Genome KpKP13

Protein target profile

Guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase

Accession: KP13_31495

Gene: AHE47006.1 gppA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GGH2
Length 499
Pocket druggability (P2Rank · AlphaFold DB model) 0.975
Direct ligand evidence 0 56 total records
Functional annotation 1 EC 5 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
No hit
Gut microbiome similarity
2.6% 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.

Structure confidence

ColabFold pLDDT
94.37 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.975
Structure A0A0H3GGH2
Pocket Pocket 1
Druggability (FPocket) 0.417
Structure A0A0H3GGH2
Pocket Pocket 31
ColabFold model
P2Rank 0.976 · Pocket 1
FPocket 0.429 · Pocket 34
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 125 / 4744 genomes with a hit
Prevalence 2.6%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSSTSLYAAIDLGSNSFHMLVVREVAGSIQTLSRIKRKVRLAAGLNSDNTLSAEAMERGWQCLRLFAERLQDIPPTQIRVVATATLRLAVNAGEFLAKAQEILGTPVQVISGEEEARLIYQGVAHTTGGADQRLVVDIGGASTELVTGTGAQTTSLFSLSMGCVTWLERYFADRSLTKENFDLAEAAAREVLLPVADVLRYHGWKVCVGASGTVQALQEIMMAQGMDERITLAKLQQLKQRAIQCGRLEELEIEGLTLERALVFPSGLAILIAIFSELNIQCMTLAGGALREGLVYGMLHLSVEQDIRSRTLRNIQRRFMIDTEQAQRVGGLASHLLSQLDGSWELDPLSRDLLLSACALHEIGLSVDFKRAPQHAAYLVNNLDLPGFTPAQKKLIATLLLNQTNAIDLSSLHQQNAVPPRVAEHLCRLLRLAILFASRRRDDLLPAIQLTAQDEQLTLILPGNWLDEHPLGREMVDQECQWQSYVHWILRVDSGDTLK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0015974 The chemical reactions and pathways resulting in the breakdown of guanine pentaphosphate (5'-pppGpp-3'), a derivative of guanine riboside with five phosphates.
  • GO:0008894 Catalysis of the reaction: guanosine 5'-triphosphate,3'-diphosphate + H2O = guanosine 5'-diphosphate,3'-diphosphate + phosphate.
  • GO:0015970 The chemical reactions and pathways resulting in the formation of guanine tetraphosphate (5'-ppGpp-3'), a derivative of guanine riboside with four phosphates.
  • GO:0015949 The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
  • GO:0042594 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
1 494 PIRSF PIRSF001267 Pyrophosphatase_GppA_Ppx
1 494 InterPro IPR030673 Pyrophosphatase, GppA/Ppx-type
306 490 SUPERFAMILY SSF109604 HD-domain/PDEase-like
20 300 Pfam PF02541 Ppx/GppA phosphatase family
20 300 InterPro IPR003695 Ppx/GppA phosphatase
304 496 Gene3D G3DSA:1.10.3210.10 Hypothetical protein af1432
1 493 Hamap MF_01550 Guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase [gppA].
1 493 InterPro IPR023709 Guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase
8 124 FunFam G3DSA:3.30.420.40:FF:000023 Guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase
304 493 FunFam G3DSA:1.10.3210.10:FF:000004 Guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase
111 288 Gene3D G3DSA:3.30.420.150 Exopolyphosphatase. Domain 2
6 127 SUPERFAMILY SSF53067 Actin-like ATPase domain
6 127 InterPro IPR043129 ATPase, nucleotide binding domain
131 299 SUPERFAMILY SSF53067 Actin-like ATPase domain
131 299 InterPro IPR043129 ATPase, nucleotide binding domain
2 469 PANTHER PTHR30005 EXOPOLYPHOSPHATASE
8 296 Gene3D G3DSA:3.30.420.40 -
111 288 FunFam G3DSA:3.30.420.150:FF:000001 Guanosine-5'-triphosphate,3'-diphosphate 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.

Download VMD script Full viewer

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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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.975
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Surrounding area
Pocket 2 P2Rank #2
0.3
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Surrounding area
Pocket 3 P2Rank #3
0.126
Likely same site as FPocket 31 1.2 Å 10 shared residues 91% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.081
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Surrounding area
Pocket 5 P2Rank #5
0.07
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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #31
0.417
Likely same site as P2Rank 3 1.2 Å 10 shared residues 91% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #33
0.41
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Surrounding area
Pocket 3 FPocket #15
0.202
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Surrounding area
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_A0A0H3GGH2
AlphaFold DB full sequence Viewing
ColabFold KP13_31495
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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
G4P PDB via homolog 603.2 Da · LogP -2.22 · TPSA 345.6 Open detail RCSB PDB
GNP PDB via homolog Detail RCSB PDB
GSP PDB via homolog Detail RCSB PDB
LMR PDB via homolog Detail RCSB PDB
MLT PDB via homolog Detail RCSB PDB

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
G4P RCSB PDB B5ZA44 603.2 Da LogP -2.22 TPSA 345.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
GNP RCSB PDB B5ZA44 522.2 Da LogP -2.76 TPSA 301.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
GSP RCSB PDB B5ZA44 539.2 Da LogP -2.22 TPSA 282.0 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
LMR RCSB PDB B5ZA44 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)O)C(=O)O
MLT RCSB PDB B5ZA44 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
TS6 RCSB PDB B5ZA44 114.1 Da LogP 0.01 TPSA 57.5 ✓ Ro5 ✓ Clean OP(=O)(O)S

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.