Protein profile

VK055_0068

dATP pyrophosphohydrolase

Genome: KpATCC43816

Gene: ntpA AIK78696.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GS12
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Amino acids 147
Annotations 7
Features 24
PDB binders 3
Druggability 0.417

Overview

Basic information about this protein and its source genome.

Accession
VK055_0068
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
ntpA AIK78696.1
Status
annotated
Amino acids
147
Structure source
AlphaFold + ColabFold
GO
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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
30.579
Human E-value
1.28e-07
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
84.828
DEG E-value
1.75e-90
Localization
Unknown
ColabFold pLDDT
96.0

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its 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
Normalized 0.026

Sequence

Primary amino-acid sequence viewer.

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

3D visualization script Full viewer

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GS12
AlphaFold — — full sequence — Viewing
ColabFold VK055_0068
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.417

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 16.35 0.777

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

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
4IJX
P50583 173.9 Da LogP -3.34 TPSA 135.6 ✓ Ro5 ✓ Clean [O-]P(=O)([O-])OP(=O)([O-])[O-]
MGP
6SCX
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
2O1C
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.