Protein target profile

VK055_0121

NUDIX domain protein

Genome: KpATCC43816 Gene: AIK78749.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQ11
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Length 192
Pocket druggability 0.455
Functional annotation 1 EC 5 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.85. Structure available AlphaFold DB model + ColabFold model

Risks to review

Human similarity Top human hit identity: 41.837%. This target also has a predicted binding pocket (FPocket 0.46) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 106 of 4744 screened genomes (2.2%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.46) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.46, 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 metabolic context No SBML/network-derived reaction evidence is loaded for this protein. 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
Hit
Human identity (%)
41.837 Lower values reduce human off-target concern.
Human E-value
1.06e-12
Gut microbiome similarity
2.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
90.06 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 0.455
Structure A0A0H3GQ11
Pocket Pocket 7
P2Rank 0.854
Structure A0A0H3GQ11
Pocket Pocket 1
ColabFold model
FPocket 0.19 · Pocket 7
P2Rank 0.805 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 106 / 4744 genomes with a hit
Prevalence 2.2%

Cross-references

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

Sequence

UniProt A0A0H3GQ11

Sequence

Primary amino-acid sequence viewer.

MADRALNLDDFLSRFQLLRPQPSRHALNQRQAAVLVPIVRRPQPGLLLTQRSPLLRKHAGQVAFPGGAVDNTDATLIAAALREAQEEVAIPPEAVEVIGVLPPVDSVTGFQVTPVVGIIPPDLHYHASQDEVSAVFEMPLAEALRLGRYHPLDIHRRGNDHRVWLSWYQHYFVWGMTAGIIRELALQIGARP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0010945 Catalysis of the reaction: an acyl-coenzyme A or its derivatives + H2O = adenosine 3',5'-bisphosphate + an acyl-4'-phosphopantetheine + 2 H+. This reaction can also use coenzyme A as a substrate.
  • GO:0009132 The chemical reactions and pathways involving a nucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with diphosphate on the sugar.
  • GO:0030145 Binding to a manganese ion (Mn).
  • GO:0016818 Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
  • GO:0000287 Binding to a magnesium (Mg) ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
30 184 CDD cd03426 CoAse
30 184 InterPro IPR045121 Coenzyme A pyrophosphatase
1 190 Hamap MF_01592 Uncharacterized Nudix hydrolase NudL [nudL].
1 190 InterPro IPR023735 Uncharacterised nudix hydrolase NudL
29 160 ProSiteProfiles PS51462 Nudix hydrolase domain profile.
29 160 InterPro IPR000086 NUDIX hydrolase domain
47 67 ProSitePatterns PS01293 Nudix CoA signature.
47 67 InterPro IPR000059 NUDIX hydrolase, NudL, conserved site
8 181 SUPERFAMILY SSF55811 Nudix
8 181 InterPro IPR015797 NUDIX hydrolase-like domain superfamily
10 187 Gene3D G3DSA:3.90.79.10 Nucleoside Triphosphate Pyrophosphohydrolase
30 143 Pfam PF00293 NUDIX domain
30 143 InterPro IPR000086 NUDIX hydrolase domain
7 185 PANTHER PTHR12992 NUDIX HYDROLASE
7 185 InterPro IPR045121 Coenzyme A pyrophosphatase

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 #7
0.455
Likely same site as P2Rank 1 2.5 Å 26 shared residues 90% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.854
Likely same site as FPocket 7 2.5 Å 26 shared residues 90% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.047
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.041
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:83-83
UniProt: Binding site:87-87
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_A0A0H3GQ11
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0121
ColabFold — — full sequence — Loaded