KpATCC43816 Protein target profile

ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family protein

Accession: VK055_4141

Gene: AIK82687.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GSY0

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Length 388

Pocket druggability (P2Rank · AlphaFold DB model) 0.944

Direct ligand evidence 0 27 total records

Functional annotation 0 EC 8 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

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.94. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 1 structural and 0 bioactivity records.

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: Hit
Human identity (%): 37.017 Lower values reduce human off-target concern.
Human E-value: 2.42e-21
Gut microbiome similarity: 2.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 53.247 Higher values support similarity to known essential genes.
DEG E-value: 3.27e-141 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 88.19 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) 0.944

Structure A0A0H3GSY0

Pocket Pocket 1

Druggability (FPocket) 0.908

Structure A0A0H3GSY0

Pocket Pocket 27

ColabFold model

P2Rank 0.947 · Pocket 1

FPocket 0.617 · Pocket 4

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 122 / 4744 genomes with a hit

Prevalence 2.6%

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.

MVGLAVACGLQGSGLRVAVLEKAEPRPLAADAPPALRVSAINAASEKLLTKLDVWREIVAQRASCYHGMEVWDKDSFGHISFDDQSMGFSHLGYIIENAVVHHALWQKAQRCADVTLLAPAELQQVAWGENEAFLSLQDGSMLTARLVIGADGANSWLRNKADIPLTFWDYHHHALVATIRTAEPHQAVARQAFHGDGILAFLPLSDPHLCSIVWSLSPGEAQRMQQADETTFNQALNIAFDNRLGLCQLASEREVFPLTGRYARQFAAHRLALVGDAAHTIHPLAGQGVNLGFMDAAELIDELKRLHAQGKDIGQHLYLRRYERSRKHSAALMLAGMQGFREMFSGSHPAKKFLRDVGLKLADTLPGVKPQLIRQAMGLNDLPAWLR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Subcellular localization

Localization: Unknown

Gene Ontology (GO)

GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
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.
GO:0019168 Catalysis of the reaction: a 2-(all-trans-polyprenyl)phenol + NADPH + O2 + H+ = a 3-(all-trans-polyprenyl)benzene-1,2-diol + NADP+ + H2O.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
1	242	FunFam	G3DSA:3.50.50.60:FF:000048	2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase
284	300	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
144	159	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
269	284	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
2	333	Pfam	PF01494	FAD binding domain
2	333	InterPro	IPR002938	FAD-binding domain
283	296	ProSitePatterns	PS01304	ubiH/COQ6 monooxygenase family signature.
283	296	InterPro	IPR018168	Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6, conserved site
251	388	Gene3D	G3DSA:3.50.50.60	-
251	388	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
1	250	Gene3D	G3DSA:3.50.50.60	-
1	250	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
244	388	FunFam	G3DSA:3.50.50.60:FF:000062	FAD-dependent 2-octaprenylphenol hydroxylase
15	388	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	14	Phobius	SIGNAL_PEPTIDE	Signal peptide region
1	373	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
1	373	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
1	384	PANTHER	PTHR43876	UBIQUINONE BIOSYNTHESIS MONOOXYGENASE COQ6, MITOCHONDRIAL
1	1	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
11	14	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	379	NCBIfam	TIGR01988	ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family
1	379	InterPro	IPR010971	Ubiquinone biosynthesis hydroxylase UbiH/COQ6
2	10	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic 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 · P2Rank

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

Pocket 1 P2Rank #1

0.944

Likely same site as FPocket 27 2.5 Å 25 shared residues 86% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.826

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Surrounding area

Pocket 3 P2Rank #3

0.427

Likely same site as FPocket 6 2.4 Å 13 shared residues 100% of smaller site

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Surrounding area

Pocket 4 P2Rank #4

0.061

Likely same site as FPocket 6 6.5 Å 4 shared residues 100% of smaller site

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Surrounding area

Pocket 5 P2Rank #5

0.01

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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 #27

0.908 Unusual size

Likely same site as P2Rank 1 2.5 Å 25 shared residues 86% of smaller site

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Surrounding area

Pocket 2 FPocket #6

0.264

Likely same site as P2Rank 3 2.4 Å 13 shared residues 100% of smaller site

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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

0.947

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Surrounding area

Pocket 2 P2Rank #2

0.912

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Surrounding area

Pocket 3 P2Rank #3

0.483

Likely same site as FPocket 4 3.1 Å 17 shared residues 100% of smaller site

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Surrounding area

Pocket 4 P2Rank #4

0.35

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Surrounding area

Pocket 5 P2Rank #5

0.135

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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_A0A0H3GSY0	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_4141	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.

