Protein profile

KP13_01733

putative ubiquinone biosynthesis protein ubiB

Genome: KpKP13

Gene: ubiB AHE46964.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GPX8
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Amino acids 546
Annotations 6
Features 18
PDB binders 2
Druggability 0.772

Overview

Basic information about this protein and its source genome.

Accession
KP13_01733
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
ubiB AHE46964.1
Status
annotated
Amino acids
546
Structure source
AlphaFold + ColabFold
EC
2.7.-.-
GO
GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme. 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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0004672 Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP. GO:0010795 Any process that modulates the frequency, rate or extent of ubiquinone biosynthesis. Ubiquinone biosynthesis consists of 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 (%)
29.858
Human E-value
1.35e-16
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
88.991
DEG E-value
0.0
Localization
CytoplasmicMembrane
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 0.772
Structure A0A0H3GPX8
Pocket Pocket 41
P2Rank 0.986
Structure A0A0H3GPX8
Pocket Pocket 1
ColabFold model
FPocket 0.979 · Pocket 25
P2Rank 0.985 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 152 / 4744 genomes with a hit
Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
  • 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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004672 Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
  • GO:0010795 Any process that modulates the frequency, rate or extent of ubiquinone biosynthesis. Ubiquinone biosynthesis consists of 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.

18 records
Show feature table
Start End DB Term Name
524 542 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
93 344 Pfam PF03109 ABC1 atypical kinase-like domain
93 344 InterPro IPR004147 ABC1 atypical kinase-like domain
94 438 SUPERFAMILY SSF56112 Protein kinase-like (PK-like)
94 438 InterPro IPR011009 Protein kinase-like domain superfamily
543 546 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
519 523 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
501 518 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
46 440 PANTHER PTHR10566 CHAPERONE-ACTIVITY OF BC1 COMPLEX CABC1 -RELATED
523 542 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 500 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
93 344 CDD cd13972 UbiB
93 344 InterPro IPR045308 UbiB domain, bacteria
6 446 NCBIfam TIGR01982 2-polyprenylphenol 6-hydroxylase
6 446 InterPro IPR010232 Probable protein kinase UbiB
501 518 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
3 542 Hamap MF_00414 Probable protein kinase UbiB [ubiB].
3 542 InterPro IPR010232 Probable protein kinase UbiB

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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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_A0A0H3GPX8
AlphaFold — — full sequence — Viewing
ColabFold KP13_01733
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
47 0.562
46 0.304
43 0.22

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 55.41 0.984
2 31.48 0.939
3 14.82 0.735
4 4.62 0.2
5 3.16 0.107

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.

83 records

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
ANP
5YK1
O53343 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ERY
5YK2
O53343 733.9 Da LogP 1.79 TPSA 193.9 2 viol. ✓ Clean CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[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.