysis of the reaction: 4-hydroxybenzoate + an all-trans-polyprenyl diphosphate = a 4-hydroxy-3-all-trans-polyprenylbenzoate + diphosphate.
  • GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

39 records
Show feature table
Start End DB Term Name
169 288 Gene3D G3DSA:1.20.120.1780 UbiA prenyltransferase
213 233 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
160 182 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
46 70 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
213 235 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
239 258 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
8 288 PANTHER PTHR11048 PRENYLTRANSFERASES
8 288 InterPro IPR039653 Prenyltransferase
45 67 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
99 132 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
259 269 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
234 238 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
288 288 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
169 288 FunFam G3DSA:1.20.120.1780:FF:000001 4-hydroxybenzoate octaprenyltransferase
6 288 Hamap MF_01635 4-hydroxybenzoate octaprenyltransferase [ubiA].
6 288 InterPro IPR006370 4-hydroxybenzoate polyprenyltransferase-like
67 89 ProSitePatterns PS00943 UbiA prenyltransferase family signature.
67 89 InterPro IPR030470 UbiA prenyltransferase conserved site
11 287 NCBIfam TIGR01474 4-hydroxybenzoate polyprenyltransferase
11 287 InterPro IPR006370 4-hydroxybenzoate polyprenyltransferase-like
23 40 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
270 287 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
28 271 Pfam PF01040 UbiA prenyltransferase family
28 271 InterPro IPR000537 UbiA prenyltransferase family
239 258 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
165 183 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
99 132 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
71 98 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
21 40 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
23 168 FunFam G3DSA:1.10.357.140:FF:000002 4-hydroxybenzoate octaprenyltransferase
41 45 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
133 164 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
184 212 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
17 286 CDD cd13959 PT_UbiA_COQ2
17 286 InterPro IPR039653 Prenyltransferase
23 168 Gene3D G3DSA:1.10.357.140 UbiA prenyltransferase
23 168 InterPro IPR044878 UbiA prenyltransferase superfamily
270 287 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.

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
0.994
Likely same site as P2Rank 1 3.3 Å 53 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #9
0.21
Likely same site as P2Rank 2 2.2 Å 7 shared residues 88% of smaller site
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.989
Likely same site as FPocket 1 3.3 Å 53 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.027
Likely same site as FPocket 9 2.2 Å 7 shared residues 88% 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_A0A0H3GKX8
AlphaFold DB full sequence Viewing
ColabFold VK055_3045
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
GST PDB via homolog 330.3 Da · LogP 3.62 · TPSA 104.1 Open detail RCSB PDB
PHB PDB via homolog Detail RCSB PDB
ZINC389804 ZINC proposed compound · Tanimoto 0.842 Detail ZINC
ZINC33246180 ZINC proposed compound · Tanimoto 0.727 Detail ZINC
ZINC3896282 ZINC proposed compound · Tanimoto 0.727 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
GST RCSB PDB Q9YBM8 330.3 Da LogP 3.62 TPSA 104.1 ✓ Ro5 ✓ Clean CC(=CCCC(=CCS[P@](=O)(O)OP(=O)(O)O)C)C
PHB RCSB PDB Q9YBM8 138.1 Da LogP 1.09 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(ccc1C(=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.