Protein target profile

KP13_03332

Leucyl-tRNA synthetase

Genome: KpKP13 Gene: AHE45711.1 leuS 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQ31
Length 868
Pocket druggability 0.782
Direct ligand evidence 0 92 total records
Functional annotation 1 EC 8 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 (%)
72.973 Lower values reduce human off-target concern.
Human E-value
9.06e-12
Gut microbiome similarity
4.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
95.507 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
93.41 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 0.782
Structure A0A0H3GQ31
Pocket Pocket 18
P2Rank 0.957
Structure A0A0H3GQ31
Pocket Pocket 1
ColabFold model
FPocket 0.706 · Pocket 34
P2Rank 0.99 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 199 / 4744 genomes with a hit
Prevalence 4.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKTGPLAAMQEQYRPEEIESKVQLHWDENRTFEVTEDESKEKYYCLSMLPYPSGRLHMGHVRNYTIGDVIARYQRMLGKNVLQPIGWDAFGLPAEGAAVKNNTAPAPWTYDNIAYMKNQLKMLGFGYDWSRELATCTPEYYRWEQKFFTELYKKGLVYKKTSAVNWCPNDQTVLANEQVIDGCCWRCDTKVERKEIPQWFIKITAYADELLNDLDKLDHWPDTVKTMQRNWIGRSEGVEISFDVNDYADKLTVYTTRPDTFMGCTYLAVAAGHPLAQQAAANNPALATFIDECRNTKVAEADMATMEKKGVDTGFKAIHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFASKYGLNIKPVILAADGSEPDLSEQALTEKGVLFNSGEFSGLDYEAGFNAIADKLAAMGVGERKVNYRLRDWGVSRQRYWGAPIPMVTLEDGTVLPTPEDQLPVILPEDVVMDGITSPIKADPEWAKTTVNGQPALRETDTFDTFMESSWYYARYTCPQYQEGMLDSKAANYWLPVDIYIGGIEHAIMHLLYFRFFHKLMRDAGMVNSDEPAKQLLCQGMVLADAFYYVGENGERNWVSPVDAIVERDEKGRIVKAKDAAGHELVYTGMSKMSKSKNNGIDPQVMVERYGADTVRLFMMFASPADMTLEWQESGVEGANRFLKRVWKLVYEHTTKGEVAALNVAALSEDQKALRRDIHKTIAKVTDDIGRRQTFNTAIAAIMELMNKLAKAPQEDEQDRALMQEALLAVVRMLNPFTPHASFTLWRELNGEGDIDNAPWPVADESAMVEDSTLVVVQVNGKVRGKITVAVDATEEQVRERAGQEHLVAKYLDGKTVRKVIYVPGKLLNLVVG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0002161 The hydrolysis of an incorrectly aminoacylated tRNA.
  • GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • GO:0006429 The process of coupling leucine to leucyl-tRNA, catalyzed by leucyl-tRNA synthetase. The leucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a leucine-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: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:0004823 Catalysis of the reaction: leucine + ATP + tRNA(Leu) = AMP + diphosphate + 2 H+ + Leu-tRNA(Leu).
  • 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.

