KpKP13 Protein target profile

Putative lysyl-tRNA synthetase

Accession: KP13_00516

Gene: AHE46750.1 poxA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQI0
Length 325
Pocket druggability (P2Rank · AlphaFold DB model) 0.949
Direct ligand evidence 0 58 total records
Functional annotation 1 EC 10 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
Hit
Human identity (%)
27.811 Lower values reduce human off-target concern.
Human E-value
6.3999999999999995e-31
Gut microbiome similarity
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
96.95 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) 0.949
Structure A0A0H3GQI0
Pocket Pocket 1
Druggability (FPocket) 0.207
Structure A0A0H3GQI0
Pocket Pocket 1
ColabFold model
P2Rank 0.954 · Pocket 1
FPocket 0.539 · Pocket 7
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 142 / 4744 genomes with a hit
Prevalence 3.0%

Sequence

Primary amino-acid sequence viewer.

MSETATWQPSAPIPNLLKRAAVMAEIRRFFTDRGVLEVETPCMSQATVTDIHLFPFETRFVGPGHSQGLNLYLMTSPEYHMKRLLAAGCGPVFQLCRSFRNEEMGRHHNPEFTMLEWYRPCYDMYRLINEVDDLLQQVLECQPAESLSYQQAFQRHLEIDPLSADKAQLREVAAKLDLSNIADTEEDRDTLLQLLFTMGVEPHIGKDRPTFIYHFPATQASLAQISPEDHRVAERFEVYYKGIELANGFHELTDAHEQRLRFEQDNRKRAARGLPQQPIDNNLLAALEAGLPDCSGVALGVDRVVMLALGAESIGEVIAFTVDRA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0006430 The process of coupling lysine to lysyl-tRNA, catalyzed by lysyl-tRNA synthetase. The lysyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a lysine-accetping tRNA.
  • 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: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:0004824 Catalysis of the reaction: ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0016880 Catalysis of the ligation of an acid to ammonia (NH4+) or an amide via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
  • GO:0000049 Binding to a transfer RNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
1 324 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
1 324 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
15 321 Pfam PF00152 tRNA synthetases class II (D, K and N)
15 321 InterPro IPR004364 Aminoacyl-tRNA synthetase, class II (D/K/N)
17 320 NCBIfam TIGR00462 EF-P lysine aminoacylase EpmA
17 320 InterPro IPR004525 Elongation factor P--(R)-beta-lysine ligase
99 116 PRINTS PR00982 Lysyl-tRNA synthetase signature
99 116 InterPro IPR018149 Lysyl-tRNA synthetase, class II, C-terminal
31 41 PRINTS PR00982 Lysyl-tRNA synthetase signature
31 41 InterPro IPR018149 Lysyl-tRNA synthetase, class II, C-terminal
149 322 PANTHER PTHR42918 LYSYL-TRNA SYNTHETASE
2 324 FunFam G3DSA:3.30.930.10:FF:000017 Elongation factor P--(R)-beta-lysine ligase
19 325 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile.
19 325 InterPro IPR006195 Aminoacyl-tRNA synthetase, class II
2 325 Hamap MF_00174 Elongation factor P--(R)-beta-lysine ligase [epmA].
2 325 InterPro IPR004525 Elongation factor P--(R)-beta-lysine ligase
14 320 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
14 320 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)

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
0.949
Likely same site as FPocket 1 4.0 Å 35 shared residues 83% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.268
Likely same site as FPocket 1 7.3 Å 15 shared residues 100% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.207 Unusual size
Likely same site as P2Rank 1 4.0 Å 35 shared residues 83% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:100-102
UniProt: Binding site:109-109
UniProt: Binding site:118-118
UniProt: Binding site:244-245
UniProt: Binding site:251-251
UniProt: Binding site:300-300
UniProt: Binding site:76-78
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_A0A0H3GQI0
AlphaFold DB full sequence Viewing
ColabFold KP13_00516
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
ACP PDB via homolog 505.2 Da · LogP -1.52 · TPSA 269.9 Open detail RCSB PDB
ADN PDB via homolog Detail RCSB PDB
B4P PDB via homolog Detail RCSB PDB
FYB PDB via homolog Detail RCSB PDB
KAA 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
ACP RCSB PDB P0A8N5 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ADN RCSB PDB Q5CR27 267.2 Da LogP -1.98 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
B4P RCSB PDB P0A8N5 836.4 Da LogP -2.45 TPSA 434.0 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
FYB RCSB PDB Q5CR27 355.3 Da LogP 2.60 TPSA 79.5 ✓ Ro5 ✓ Clean c1cc2c(cc1F)C(=O)C=C(O2)C(=O)NCC3(CCC(CC3)(F)F)O
KAA RCSB PDB P0A8N7 474.5 Da LogP -3.14 TPSA 243.8 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
KRS RCSB PDB A0PV47 292.3 Da LogP 2.53 TPSA 76.0 ✓ Ro5 ✓ Clean C[C@H]1CCC[C@@H](O1)C[C@H]2Cc3cc(cc(c3C(=O)O2)O…
LYN RCSB PDB Q9RHV9 146.2 Da LogP -1.79 TPSA 96.8 ✓ Ro5 ✓ Clean C(CC[NH3+])C[C@@H](C(=O)N)N
XAH RCSB PDB Q9RHV9 490.4 Da LogP -2.35 TPSA 256.2 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.