KpATCC43816 Protein target profile

cobyrinic acid a,c-diamide synthase

Accession: VK055_4326

Gene: cobB AIK82871.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GWZ7
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Length 458
Pocket druggability (P2Rank · AlphaFold DB model) 0.965
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.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.96. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 46 of 4744 screened genomes (1.0%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.96) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.91, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

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
1.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
95.17 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) 0.965
Structure A0A0H3GWZ7
Pocket Pocket 1
Druggability (FPocket) 0.906
Structure A0A0H3GWZ7
Pocket Pocket 3
ColabFold model
P2Rank 0.961 · Pocket 1
FPocket 0.888 · Pocket 19
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 46 / 4744 genomes with a hit
Prevalence 1.0%

Cross-references

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

Sequence

UniProt A0A0H3GWZ7

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.

MATRRAFILAGTGSGCGKTTVTLGLLSLLQQRGMRVQPCKVGPDYLDTAWHTAISGIASRNLDSFMLPAPILNALFTEQLQQADIAVIEGVMGLYDGYGTDPNYCSSAAMAKQLGCPVILLVDGKAVSTSIAATVMGFQHFDPALDIAGVIVNRVNSDAHFQLLKSAIERYCRVPVLGYVPRVEGVALPERHLGLVTARESVVNQQAWRDFASLLGRSLDIDRLLALSELAAMPIGEWGEQLAADAGEGLTLALADDEAFNFYYPDNLALLARCGVKMVRFSPLRDRQLPACQMIWLGGGYPELHAAGLSANHEMLTQLHAAHRRGVAIYAECGGLMYLGTTLEVTSGERYTMADIIPGHSRMGTRLTRFGYCEAQAQQQTLLAAPGEWLRGHEFHYSDFSPATPAVLACRKQRDGKTLQQWQGGWQSGSAFASYLHVHFAQRPTMLNHWLRAARRAL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0042242 Catalysis of the conversion of cobyrinic acid to cobyrinic acid a,c-diamide via the intermediate formation of cobyrinic acid c-monoamide.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
46 191 Gene3D G3DSA:3.40.50.300 -
46 191 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
5 197 CDD cd05388 CobB_N
252 453 SUPERFAMILY SSF52317 Class I glutamine amidotransferase-like
252 453 InterPro IPR029062 Class I glutamine amidotransferase-like
3 43 Gene3D G3DSA:3.40.50.300 -
3 43 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
8 453 NCBIfam TIGR00379 hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolyzing)
8 453 InterPro IPR004484 Cobyrinic acid a,c-diamide synthase CbiA
259 457 Gene3D G3DSA:3.40.50.880 -
259 457 InterPro IPR029062 Class I glutamine amidotransferase-like
251 445 ProSiteProfiles PS51274 CobBQ-type GATase domain profile.
4 444 Hamap MF_00027 Hydrogenobyrinate a,c-diamide synthase [cobB].
4 444 InterPro IPR004484 Cobyrinic acid a,c-diamide synthase CbiA
1 16 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.
5 200 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
5 200 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
8 193 Pfam PF01656 CobQ/CobB/MinD/ParA nucleotide binding domain
8 193 InterPro IPR002586 CobQ/CobB/MinD/ParA nucleotide binding domain
252 443 Pfam PF07685 CobB/CobQ-like glutamine amidotransferase domain
252 443 InterPro IPR011698 CobB/CobQ-like glutamine amidotransferase
252 451 CDD cd03130 GATase1_CobB
6 454 PANTHER PTHR43873 COBYRINATE A,C-DIAMIDE SYNTHASE
6 454 InterPro IPR004484 Cobyrinic acid a,c-diamide synthase CbiA

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
0.965
Likely same site as FPocket 3 6.0 Å 19 shared residues 90% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.1
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Surrounding area
Pocket 3 P2Rank #3
0.084
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Surrounding area
Pocket 4 P2Rank #4
0.053
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Surrounding area
Pocket 5 P2Rank #5
0.005
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #3
0.906 Unusual size
Likely same site as P2Rank 1 6.0 Å 19 shared residues 90% of smaller site
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Surrounding area
Residue sets
UniProt: Active site:333-333 Nucleophile
UniProt: Site:437-437 Increases nucleophilicity of active site Cys
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_A0A0H3GWZ7
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4326
ColabFold — — full sequence — Loaded