Protein profile

KP13_03332

Leucyl-tRNA synthetase

Genome: KpKP13

Gene: leuS AHE45711.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ31
Amino acids 868
Annotations 9
Features 55
PDB binders 11
Druggability 0.782

Overview

Basic information about this protein and its source genome.

Accession
KP13_03332
Gene
leuS AHE45711.1
Status
annotated
Amino acids
868
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
72.973
Human E-value
9.06e-12
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
95.507
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
93.41

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its 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
Normalized 0.042

Sequence

Primary amino-acid sequence viewer.

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GQ31
AlphaFold full sequence Viewing
ColabFold KP13_03332
ColabFold full sequence Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
18 0.782
40 0.51
26 0.218
15 0.217

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 25.69 0.908
2 6.48 0.328
3 2.49 0.069
4 2.36 0.062
5 1.43 0.019

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

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 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 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 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 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 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 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 Q72GM3 117.1 Da LogP 0.20 TPSA 63.3 ✓ Ro5 ✓ Clean CCC[C@@H](C(=O)O)N
OV8 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 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 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 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.