Protein target profile

VK055_4327

cobalamin biosynthesis protein CobD

Genome: KpATCC43816 Gene: AIK82872.1 cobD 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GXL8
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Length 319
Pocket druggability 0.865
Metabolic reactions 2
Chokepoint No
Functional annotation 0 EC 5 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.

Main supporting evidence

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.86, P2Rank 0.94). Use the 3D pocket comparison to verify whether they identify the same site. Central metabolic position More central than 91.4% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Review the complete evidence below

Risks to review

Microbiome similarity 66 of 4744 screened genomes (1.4%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.86) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence gaps

No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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
1.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
94.14 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 0.865
Structure A0A0H3GXL8
Pocket Pocket 3
P2Rank 0.94
Structure A0A0H3GXL8
Pocket Pocket 1
ColabFold model
FPocket 0.856 · Pocket 2
P2Rank 0.943 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 66 / 4744 genomes with a hit
Prevalence 1.4%

Cross-references

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

Sequence

UniProt A0A0H3GXL8

Pathways

KEGG R06529 BioCyc RXN-6261 KEGG R07302 BioCyc 6.3.1.10-RXN

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 91.4% of genes in this genome, no human homolog detected.

Relative network centrality 91.4% more central than 91.4% of genes in this genome
Chokepoint Not a chokepoint
Pathways
Porphyrin metabolism
Catalyzed reactions

2 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.

MTLLAWCVAWILDVVIGDPPHWPHPVRWIGRLIAVSQRVVRRVCHSDRALRIGGGVMWLVVIGLTWGVAWGVLALAHGIHPWLGWLAEVWMIFTALAGRCLAQSAMAVARPLQAGDLAESRHKLSWIVGRDTSQLQPAQINRAVVETVAENTVDGIIAPLFFLLLGGAPLAMAYKAVNTLDSMVGYKHEKYRAIGMVSARLDDVANFLPARLSWLLLSLAAVLCREDGARALRTGWRDRYQHSSPNCAWPEATVAGALGIRLGGPNDYFGQRVEKPWIGDAVRDIAVDDISRTIRLMWVASSLALALFIGVRYWLVGAA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0048472 Catalysis of the reaction: O-phospho-L-threonine + H+ = (R)-1-aminopropan-2-yl phosphate + CO2.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0015420 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: vitamin B12(out) + ATP + H2O = ADP + an vitamin B12(in) + H+ + phosphate. Vitamin B12 is alkylcob(III)alamin.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
56 76 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
2 12 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
296 315 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 17 SignalP_EUK SignalP-TM SignalP-TM
1 17 Phobius SIGNAL_PEPTIDE Signal peptide region
316 319 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
82 102 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
18 26 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
77 81 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 318 Hamap MF_00024 Cobalamin biosynthesis protein CbiB [cbiB].
1 318 InterPro IPR004485 Cobalamin biosynthesis CobD/CbiB
156 177 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
2 316 PANTHER PTHR34308 COBALAMIN BIOSYNTHESIS PROTEIN CBIB
2 316 InterPro IPR004485 Cobalamin biosynthesis CobD/CbiB
204 224 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
45 55 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
27 44 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
178 203 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
52 74 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
8 307 NCBIfam TIGR00380 adenosylcobinamide-phosphate synthase CbiB
8 307 InterPro IPR004485 Cobalamin biosynthesis CobD/CbiB
103 155 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
294 316 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
155 177 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
7 297 Pfam PF03186 CobD/Cbib protein
7 297 InterPro IPR004485 Cobalamin biosynthesis CobD/CbiB
225 295 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
13 17 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.

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 #3
0.865
Likely same site as P2Rank 3 1.0 Å 12 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
0.94
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Surrounding area
Site 2 P2Rank #2
0.524
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Surrounding area
Site 3 P2Rank #3
0.239
Likely same site as FPocket 3 1.0 Å 12 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.131
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Surrounding area
Site 5 P2Rank #5
0.106
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Surrounding area
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_A0A0H3GXL8
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4327
ColabFold — — full sequence — Loaded