Protein target profile

VK055_4140

2-polyprenyl-6-methoxyphenol 4-hydroxylase

Genome: KpATCC43816 Gene: ubiH AIK82686.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 5 reactions UniProt A0A0H3GY55
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Length 392
Pocket druggability 0.954
Metabolic reactions 5
Chokepoint No
Direct ligand evidence 0 63 total records
Functional annotation 0 EC 7 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.99. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Low human similarity A human hit was flagged, but identity is only 28.117% - a weak match, lower risk than a close homolog. This target also has a predicted binding pocket (FPocket 0.95) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 114 of 4744 screened genomes (2.4%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.95) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.95, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

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
Hit
Human identity (%)
28.117 Lower values reduce human off-target concern.
Human E-value
4.220000000000001e-33
Gut microbiome similarity
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Unknown

Structure confidence

ColabFold pLDDT
90.01 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 0.954
Structure A0A0H3GY55
Pocket Pocket 9
P2Rank 0.991
Structure A0A0H3GY55
Pocket Pocket 1
ColabFold model
FPocket 0.959 · Pocket 1
P2Rank 0.983 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 114 / 4744 genomes with a hit
Prevalence 2.4%

Cross-references

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

Sequence

UniProt A0A0H3GY55

Chemistry

ChEMBL CHEMBL130259

Pathways

BioCyc RXN3O-12 BioCyc RXN-9226 BioCyc RXN-9241 BioCyc RXN-9234 BioCyc 2-OCTAPRENYL-6-METHOXYPHENOL-HYDROX-RXN

Metabolic context

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

Explore metabolic network
Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
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

5 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.

MSVLIVGGGMTGATLALAISRLTGGALPVHLIEAQDPHSSRHPGFDDRAIALAAGTCQQLARIGIWQRLAERATPIQRVHVSDRGHAGFVNLAAADYGLSALGQVVELHDVGQRLFGLLREAPGVTLHCPAKVEAVSRSQESVSLTLEGGKIINGKLLVAADGSRSALGARCGISWQQQPYEQIAIIANVSTALPHEGRAFERFTEHGPLAMLPMSQGRCSLVWCHPQSRRDEVQSWSDERFCQELQQAFGWRLGRITHAGKRSVYPLALTTASRAVSHRLALVGNAAQTLHPIAGQGFNLGLRDVMSLAELLADAHLSGEDVGHYPLLCRYQARRAGDKAATIGVTDGLVHLFANRWAPLVAGRNVGLMAMELFTPARDALAQRTLGWVPR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • GO:0008681 Catalysis of the reaction: 2-methoxy-6-(all-trans-octaprenyl)phenol + H+ + NADPH + O2 = 2-methoxy-6-all-trans-octaprenyl-1,4-benzoquinol + H2O + NADP+.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • GO:0016705 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
  • GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
  • GO:0016709 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and one atom of oxygen is incorporated into one donor.
  • GO:0110142 A protein complex composed of enzymes and accessory factors of the ubiquinone (CoQ) biosynthesis pathway. In E. coli, the complex is composed of seven proteins: UbiE, F, G, H, I, J and K. In eukaryotes, the complex is located on the matrix face of the inner mitochondrial membrane and includes COQ3, COQ4, COQ5, COQ6, COQ7, COQ9.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
293 309 PRINTS PR00420 Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
278 293 PRINTS PR00420 Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
2 24 PRINTS PR00420 Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
154 169 PRINTS PR00420 Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
1 18 Phobius SIGNAL_PEPTIDE Signal peptide region
258 388 FunFam G3DSA:3.50.50.60:FF:000021 Ubiquinone biosynthesis monooxygenase COQ6
292 305 ProSitePatterns PS01304 ubiH/COQ6 monooxygenase family signature.
292 305 InterPro IPR018168 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6, conserved site
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
253 391 Gene3D G3DSA:3.50.50.60 -
253 391 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
1 203 Gene3D G3DSA:3.50.50.60 -
1 203 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
3 383 PANTHER PTHR43876 UBIQUINONE BIOSYNTHESIS MONOOXYGENASE COQ6, MITOCHONDRIAL
3 387 NCBIfam TIGR01988 ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family
3 387 InterPro IPR010971 Ubiquinone biosynthesis hydroxylase UbiH/COQ6
3 13 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
19 392 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
3 388 NCBIfam TIGR01984 2-octaprenyl-6-methoxyphenyl hydroxylase
3 388 InterPro IPR011295 2-polyprenyl-6-methoxyphenol 4-hydroxylase
2 336 Pfam PF01494 FAD binding domain
2 336 InterPro IPR002938 FAD-binding domain
1 213 FunFam G3DSA:3.50.50.60:FF:000123 2-octaprenyl-6-methoxyphenyl hydroxylase
2 380 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
2 380 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
14 18 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.

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 #9
0.954
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.991
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.056
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.056
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.005
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_A0A0H3GY55
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4140
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.

63 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 13 records from similar proteins
Structural ligands 12 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
61M PDB via homolog 179.2 Da · LogP 0.93 · TPSA 80.4 Open detail RCSB PDB
APR PDB via homolog Detail RCSB PDB
BHA PDB via homolog Detail RCSB PDB
CTC PDB via homolog Detail RCSB PDB
DHB 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
61M RCSB PDB
6SW2
Q9HWJ1 179.2 Da LogP 0.93 TPSA 80.4 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)CC(=O)O)N
APR RCSB PDB
2PHH
P00438 559.3 Da LogP -3.28 TPSA 291.5 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BHA RCSB PDB
1PBC
P00438 153.1 Da LogP 0.67 TPSA 83.5 ✓ Ro5 ✓ Clean c1cc(c(cc1N)O)C(=O)O
CTC RCSB PDB
5TUI
A0A059WYP6 478.9 Da LogP 0.44 TPSA 181.6 1 viol. ✓ Clean C[C@]1(c2c(ccc(c2C(=O)C3=C([C@]4([C@@H](C[C@@H]…
DHB RCSB PDB
6JU1
P20586 154.1 Da LogP 0.80 TPSA 77.8 ✓ Ro5 Alert c1cc(c(cc1C(=O)O)O)O
DOB RCSB PDB
1DOD
P20586 154.1 Da LogP 0.80 TPSA 77.8 ✓ Ro5 ✓ Clean c1cc(c(cc1O)O)C(=O)O
FAS RCSB PDB
1PDH
P00438 785.6 Da LogP -2.42 TPSA 362.9 3 viol. ✓ Clean Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@H]([C@@…
PAB RCSB PDB
1IUS
P20586 137.1 Da LogP 0.97 TPSA 63.3 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)O)N
PHB RCSB PDB
1D7L
P20586 138.1 Da LogP 1.09 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)O)O
PSL RCSB PDB
1YKJ
P20586 176.1 Da LogP -2.08 TPSA 123.6 ✓ Ro5 ✓ Clean [O-]S(=O)(=O)OS(=O)(=O)[O-]
RFL RCSB PDB
1D7L
P20586 814.6 Da LogP -2.67 TPSA 366.2 3 viol. ✓ Clean Cc1cc2c(cc1N(C)C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]…
RFP RCSB PDB
6BRD
F2R776 823.0 Da LogP 4.34 TPSA 220.1 3 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…

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.