Protein target profile

VK055_0068

dATP pyrophosphohydrolase

Genome: KpATCC43816 Gene: AIK78696.1 ntpA 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GS12
Length 147
Pocket druggability 0.417
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 53 total records
Functional annotation 0 EC 7 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.

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 (%)
30.579 Lower values reduce human off-target concern.
Human E-value
1.28e-07
Gut microbiome similarity
2.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
84.828 Higher values support similarity to known essential genes.
DEG E-value
1.75e-90 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Unknown

Structure confidence

ColabFold pLDDT
96.0 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 0.417
Structure A0A0H3GS12
Pocket Pocket 1
P2Rank 0.877
Structure A0A0H3GS12
Pocket Pocket 1
ColabFold model
FPocket 0.817 · Pocket 1
P2Rank 0.912 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 122 / 4744 genomes with a hit
Prevalence 2.6%

Cross-references

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

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 88.9% of genes in this genome.

Relative network centrality 88.9% more central than 88.9% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reaction

1 reaction 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.

MSFKLPVSVLVVIYAEDTKRVLMLQRRDDPAFWQSVTGSLEAGETALQAAAREVKEEVAIDVACEQLTLIDCQRTVEFEIFSHLRHRYAPGVERNTEFWFCLALPHEREITFTEHLAYRWVSATEAAALTKSWSNRQAIEEFVINAA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0019177 Catalysis of the reaction: dihydroneopterin triphosphate = dihydroneopterin phosphate + diphosphate.
  • GO:0046656 The chemical reactions and pathways resulting in the formation of folic acid, pteroylglutamic acid.
  • GO:0008828 Catalysis of the reaction: dATP + H2O = dAMP + H+ + diphosphate.
  • GO:0004081 Catalysis of the reaction: P(1),P(4)-bis(5'-nucleosyl)tetraphosphate + H2O = NTP + NMP. Acts on bis(5'-guanosyl)-, bis(5'-xanthosyl)-, bis(5'-adenosyl)- and bis(5'-uridyl)-tetraphosphate.
  • GO:0046872 Binding to a metal ion.
  • GO:0006167 The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.
  • GO:0006754 The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
1 147 Gene3D G3DSA:3.90.79.10 Nucleoside Triphosphate Pyrophosphohydrolase
5 11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
4 142 PANTHER PTHR21340 DIADENOSINE 5,5-P1,P4-TETRAPHOSPHATE PYROPHOSPHOHYDROLASE MUTT
1 15 Phobius SIGNAL_PEPTIDE Signal peptide region
4 143 ProSiteProfiles PS51462 Nudix hydrolase domain profile.
4 143 InterPro IPR000086 NUDIX hydrolase domain
1 4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
5 141 Pfam PF00293 NUDIX domain
5 141 InterPro IPR000086 NUDIX hydrolase domain
12 15 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
3 140 SUPERFAMILY SSF55811 Nudix
3 140 InterPro IPR015797 NUDIX hydrolase-like domain superfamily
16 147 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
6 140 CDD cd04664 Nudix_Hydrolase_7
99 120 PRINTS PR01404 DATP pyrophosphohydrolase signature
99 120 InterPro IPR003564 Dihydroneopterin triphosphate diphosphatase
126 139 PRINTS PR01404 DATP pyrophosphohydrolase signature
126 139 InterPro IPR003564 Dihydroneopterin triphosphate diphosphatase
71 90 PRINTS PR01404 DATP pyrophosphohydrolase signature
71 90 InterPro IPR003564 Dihydroneopterin triphosphate diphosphatase
3 20 PRINTS PR01404 DATP pyrophosphohydrolase signature
3 20 InterPro IPR003564 Dihydroneopterin triphosphate diphosphatase
20 41 PRINTS PR01404 DATP pyrophosphohydrolase signature
20 41 InterPro IPR003564 Dihydroneopterin triphosphate diphosphatase

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 #1
0.417
Likely same site as P2Rank 1 0.8 Å 23 shared residues 96% of smaller site
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.877
Likely same site as FPocket 1 0.8 Å 23 shared residues 96% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.015
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:114-114
UniProt: Binding site:132-132
UniProt: Binding site:26-26
UniProt: Binding site:37-37
UniProt: Binding site:4-4
UniProt: Binding site:53-53
UniProt: Binding site:57-57
UniProt: Binding site:78-81
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_A0A0H3GS12
AlphaFold DB full sequence Viewing
ColabFold VK055_0068
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
DPO PDB via homolog 173.9 Da · LogP -3.34 · TPSA 135.6 Open detail RCSB PDB
MGP PDB via homolog Detail RCSB PDB
PPV PDB via homolog Detail RCSB PDB
ZINC15521877 ZINC proposed compound · Tanimoto 0.982 Detail ZINC
ZINC6827739 ZINC proposed compound · Tanimoto 0.692 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
DPO RCSB PDB P50583 173.9 Da LogP -3.34 TPSA 135.6 ✓ Ro5 ✓ Clean [O-]P(=O)([O-])OP(=O)([O-])[O-]
MGP RCSB PDB Q9BQG2 538.2 Da LogP -2.91 TPSA 290.1 3 viol. ✓ Clean C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H](…
PPV RCSB PDB P0AFC0 178.0 Da LogP -0.81 TPSA 124.3 ✓ Ro5 ✓ Clean OP(=O)(O)OP(=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.