Protein target profile

KP13_01731

Ubiquinone/menaquinone biosynthesis methyltransferase ubiE

Genome: KpKP13 Gene: AHE46966.1 ubiE 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GLM9
Length 251
Pocket druggability 0.988
Direct ligand evidence 0 58 total records
Functional annotation 2 EC 6 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.

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 (%)
56.0 Lower values reduce human off-target concern.
Human E-value
9.14e-11
Gut microbiome similarity
5.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
91.25 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 0.988
Structure A0A0H3GLM9
Pocket Pocket 1
P2Rank 0.976
Structure A0A0H3GLM9
Pocket Pocket 1
ColabFold model
FPocket 0.986 · Pocket 1
P2Rank 0.948 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 241 / 4744 genomes with a hit
Prevalence 5.1%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MVEDSQETTHFGFQTVAKEQKADMVAHVFHSVAAKYDVMNDLMSFGIHRLWKRFTIDCSGVRRGQTVLDLAGGTGDLTAKFSRLVGETGRVMLADINDSMLKMGREKLRNIGIVGNVEYVQANAEALPFADNTFDCITISFGLRNVTDKEKALRSMYRVLKPGGRLLVLEFSKPILEPLSKAYDAYSFHILPKVGELVAKDGDSYRYLAESIRMHPDQETLKGMMQDAGFENVDYYNLTAGIVALHRGYKF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 6 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

6
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • GO:0008425 Catalysis of the reaction: a 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol + S-adenosyl-L-methionine = a 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol + S-adenosyl-L-homocysteine + H+.
  • GO:0043770 Catalysis of the reaction: a 2-demethylmenaquinol + S-adenosyl-L-methionine = a menaquinol + H+ + S-adenosyl-L-homocysteine. Reaction substrates can have varying polyprenyl side chain length.
  • GO:0009060 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
  • GO:0009234 The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
36 51 ProSitePatterns PS01183 ubiE/COQ5 methyltransferase family signature 1.
36 51 InterPro IPR023576 UbiE/COQ5 methyltransferase, conserved site
27 233 PANTHER PTHR43591 METHYLTRANSFERASE
25 250 NCBIfam TIGR01934 ubiquinone/menaquinone biosynthesis methyltransferase
25 250 InterPro IPR004033 UbiE/COQ5 methyltransferase
18 249 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
18 249 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
31 251 FunFam G3DSA:3.40.50.150:FF:000014 Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE
16 250 Hamap MF_01813 Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE [ubiE].
16 250 InterPro IPR004033 UbiE/COQ5 methyltransferase
20 250 ProSiteProfiles PS51608 UbiE family SAM-binding methyltransferase profile.
20 250 InterPro IPR004033 UbiE/COQ5 methyltransferase
31 251 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
31 251 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
15 250 Pfam PF01209 ubiE/COQ5 methyltransferase family
66 168 CDD cd02440 AdoMet_MTases
158 172 ProSitePatterns PS01184 ubiE/COQ5 methyltransferase family signature 2.
158 172 InterPro IPR023576 UbiE/COQ5 methyltransferase, conserved site

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 #1
0.988
Likely same site as P2Rank 1 4.9 Å 28 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #2
0.978
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.976
Likely same site as FPocket 1 4.9 Å 28 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.113
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:123-124
UniProt: Binding site:140-140
UniProt: Binding site:74-74
UniProt: Binding site:95-95
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_A0A0H3GLM9
AlphaFold DB full sequence Viewing
ColabFold KP13_01731
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.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ARS PDB via homolog 74.9 Da · LogP -0.38 · TPSA 0.0 Open detail RCSB PDB
BY9 PDB via homolog Detail RCSB PDB
DTT PDB via homolog Detail RCSB PDB
MLI PDB via homolog Detail RCSB PDB
PA0 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
ARS RCSB PDB C0JV69 74.9 Da LogP -0.38 TPSA 0.0 ✓ Ro5 ✓ Clean [As]
BY9 RCSB PDB Q0H2W9 487.5 Da LogP 1.29 TPSA 157.0 1 viol. ✓ Clean c1ccc2c(c1)c3c4c(c5c6ccccc6n(c5c3[nH]2)[C@H]7[C…
DTT RCSB PDB C0JV69 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
MLI RCSB PDB Q9ALM7 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PA0 RCSB PDB C0JV69 168.0 Da LogP 0.36 TPSA 17.1 ✓ Ro5 ✓ Clean c1ccc(cc1)[As]=O
PC RCSB PDB Q9FR44 184.2 Da LogP -0.20 TPSA 66.8 ✓ Ro5 ✓ Clean C[N+](C)(C)CCOP(=O)(O)O
RXO RCSB PDB C0JV69 215.0 Da LogP -0.44 TPSA 63.4 ✓ Ro5 ✓ Clean c1cc(c(cc1[AsH2])[N+](=O)[O-])O
TEX RCSB PDB A0A077K7L1 437.6 Da LogP 4.85 TPSA 68.4 ✓ Ro5 Alert CC(C)[C@H]1C(=O)N[C@@H](Cc2c[nH]c3c2c(ccc3[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.