Protein target profile

VK055_0207

peptidyl-tRNA hydrolase

Genome: KpATCC43816 Gene: pth AIK78835.1 3D evidence: Experimental + ColabFold model UniProt A6TAP7
Length 194
Pocket druggability 0.769
Direct ligand evidence 0 60 total records
Functional annotation 0 EC 1 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 (%)
35.227 Lower values reduce human off-target concern.
Human E-value
2.63e-20
Gut microbiome similarity
4.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
91.753 Higher values support similarity to known essential genes.
DEG E-value
1.11e-125 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.31 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.769
Structure 7BRD
Pocket Pocket 1
P2Rank 0.448
Structure 7BRD
Pocket Pocket 1
ColabFold model
FPocket 0.694 · Pocket 6
P2Rank 0.291 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 231 / 4744 genomes with a hit
Prevalence 4.9%

Cross-references

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

Structure

Sequence

Primary amino-acid sequence viewer.

MTIKLIVGLANPGAEYAATRHNAGAWYVDLLADRHRAPLREESKFFGYTSRINLAGEDVRLLVPTTFMNLSGKAVAAMATFYRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRVGIGHPGDKNKVVGFVLGKPPASEQKLIDDAVDEAARCTEIWLKDGLTKATNRLHAFKAQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • GO:0004045 Catalysis of the reaction: an N-acyl-L-alpha-aminoacyl-tRNA + H2O = an N-acyl-L-amino acid + a tRNA + H+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
4 175 NCBIfam TIGR00447 aminoacyl-tRNA hydrolase
4 175 InterPro IPR001328 Peptidyl-tRNA hydrolase
1 194 Gene3D G3DSA:3.40.50.1470 -
1 194 InterPro IPR036416 Peptidyl-tRNA hydrolase superfamily
3 182 Hamap MF_00083 Peptidyl-tRNA hydrolase [pth].
3 182 InterPro IPR001328 Peptidyl-tRNA hydrolase
110 120 ProSitePatterns PS01196 Peptidyl-tRNA hydrolase signature 2.
110 120 InterPro IPR018171 Peptidyl-tRNA hydrolase, conserved site
4 187 PANTHER PTHR17224 PEPTIDYL-TRNA HYDROLASE
4 187 InterPro IPR001328 Peptidyl-tRNA hydrolase
5 177 CDD cd00462 PTH
5 177 InterPro IPR001328 Peptidyl-tRNA hydrolase
16 29 ProSitePatterns PS01195 Peptidyl-tRNA hydrolase signature 1.
16 29 InterPro IPR018171 Peptidyl-tRNA hydrolase, conserved site
3 192 SUPERFAMILY SSF53178 Peptidyl-tRNA hydrolase-like
3 192 InterPro IPR036416 Peptidyl-tRNA hydrolase superfamily
1 192 FunFam G3DSA:3.40.50.1470:FF:000001 Peptidyl-tRNA hydrolase
5 189 Pfam PF01195 Peptidyl-tRNA hydrolase
5 189 InterPro IPR001328 Peptidyl-tRNA hydrolase

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
0.769
Likely same site as P2Rank 2 1.5 Å 14 shared residues 93% of smaller site
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.448
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.249
Likely same site as FPocket 1 1.5 Å 14 shared residues 93% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.0
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Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 7BRD
X-ray A Viewing
ColabFold VK055_0207
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.

60 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 10 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0L1 PDB via homolog 146.1 Da · LogP 0.72 · TPSA 74.6 Open detail RCSB PDB
3NZ PDB via homolog Detail RCSB PDB
5AE PDB via homolog Detail RCSB PDB
AR3 PDB via homolog Detail RCSB PDB
CTN 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
0L1 RCSB PDB Q9HVC3 146.1 Da LogP 0.72 TPSA 74.6 ✓ Ro5 ✓ Clean C(CCC(=O)O)CC(=O)O
3NZ RCSB PDB Q9HVC3 443.5 Da LogP -1.28 TPSA 183.7 1 viol. ✓ Clean COc1ccc(cc1)C[C@@H](C(=O)N[C@@H]2[C@H](O[C@H]([…
5AE RCSB PDB Q9HVC3 244.2 Da LogP -3.17 TPSA 143.7 ✓ Ro5 ✓ Clean C1=NC(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)CO)…
AR3 RCSB PDB D0C9L6 243.2 Da LogP -2.56 TPSA 130.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H]([C@H](O2)CO…
CTN RCSB PDB D0C9L6 243.2 Da LogP -2.56 TPSA 130.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
FLC RCSB PDB Q5SHZ2 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
PML RCSB PDB Q9HVC3 160.2 Da LogP 1.11 TPSA 74.6 ✓ Ro5 ✓ Clean C(CCC(=O)O)CCC(=O)O
POL RCSB PDB D0C9L6 60.1 Da LogP 0.39 TPSA 20.2 ✓ Ro5 ✓ Clean CCCO
TLA RCSB PDB D0C9L6 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O
URI RCSB PDB D0C9L6 244.2 Da LogP -2.85 TPSA 124.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…

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.