27 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 26 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

ZINC13356583 ZINC proposed compound · Tanimoto 0.667 Detail ZINC

ZINC343704 ZINC proposed compound · Tanimoto 0.643 Detail ZINC

ZINC1059491 ZINC proposed compound · Tanimoto 0.633 Detail ZINC

ZINC1612530 ZINC proposed compound · Tanimoto 0.594 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
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`

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
ZINC13356583 ZINC	0.667	207.2 Da LogP 1.71 TPSA 80.4	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)CCCC(=O)O`
ZINC343704 ZINC	0.643	208.2 Da LogP 1.04 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CC(=O)c1ccccc1C(=O)O`
ZINC1059491 ZINC	0.633	211.3 Da LogP 2.69 TPSA 43.1	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)Cc1ccccc1`
ZINC1612530 ZINC	0.594	225.3 Da LogP 3.08 TPSA 43.1	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)CCc1ccccc1`
ZINC4235287 ZINC	0.594	213.3 Da LogP 1.44 TPSA 47.0	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)C[n+]1ccccc1`
ZINC1715395 ZINC	0.581	214.2 Da LogP 2.50 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CC(=O)c1cccc2ccccc12`
ZINC895186 ZINC	0.576	208.2 Da LogP 0.25 TPSA 106.4	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)C[C@H](N)C(=O)O`
ZINC901103 ZINC	0.576	208.2 Da LogP 0.25 TPSA 106.4	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)C[C@@H](N)C(=O)O`
ZINC216654421 ZINC	0.563	214.2 Da LogP -0.26 TPSA 103.2	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)CS(N)(=O)=O`
ZINC34352328 ZINC	0.559	207.2 Da LogP 1.40 TPSA 69.4	✓ Ro5	✓ Clean	`COC(=O)CCC(=O)c1ccccc1N`
ZINC36047644 ZINC	0.559	208.2 Da LogP 0.47 TPSA 92.4	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)NCCC(=O)O`
ZINC5162233 ZINC	0.556	212.3 Da LogP 2.08 TPSA 69.1	✓ Ro5	Alert	`Nc1ccccc1C(=O)c1ccccc1N`
ZINC2228897 ZINC	0.548	298.3 Da LogP 1.01 TPSA 110.2	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)NCCNC(=O)c1ccccc1N`
ZINC1616708 ZINC	0.543	269.3 Da LogP 2.78 TPSA 80.4	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)CCc1ccccc1C(=O)O`
ZINC150129 ZINC	0.531	212.3 Da LogP 2.52 TPSA 55.1	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)Nc1ccccc1`
ZINC3886415 ZINC	0.529	226.3 Da LogP 2.20 TPSA 55.1	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)NCc1ccccc1`
ZINC85434286 ZINC	0.529	245.7 Da LogP 3.35 TPSA 43.1	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)Cc1ccccc1Cl`
ZINC32314 ZINC	0.516	241.2 Da LogP 2.20 TPSA 80.4	✓ Ro5	Alert	`Nc1ccccc1C(=O)c1ccccc1C(=O)O`
ZINC40564460 ZINC	0.516	216.0 Da LogP 1.73 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)O)c1Br`
ZINC3083759 ZINC	0.514	255.3 Da LogP 2.31 TPSA 69.4	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)OCC(=O)c1ccccc1`
ZINC128305 ZINC	0.500	240.3 Da LogP 2.24 TPSA 55.1	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)NCCc1ccccc1`
ZINC1875257564 ZINC	0.500	241.3 Da LogP 1.78 TPSA 81.1	✓ Ro5	✓ Clean	`Nc1ccccc1CNC(=O)c1ccccc1N`
ZINC2169730 ZINC	0.500	227.3 Da LogP 2.63 TPSA 52.3	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)OCc1ccccc1`
ZINC22577051 ZINC	0.500	384.5 Da LogP 0.19 TPSA 134.3	1 viol.	✓ Clean	`Nc1ccccc1C(=O)NCCNCCNCCNC(=O)c1ccccc1N`
ZINC4343010 ZINC	0.500	217.3 Da LogP 2.76 TPSA 43.1	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)Cc1cccs1`
ZINC70286739 ZINC	0.500	242.3 Da LogP 2.13 TPSA 64.4	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)NOCc1ccccc1`

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 A0A0H3GSY0