Protein target profile

KP13_01005

putative Nudix hydrolase

Genome: KpKP13 Gene: AHE43467.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H120
Export view
Length 183
Pocket druggability 0.071
Functional annotation 0 EC 2 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

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 0.86. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 117 of 4744 screened genomes (2.5%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.07.

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
No hit
Gut microbiome similarity
2.5% 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
91.17 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 0.071
Structure A0A0H3H120
Pocket Pocket 4
P2Rank 0.859
Structure A0A0H3H120
Pocket Pocket 1
ColabFold model
FPocket 0.111 · Pocket 3
P2Rank 0.889 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 117 / 4744 genomes with a hit
Prevalence 2.5%

Cross-references

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

Sequence

UniProt A0A0H3H120

Sequence

Primary amino-acid sequence viewer.

MAEQNHLASTEWVDIVNENNEVIAQSSREQMRAQCLRHRATYIVVHDGMGKILVQRRTETKDFHPGMLDATAGGVVQADEQLLESARREAEEELGIAGVPFADHGQFYYEDKFCRVWGSLFSCVSHGPFALQEEEVSEVCWLTPEEITARCDEFTPDSLKALALWMTRNAGNEYDDAEESERE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
39 162 CDD cd04697 Nudix_Hydrolase_38
37 155 Pfam PF00293 NUDIX domain
37 155 InterPro IPR000086 NUDIX hydrolase domain
2 181 Gene3D G3DSA:3.90.79.10 Nucleoside Triphosphate Pyrophosphohydrolase
10 166 SUPERFAMILY SSF55811 Nudix
10 166 InterPro IPR015797 NUDIX hydrolase-like domain superfamily
1 171 PIRSF PIRSF017340 Nudix_hydro
1 171 InterPro IPR024195 NUDIX hydrolase, YfcD, predicted
36 164 ProSiteProfiles PS51462 Nudix hydrolase domain profile.
36 164 InterPro IPR000086 NUDIX hydrolase domain
3 152 PANTHER PTHR10885 ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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

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

Site 1 P2Rank #1
0.859
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.228
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:89-89
UniProt: Binding site:93-93
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_A0A0H3H120
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_01005
ColabFold — — full sequence — Loaded