Protein profile

VK055_4141

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

Genome: KpATCC43816

Gene: AIK82687.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GSY0

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Amino acids 388

Annotations 8

Features 23

PDB binders 1

Druggability 0.908

Overview

Basic information about this protein and its source genome.

Accession: VK055_4141
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK82687.1
Status: annotated
Amino acids: 388
Structure source: AlphaFold + ColabFold

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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 37.017
Human E-value: 2.42e-21
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 53.247
DEG E-value: 3.27e-141
Localization: Unknown
ColabFold pLDDT: 88.19

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.908

Structure A0A0H3GSY0

Pocket Pocket 27

P2Rank 0.944

Structure A0A0H3GSY0

Pocket Pocket 1

ColabFold model

FPocket 0.617 · Pocket 4

P2Rank 0.947 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 122 / 4744 genomes with a hit

Normalized 0.026

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GSY0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_4141	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
27				0.908
6				0.264

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	27.37	0.92
2	13.22	0.678
3	7.02	0.363
4	4.2	0.171
5	2.37	0.062

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
4				0.617

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	27.71	0.922
2	15.78	0.762
3	5.8	0.283
4	5.61	0.27
5	3.08	0.103

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

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