Protein target profile
VK055_0068
dATP pyrophosphohydrolase
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
Risks to review
Evidence coverage
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 modelThe 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.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.
Sequence
Pathways
Sequence
Primary amino-acid sequence viewer.
MSFKLPVSVLVVIYAEDTKRVLMLQRRDDPAFWQSVTGSLEAGETALQAAAREVKEEVAIDVACEQLTLIDCQRTVEFEIFSHLRHRYAPGVERNTEFWFCLALPHEREITFTEHLAYRWVSATEAAALTKSWSNRQAIEEFVINAA
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
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.
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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Residue sets
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Residue sets
All structural evidence
Structural evidence
0 + 2Experimental 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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
| 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
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC15521877 ZINC | 0.982 | 458.2 Da LogP -3.02 TPSA 243.6 | 2 viol. | ✓ Clean |
C[n+]1cn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O…
|
| ZINC6827739 ZINC | 0.692 | 258.0 Da LogP -0.69 TPSA 170.8 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)OP(=O)(O)OP(=O)(O)O
|
| ZINC12371988 ZINC | 0.683 | 298.3 Da LogP -3.26 TPSA 150.5 | ✓ Ro5 | ✓ Clean |
C[n+]1cn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c2n…
|
| ZINC12371989 ZINC | 0.683 | 298.3 Da LogP -3.26 TPSA 150.5 | ✓ Ro5 | ✓ Clean |
C[n+]1cn([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c2…
|
| ZINC14591885 ZINC | 0.683 | 298.3 Da LogP -3.26 TPSA 150.5 | ✓ Ro5 | ✓ Clean |
C[n+]1cn([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c2n…
|
| ZINC18130229 ZINC | 0.683 | 298.3 Da LogP -3.26 TPSA 150.5 | ✓ Ro5 | ✓ Clean |
C[n+]1cn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c2nc…
|
| ZINC19939880 ZINC | 0.683 | 298.3 Da LogP -3.26 TPSA 150.5 | ✓ Ro5 | ✓ Clean |
C[n+]1cn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c2nc…
|
| ZINC28523740 ZINC | 0.683 | 298.3 Da LogP -3.26 TPSA 150.5 | ✓ Ro5 | ✓ Clean |
C[n+]1cn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)c2nc(…
|
| ZINC5893253 ZINC | 0.683 | 298.3 Da LogP -3.26 TPSA 150.5 | ✓ Ro5 | ✓ Clean |
C[n+]1cn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c2nc…
|
| ZINC104869865 ZINC | 0.682 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…
|
| ZINC12504289 ZINC | 0.682 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC34541308 ZINC | 0.682 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC35000839 ZINC | 0.682 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC45284491 ZINC | 0.682 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC80639694 ZINC | 0.682 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC8215481 ZINC | 0.682 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC32303987 ZINC | 0.606 | 499.2 Da LogP -2.51 TPSA 290.6 | 2 viol. | ✓ Clean |
Nc1nc(=O)n([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)…
|
| ZINC59066138 ZINC | 0.606 | 499.2 Da LogP -2.51 TPSA 290.6 | 2 viol. | ✓ Clean |
Nc1nc(=O)n([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=…
|
| ZINC100058967 ZINC | 0.594 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc(=O)c2ncn([C@H]3O[C@H](CO[P@](=O)(O)OP(=O)…
|
| ZINC12504287 ZINC | 0.594 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc(=O)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(…
|
| ZINC12504288 ZINC | 0.594 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc(=O)c2ncn([C@H]3O[C@@H](CO[P@@](=O)(O)OP(=…
|
| ZINC31308647 ZINC | 0.594 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc(=O)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(…
|
| ZINC12502055 ZINC | 0.591 | 483.2 Da LogP -2.21 TPSA 270.4 | 2 viol. | ✓ Clean |
Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…
|
| ZINC12502057 ZINC | 0.591 | 483.2 Da LogP -2.21 TPSA 270.4 | 2 viol. | ✓ Clean |
Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…
|
| ZINC12502058 ZINC | 0.591 | 483.2 Da LogP -2.21 TPSA 270.4 | 2 viol. | ✓ Clean |
Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…
|
| ZINC13431057 ZINC | 0.591 | 483.2 Da LogP -2.21 TPSA 270.4 | 2 viol. | ✓ Clean |
Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…
|
| ZINC13431059 ZINC | 0.591 | 483.2 Da LogP -2.21 TPSA 270.4 | 2 viol. | ✓ Clean |
Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…
|
| ZINC25726736 ZINC | 0.591 | 483.2 Da LogP -2.21 TPSA 270.4 | 2 viol. | ✓ Clean |
Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…
|
| ZINC3861746 ZINC | 0.591 | 483.2 Da LogP -2.21 TPSA 270.4 | 2 viol. | ✓ Clean |
Nc1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@@](=O)(O)…
|
| ZINC53683723 ZINC | 0.591 | 483.2 Da LogP -2.21 TPSA 270.4 | 2 viol. | ✓ Clean |
Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…
|
| ZINC82142138 ZINC | 0.591 | 483.2 Da LogP -2.21 TPSA 270.4 | 2 viol. | ✓ Clean |
Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…
|
| ZINC82142140 ZINC | 0.591 | 483.2 Da LogP -2.21 TPSA 270.4 | 2 viol. | ✓ Clean |
Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…
|
| ZINC13548083 ZINC | 0.583 | 459.2 Da LogP -2.76 TPSA 241.2 | 2 viol. | ✓ Clean |
CN1CN([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[C…
|
| ZINC13519607 ZINC | 0.582 | 498.2 Da LogP -2.19 TPSA 264.4 | 2 viol. | ✓ Clean |
Cc1cn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)OP…
|
| ZINC31298140 ZINC | 0.582 | 498.2 Da LogP -2.19 TPSA 264.4 | 2 viol. | ✓ Clean |
Cc1cn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)…
|
| ZINC81168754 ZINC | 0.582 | 498.2 Da LogP -2.19 TPSA 264.4 | 2 viol. | ✓ Clean |
Cc1cn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)…
|
| ZINC81168756 ZINC | 0.582 | 498.2 Da LogP -2.19 TPSA 264.4 | 2 viol. | ✓ Clean |
Cc1cn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)…
|
| ZINC12501413 ZINC | 0.574 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…
|
| ZINC12958448 ZINC | 0.574 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…
|
| ZINC1532555 ZINC | 0.574 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…
|
| ZINC16546189 ZINC | 0.574 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…
|
| ZINC2159505 ZINC | 0.574 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…
|
| ZINC3073318 ZINC | 0.574 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…
|
| ZINC3869963 ZINC | 0.574 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…
|
| ZINC3869965 ZINC | 0.574 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…
|
| ZINC9334496 ZINC | 0.574 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…
|
| ZINC13431045 ZINC | 0.561 | 403.2 Da LogP -2.33 TPSA 223.9 | 2 viol. | ✓ Clean |
Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…
|
| ZINC13431047 ZINC | 0.561 | 403.2 Da LogP -2.33 TPSA 223.9 | 2 viol. | ✓ Clean |
Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…
|
| ZINC33913782 ZINC | 0.561 | 403.2 Da LogP -2.33 TPSA 223.9 | 2 viol. | ✓ Clean |
Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…
|
| ZINC8215624 ZINC | 0.561 | 403.2 Da LogP -2.33 TPSA 223.9 | 2 viol. | ✓ Clean |
Nc1ccn([C@@H]2O[C@H](CO[P@@](=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.