KpKP13 Protein target profile

ATP phosphoribosyltransferase

Accession: KP13_03767

Gene: AHE43696.1 hisG 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H0I5
Length 299
Pocket druggability (P2Rank · AlphaFold DB model) 0.271
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 5 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.

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
3.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
71.525 Higher values support similarity to known essential genes.
DEG E-value
1.23e-152 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.36 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) 0.271
Structure A0A0H3H0I5
Pocket Pocket 1
Druggability (FPocket) 0.29
Structure A0A0H3H0I5
Pocket Pocket 19
ColabFold model
P2Rank 0.244 · Pocket 1
FPocket 0.341 · Pocket 9
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 168 / 4744 genomes with a hit
Prevalence 3.5%

Sequence

Primary amino-acid sequence viewer.

MLDNTRLRIAIQKSGRLSEDSRELLSRCGIKVNLHTQRLIALAENMPIDILRVRDDDIPGLVMDGVVDLGIIGENVLEEELLSRRAQGEDPRYFTLRRLDFGGCRLSLATPVDEAWNGPAALDGKRIATSYPHLLKRYLDQKGISFKSCLLNGSVEVAPRAGLADAICDLVSTGATLEANGLREVEVIYRSKACLIQRDGEMADAKQQLIDRLLTRIQGVIQARESKYIMMHAPTERLEEVVALLPGAERPTILPLAGDKQRVAMHMVSSETLFWETMEKLKALGASSILVLPIEKMME

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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0000105 The chemical reactions and pathways resulting in the formation of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
  • GO:0003879 Catalysis of the reaction: 1-(5-phospho-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0005524 Binding to 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
200 298 NCBIfam TIGR03455 ATP phosphoribosyltransferase, C-terminal domain
200 298 InterPro IPR013115 Histidine biosynthesis HisG, C-terminal
6 220 CDD cd13592 PBP2_HisGL2
7 221 Gene3D G3DSA:3.40.190.10 -
102 191 Gene3D G3DSA:3.40.190.10 -
104 191 FunFam G3DSA:3.40.190.10:FF:000008 ATP phosphoribosyltransferase
2 298 PANTHER PTHR21403 ATP PHOSPHORIBOSYLTRANSFERASE ATP-PRTASE
2 298 InterPro IPR001348 ATP phosphoribosyltransferase HisG
226 299 FunFam G3DSA:3.30.70.120:FF:000002 ATP phosphoribosyltransferase
156 177 ProSitePatterns PS01316 ATP phosphoribosyltransferase signature.
156 177 InterPro IPR018198 ATP phosphoribosyltransferase, conserved site
226 299 Gene3D G3DSA:3.30.70.120 -
226 299 InterPro IPR015867 Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal
7 197 NCBIfam TIGR00070 ATP phosphoribosyltransferase
7 197 InterPro IPR013820 ATP phosphoribosyltransferase, catalytic domain
54 219 Pfam PF01634 ATP phosphoribosyltransferase
54 219 InterPro IPR013820 ATP phosphoribosyltransferase, catalytic domain
226 298 SUPERFAMILY SSF54913 GlnB-like
226 298 InterPro IPR011322 Nitrogen regulatory PII-like, alpha/beta
6 299 Hamap MF_00079 ATP phosphoribosyltransferase [hisG].
6 299 InterPro IPR020621 ATP phosphoribosyltransferase HisG, long form
223 296 Pfam PF08029 HisG, C-terminal domain
223 296 InterPro IPR013115 Histidine biosynthesis HisG, C-terminal
6 224 SUPERFAMILY SSF53850 Periplasmic binding protein-like II

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 · P2Rank

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

Pocket 1 P2Rank #1
0.271
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Surrounding area
Pocket 2 P2Rank #2
0.013
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Surrounding area
Pocket 3 P2Rank #3
0.009
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #19
0.29
Show in viewer
Surrounding area
Pocket 2 FPocket #3
0.275
Show in viewer
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_A0A0H3H0I5
AlphaFold DB full sequence Viewing
ColabFold KP13_03767
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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
PRT PDB via homolog 719.3 Da · LogP -3.60 · TPSA 385.5 Open detail RCSB PDB
TIH PDB via homolog Detail RCSB PDB
TLA PDB via homolog Detail RCSB PDB
WO4 PDB via homolog Detail RCSB PDB
ZINC1671208 ZINC proposed compound · Tanimoto 0.700 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
PRT RCSB PDB P60757 719.3 Da LogP -3.60 TPSA 385.5 3 viol. ✓ Clean [H]/N=C\1/c2c(n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O…
TIH RCSB PDB P9WMN1 171.2 Da LogP 0.70 TPSA 63.3 ✓ Ro5 ✓ Clean c1cc(sc1)C[C@@H](C(=O)O)N
TLA RCSB PDB P60757 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O
WO4 RCSB PDB Q02129 247.8 Da LogP -2.62 TPSA 80.3 ✓ Ro5 ✓ Clean [O-][W](=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.

Cross-references

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