KpATCC43816 Protein target profile

tRNA (mo5U34)-methyltransferase

Accession: VK055_0062

Gene: cmoB AIK78690.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3H064
Length 334
Pocket druggability (P2Rank · AlphaFold DB model) 0.905
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 4 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
No hit
Gut microbiome similarity
3.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
97.06 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) 0.905
Structure A0A0H3H064
Pocket Pocket 1
Druggability (FPocket) 0.744
Structure A0A0H3H064
Pocket Pocket 20
ColabFold model
P2Rank 0.922 · Pocket 1
FPocket 0.308 · Pocket 3
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 151 / 4744 genomes with a hit
Prevalence 3.2%

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.

MIDFSNFYQLIAKSPLSHWLETLPAQVAAWQRDALHGKFREWERAVEFLPELTPWRLDLLHSVTAESETPLSEGHQRRIENLLKNLMPWRKGPYSLYGINIDTEWRSDWKWERVLPHLSDLTGRTILDVGCGSGYHMWRMIGAGAHLAVGIDPTQLFLCQFEAVRKLLGNDQRAHLLPLGIEQLPALEAFDTVFSMGVLYHRRSPLDHLWQLKDQLAPGGELVLETLVVEGDENTVLVPGDRYAQMRNVYFIPSAAALKMWLEKCGFIDVRIVDACVTSTEEQRRTEWMTTESLADFLDPQDQRKTVEGYPAPLRAVIIATKPETQQSLAKKAR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
  • GO:0002098 The process in which a uridine at position 34 of a tRNA is post-transcriptionally modified. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • 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.

13 records
Show feature table
Start End DB Term Name
125 229 CDD cd02440 AdoMet_MTases
99 318 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
99 318 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
12 322 Hamap MF_01590 tRNA U34 carboxymethyltransferase [cmoB].
12 322 InterPro IPR010017 tRNA U34 carboxymethyltransferase
95 323 FunFam G3DSA:3.40.50.150:FF:000080 tRNA U34 carboxymethyltransferase
7 322 Pfam PF08003 Protein of unknown function (DUF1698)
7 322 InterPro IPR027555 tRNA (Mo5U34)-methyltransferase-like
30 230 PANTHER PTHR43464 METHYLTRANSFERASE
7 321 NCBIfam TIGR00452 tRNA 5-methoxyuridine(34)/uridine 5-oxyacetic acid(34) synthase CmoB
7 321 InterPro IPR010017 tRNA U34 carboxymethyltransferase
91 323 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
91 323 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily

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
0.905
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.013
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #20
0.744
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:105-105
UniProt: Binding site:110-110
UniProt: Binding site:130-130
UniProt: Binding site:152-154
UniProt: Binding site:181-182
UniProt: Binding site:196-196
UniProt: Binding site:200-200
UniProt: Binding site:315-315
UniProt: Binding site:91-91
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_A0A0H3H064
AlphaFold DB full sequence Viewing
ColabFold VK055_0062
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
BTB PDB via homolog 209.2 Da · LogP -3.01 · TPSA 104.4 Open detail RCSB PDB
GEK PDB via homolog Detail RCSB PDB
MLI PDB via homolog Detail RCSB PDB
ZINC1615342 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC12371977 ZINC proposed compound · Tanimoto 0.600 Detail ZINC

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
BTB RCSB PDB Q87XG5 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
GEK RCSB PDB A1AC32 442.5 Da LogP -5.85 TPSA 227.2 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
MLI RCSB PDB Q8DAP0 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]

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.