55 records
Show feature table
Start End DB Term Name
579 632 Gene3D G3DSA:2.20.28.290 -
13 867 NCBIfam TIGR00396 bacterial-type leucine--tRNA ligase
13 867 InterPro IPR002302 Leucine-tRNA ligase
50 61 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
50 61 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
633 805 Gene3D G3DSA:1.10.730.10 -
12 867 Hamap MF_00049_B Leucine--tRNA ligase [leuS].
12 867 InterPro IPR002302 Leucine-tRNA ligase
806 868 FunFam G3DSA:3.10.20.590:FF:000001 Leucine--tRNA ligase
40 242 Gene3D G3DSA:3.40.50.620 HUPs
40 242 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
234 423 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain
234 423 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
40 257 FunFam G3DSA:3.40.50.620:FF:000003 Leucine--tRNA ligase
666 784 CDD cd07958 Anticodon_Ia_Leu_BEm
23 179 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
23 179 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
425 580 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
425 580 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
626 660 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
626 660 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
417 578 Gene3D G3DSA:3.40.50.620 HUPs
417 578 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
161 177 PRINTS PR00985 Leucyl-tRNA synthetase signature
161 177 InterPro IPR002302 Leucine-tRNA ligase
193 206 PRINTS PR00985 Leucyl-tRNA synthetase signature
193 206 InterPro IPR002302 Leucine-tRNA ligase
135 152 PRINTS PR00985 Leucyl-tRNA synthetase signature
135 152 InterPro IPR002302 Leucine-tRNA ligase
223 242 PRINTS PR00985 Leucyl-tRNA synthetase signature
223 242 InterPro IPR002302 Leucine-tRNA ligase
565 575 PRINTS PR00985 Leucyl-tRNA synthetase signature
565 575 InterPro IPR002302 Leucine-tRNA ligase
493 511 PRINTS PR00985 Leucyl-tRNA synthetase signature
493 511 InterPro IPR002302 Leucine-tRNA ligase
532 554 PRINTS PR00985 Leucyl-tRNA synthetase signature
532 554 InterPro IPR002302 Leucine-tRNA ligase
9 51 FunFam G3DSA:1.10.730.10:FF:000002 Leucine--tRNA ligase
670 867 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
670 867 InterPro IPR009080 Aminoacyl-tRNA synthetase, class Ia, anticodon-binding
243 416 Gene3D G3DSA:3.90.740.10 -
243 416 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
10 867 PANTHER PTHR43740 LEUCYL-TRNA SYNTHETASE
10 867 InterPro IPR002302 Leucine-tRNA ligase
243 417 FunFam G3DSA:3.90.740.10:FF:000012 Leucine--tRNA ligase
13 676 SUPERFAMILY SSF52374 Nucleotidylyl transferase
577 632 FunFam G3DSA:2.20.28.290:FF:000001 Leucine--tRNA ligase
42 666 CDD cd00812 LeuRS_core
398 579 FunFam G3DSA:3.40.50.620:FF:000124 Leucine--tRNA ligase
229 411 Pfam PF13603 Leucyl-tRNA synthetase, Domain 2
229 411 InterPro IPR025709 Leucyl-tRNA synthetase, editing domain
807 868 Gene3D G3DSA:3.10.20.590 -
621 806 FunFam G3DSA:1.10.730.10:FF:000002 Leucine--tRNA ligase
708 829 Pfam PF08264 Anticodon-binding domain of tRNA ligase
708 829 InterPro IPR013155 Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding

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 #18
0.782
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Surrounding area
Site 2 FPocket #40
0.51
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Surrounding area
Site 3 FPocket #26
0.218
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Surrounding area
Site 4 FPocket #15
0.217
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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
0.957
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Surrounding area
Site 2 P2Rank #2
0.426
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Surrounding area
Site 3 P2Rank #3
0.329
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Surrounding area
Site 4 P2Rank #4
0.177
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Surrounding area
Site 5 P2Rank #5
0.064
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Surrounding area
Residue sets
UniProt: Binding site:622-622
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_A0A0H3GQ31
AlphaFold DB full sequence Viewing
ColabFold KP13_03332
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.

92 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 42 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 31 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2AD PDB via homolog 266.3 Da · LogP -2.01 · TPSA 145.3 Open detail RCSB PDB
84T PDB via homolog Detail RCSB PDB
9YN PDB via homolog Detail RCSB PDB
FGX PDB via homolog Detail RCSB PDB
ILA 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
2AD RCSB PDB Q7SIE4 266.3 Da LogP -2.01 TPSA 145.3 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
84T RCSB PDB P07813 460.4 Da LogP -1.33 TPSA 215.2 2 viol. ✓ Clean CC(C)[C@H]([C@@H](C(=O)NP(=O)(O)OC[C@@H]1C[C@@H…
9YN RCSB PDB P07813 379.4 Da LogP -1.48 TPSA 174.4 ✓ Ro5 ✓ Clean CC(C)C[C@@H](C(=O)N[C@@H]1[C@@H]([C@H](O[C@H]1n…
FGX RCSB PDB B8ZKS5 655.4 Da LogP 1.43 TPSA 204.5 2 viol. ✓ Clean [B-]12(CCc3c1cc(cc3)[C@@H](c4ccc(cc4)SCC(=O)C)O…
ILA RCSB PDB P07813 458.5 Da LogP -2.65 TPSA 220.6 2 viol. ✓ Clean CC[C@H](C)[C@@H](C(=O)NS(=O)(=O)NC[C@@H]1[C@H](…
LMS RCSB PDB P07813 346.3 Da LogP -2.75 TPSA 188.7 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
NVA RCSB PDB Q72GM3 117.1 Da LogP 0.20 TPSA 63.3 ✓ Ro5 ✓ Clean CCC[C@@H](C(=O)O)N
OV8 RCSB PDB Q5FAJ3 478.6 Da LogP -2.00 TPSA 204.9 1 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
OVZ RCSB PDB Q5FAJ3 568.7 Da LogP -0.16 TPSA 190.9 2 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
VRT RCSB PDB P07813 365.4 Da LogP -1.73 TPSA 174.4 ✓ Ro5 ✓ Clean CCCC(C(=O)N[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2n…
WMP RCSB PDB B8ZKS5 568.3 Da LogP 0.66 TPSA 193.5 2 viol. ✓ Clean [B-]12(c3cc(ccc3CO1)[C@@H](c4ccccc4)O)O[C@H]5[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.