Protein target profile

VK055_4343

cobU

Genome: KpATCC43816 Gene: AIK82888.1 cobU 3D evidence: Experimental + ColabFold model Metabolism 5 reactions UniProt A0A0H3GSH0
Length 181
Pocket druggability 0.345
Metabolic reactions 5
Chokepoint Yes
Direct ligand evidence 0 52 total records
Functional annotation 2 EC 6 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
1.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
34.783 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
94.33 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.345
Structure 7TM8
Pocket Pocket 8
P2Rank 0.185
Structure 7TM8
Pocket Pocket 1
ColabFold model
FPocket 0.6 · Pocket 3
P2Rank 0.565 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 58 / 4744 genomes with a hit
Prevalence 1.2%

Cross-references

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

Structure

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a producing & consuming chokepoint reaction in Porphyrin metabolism, no isoenzyme backup detected, more central than 96.5% of genes in this genome, no human homolog detected.

Relative network centrality 96.5% more central than 96.5% of genes in this genome
Chokepoint Chokepoint gene
Catalyzed reactions

5 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MLTLVTGGARSGKSRHAEALIADAPQVLYIATSQIFDDEMAARIQHHRDGRPAHWRTAERWQQLDELITPAIAPEEAILLECITTMVTNLLFALGGDSDPDGWDYAAMEQAIDDEIGVLIAACQRCPAHVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADAVWLVVSGIGVKIK

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:0043752 Catalysis of the reaction: RTP + adenosylcobinamide = adenosylcobinamide phosphate + RDP (where RTP is either ATP or GTP).
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • GO:0009236 The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0008820 Catalysis of the reaction: adenosylcobinamide phosphate + GTP + 2 H+ = adenosylcobinamide-GDP + diphosphate.
  • GO:0005525 Binding to GTP, guanosine triphosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
3 178 CDD cd00544 CobU
3 178 InterPro IPR003203 Bifunctional adenosylcobalamin biosynthesis protein CobU/CobP
3 180 Pfam PF02283 Cobinamide kinase / cobinamide phosphate guanyltransferase
3 180 InterPro IPR003203 Bifunctional adenosylcobalamin biosynthesis protein CobU/CobP
1 181 PIRSF PIRSF006135 CobU
1 181 InterPro IPR003203 Bifunctional adenosylcobalamin biosynthesis protein CobU/CobP
2 181 FunFam G3DSA:3.40.50.300:FF:000632 Bifunctional adenosylcobalamin biosynthesis protein
1 181 PANTHER PTHR34848 -
2 181 Gene3D G3DSA:3.40.50.300 -
2 181 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
2 181 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases

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 #8
0.345
Likely same site as P2Rank 4 1.9 Å 4 shared residues 100% of smaller site
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.185
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Surrounding area
Site 2 P2Rank #2
0.033
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Surrounding area
Site 3 P2Rank #3
0.006
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Surrounding area
Site 4 P2Rank #4
0.004
Likely same site as FPocket 8 1.9 Å 4 shared residues 100% of smaller site
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Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 7TM8
X-ray 1.65 Å A,B,C
100.0% 1-181
Viewing
ColabFold VK055_4343
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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5GP PDB via homolog 363.2 Da · LogP -2.57 · TPSA 206.0 Open detail RCSB PDB
POP PDB via homolog Detail RCSB PDB
ZINC12501413 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC12958448 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1532555 ZINC proposed compound · Tanimoto 1.000 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
5GP RCSB PDB Q05599 363.2 Da LogP -2.57 TPSA 206.0 1 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
POP RCSB PDB Q05599 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(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.