Protein profile

VK055_3045

4-hydroxybenzoate polyprenyl transferase

Genome: KpATCC43816

Gene: ubiA AIK81630.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GKX8

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Amino acids 288

Annotations 7

Features 39

PDB binders 2

Druggability 0.994

Overview

Basic information about this protein and its source genome.

Accession: VK055_3045
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: ubiA AIK81630.1
Status: annotated
Amino acids: 288
Structure source: AlphaFold + ColabFold

2.5.1.39

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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 39.583
Human E-value: 2.5e-25
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 89.199
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 92.92

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 0.994

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

Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

2.5.1.39

Gene Ontology (GO)

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 Features

Domain/signature hits 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; 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_A0A0H3GKX8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3045	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
1				0.994

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				55.27	0.984

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
1				0.891
13				0.869

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	56.95	0.985
2	1.44	0.019
3	0.94	0.004

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

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
GST	4OD5	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	4OD5	Q9YBM8	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)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	0.842	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(O)cc2)cc1`
ZINC33246180	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccc(O)cc2)cc1`
ZINC3896282	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccc(O)cc2)cc1`
ZINC392302	0.727	230.2 Da LogP 2.88 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(O)cc2)cc1`
ZINC289893	0.696	278.3 Da LogP 1.92 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(S(=O)(=O)c2ccc(O)cc2)cc1`
ZINC114185151	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	0.667	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccc(O)cc1`
ZINC3156317	0.640	258.2 Da LogP 2.31 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(=O)c2ccc(O)cc2)cc1`
ZINC4903179	0.640	257.2 Da LogP 2.34 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2ccc(O)cc2)cc1`
ZINC134079	0.632	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1640789	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	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	0.632	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(O)cc1`
ZINC3147211	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	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	0.619	226.2 Da LogP 2.46 TPSA 54.4	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccccc1`
ZINC1532829	0.595	234.2 Da LogP 2.79 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/COP(=O)(O)O`
ZINC6338454	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`
ZINC65340137	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`
ZINC2556391	0.579	302.4 Da LogP 4.51 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)O`
ZINC8215849	0.575	314.2 Da LogP 2.91 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CO[P@@](=O)(O)OP(=O)(O)O`
ZINC167246	0.571	248.0 Da LogP 1.99 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)cc1`
ZINC3269660	0.571	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC34573580	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	0.571	201.0 Da LogP 2.15 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Br)cc1`
ZINC12494625	0.561	382.3 Da LogP 4.63 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/CO[P@@](=O)(O)OP(=O)…`
ZINC2356589248	0.561	382.3 Da LogP 4.63 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCCC(C)=CCCC(C)=CCO[P@](=O)(O)OP(=O)(O)O`
ZINC5234593	0.552	293.3 Da LogP 1.89 TPSA 103.7	✓ Ro5	Alert	`O=C(O)c1ccc(S(=O)(=O)Nc2ccc(O)cc2)cc1`
ZINC34661063	0.548	394.2 Da LogP 3.02 TPSA 159.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CO[P@@](=O)(O)O[P@@](=O)(O)OP(…`
ZINC13375284	0.545	270.2 Da LogP 3.50 TPSA 99.3	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccc(C(=O)O)cc2)cc1`
ZINC156520	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`
ZINC1651850	0.545	270.3 Da LogP 2.87 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(CCc2ccc(C(=O)O)cc2)cc1`
ZINC1759946	0.545	256.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Cc2ccc(C(=O)O)cc2)cc1`
ZINC1857524265	0.545	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C=Cc2ccc(C(=O)O)cc2)cc1`
ZINC188555	0.545	350.3 Da LogP 4.67 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(Oc3ccc(C(=O)O)cc3)cc2)cc1`
ZINC241160	0.545	258.2 Da LogP 2.88 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(C(=O)O)cc2)cc1`
ZINC2504355	0.545	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC32299177	0.545	266.3 Da LogP 2.48 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C#Cc2ccc(C(=O)O)cc2)cc1`
ZINC34009333	0.545	376.4 Da LogP 3.96 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(c2ccc(C(=O)O)cc2)c2ccc(C(=O)O)cc2…`
ZINC34057267	0.545	274.3 Da LogP 4.72 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccccc3)cc2)cc1`
ZINC346855	0.545	274.3 Da LogP 3.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Sc2ccc(C(=O)O)cc2)cc1`
ZINC4309722	0.545	270.2 Da LogP 3.50 TPSA 99.3	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccc(C(=O)O)cc2)cc1`
ZINC4792283	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`
ZINC59301968	0.545	394.3 Da LogP 2.54 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc(P(c2ccc(C(=O)O)cc2)c2ccc(C(=O)O)cc2…`
ZINC8418684	0.545	257.2 Da LogP 2.83 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Nc2ccc(C(=O)O)cc2)cc1`
ZINC95080304	0.545	377.4 Da LogP 4.25 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(N(c2ccc(C(=O)O)cc2)c2ccc(C(=O)O)cc2…`
ZINC96024941	0.545	366.4 Da LogP 3.88 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C#Cc2ccc(C#Cc3ccc(C(=O)O)cc3)cc2)cc1`
ZINC104242579	0.542	240.3 Da LogP 2.85 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(CC(=O)c1ccc(O)cc1)c1ccccc1`
ZINC3099517	0.542	210.2 Da LogP 2.53 TPSA 37.3	✓ Ro5	✓ Clean	`CCP(CC)c1ccc(C(=O)O)cc1`
ZINC642881183	0.542	350.3 Da LogP 3.83 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2cc(O)c(-c3ccc(C(=O)O)cc3)cc2O)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.