Protein target profile

KP13_00709

Tryptophanyl-tRNA synthetase

Genome: KpKP13 Gene: AHE42327.1 trpS 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GU65
Length 334
Pocket druggability 0.401
Direct ligand evidence 0 58 total records
Functional annotation 1 EC 7 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 (%)
42.296 Lower values reduce human off-target concern.
Human E-value
5.96e-87
Gut microbiome similarity
31.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
95.21 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
94.28 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.401
Structure A0A0H3GU65
Pocket Pocket 26
P2Rank 0.851
Structure A0A0H3GU65
Pocket Pocket 1
ColabFold model
FPocket 0.369 · Pocket 1
P2Rank 0.88 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1492 / 4744 genomes with a hit
Prevalence 31.5%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MTKPIVFSGAQPSGELTIGNYMGALRQWVNMQDDYHCIYCIVDQHAITVRQDPQQLRKATLDTLALYLACGIDPQKSTIFVQSHVPEHAQLGWALNCYTYFGELSRMTQFKDKSARYAENINAGLFDYPVLMAADILLYQTNQVPVGEDQKQHLELSRDIAQRFNAIYGDIFKVPEPFIPKSGARVMSLLEPTKKMSKSDDNRNNVIGLLEDPKSVVKKIKRAVTDSDEPPVVRYDLKEKAGVSNLLDILSAVTGKTIPELEQHFEGKMYGHLKGEVAEAVSGMLIDLQERYHRFRNDEAFLNQVMKDGAEKASARASQTLKAVYEAIGFVAKP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • GO:0006436 The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-tRNA synthetase. The tryptophanyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tryptophan-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
  • GO:0006418 The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, to be used in ribosome-mediated polypeptide synthesis.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004830 Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp).
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
142 163 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature
142 163 InterPro IPR002306 Tryptophan-tRNA ligase
195 205 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature
195 205 InterPro IPR002306 Tryptophan-tRNA ligase
16 32 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature
16 32 InterPro IPR002306 Tryptophan-tRNA ligase
66 85 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature
66 85 InterPro IPR002306 Tryptophan-tRNA ligase
3 285 Pfam PF00579 tRNA synthetases class I (W and Y)
3 285 InterPro IPR002305 Aminoacyl-tRNA synthetase, class Ic
186 298 FunFam G3DSA:1.10.240.10:FF:000002 Tryptophan--tRNA ligase
6 212 FunFam G3DSA:3.40.50.620:FF:000024 Tryptophan--tRNA ligase
5 284 CDD cd00806 TrpRS_core
5 284 InterPro IPR002306 Tryptophan-tRNA ligase
3 331 Hamap MF_00140_B Tryptophan--tRNA ligase [trpS].
3 331 InterPro IPR024109 Tryptophan-tRNA ligase, bacterial-type
6 329 Gene3D G3DSA:3.40.50.620 HUPs
6 329 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
12 21 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
12 21 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
3 330 NCBIfam TIGR00233 tryptophan--tRNA ligase
3 330 InterPro IPR002306 Tryptophan-tRNA ligase
3 330 PANTHER PTHR43766 TRYPTOPHAN--TRNA LIGASE, MITOCHONDRIAL
5 330 SUPERFAMILY SSF52374 Nucleotidylyl transferase
186 298 Gene3D G3DSA:1.10.240.10 -

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 #26
0.401
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Surrounding area
Site 2 FPocket #2
0.262
Likely same site as P2Rank 1 5.4 Å 18 shared residues 67% of smaller site
Unusual size
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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
0.851
Likely same site as FPocket 2 5.4 Å 18 shared residues 67% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.055
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.009
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:11-13
UniProt: Binding site:135-135
UniProt: Binding site:147-149
UniProt: Binding site:186-186
UniProt: Binding site:19-20
UniProt: Binding site:195-199
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_A0A0H3GU65
AlphaFold DB full sequence Viewing
ColabFold KP13_00709
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.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5BX PDB via homolog 257.3 Da · LogP 1.77 · TPSA 66.5 Open detail RCSB PDB
9E0 PDB via homolog Detail RCSB PDB
ANL PDB via homolog Detail RCSB PDB
AQP PDB via homolog Detail RCSB PDB
LTN 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
5BX RCSB PDB P00953 257.3 Da LogP 1.77 TPSA 66.5 ✓ Ro5 ✓ Clean C[C@H](c1c[nH]c2c1cccc2)[C@H]3C(=O)N=C(O3)NC
9E0 RCSB PDB P00953 233.3 Da LogP 2.83 TPSA 53.1 ✓ Ro5 ✓ Clean C[C@H]1c2c[nH]c3c2c(ccc3)S[C@H]1C(=O)O
ANL RCSB PDB P00953 93.1 Da LogP 1.27 TPSA 26.0 ✓ Ro5 ✓ Clean c1ccc(cc1)N
AQP RCSB PDB P00953 587.2 Da LogP -1.51 TPSA 325.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
LTN RCSB PDB P00953 203.2 Da LogP 0.52 TPSA 84.9 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)N)N
NH4 RCSB PDB P00953 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
TYM RCSB PDB P00953 533.4 Da LogP -0.26 TPSA 233.9 3 viol. ✓ Clean c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O[P@](=O)(O)OC…
WSA RCSB PDB P75510 532.5 Da LogP -1.54 TPSA 233.6 3 viol. ✓ Clean c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)NS(=O)(=O)OC[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.