Protein profile

VK055_1858

leucine--tRNA ligase

Genome: KpATCC43816

Gene: leuS AIK80464.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ31
Amino acids 860
Annotations 9
Features 55
PDB binders 11
Druggability 0.782

Overview

Basic information about this protein and its source genome.

Accession
VK055_1858
Gene
leuS AIK80464.1
Status
annotated
Amino acids
860
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
72.973
Human E-value
9.14e-12
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
95.698
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
93.84

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 0.787 · Pocket 36
P2Rank 0.969 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 200 / 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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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: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: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: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
390 571 FunFam G3DSA:3.40.50.620:FF:000124 Leucine--tRNA ligase
417 572 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
417 572 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
15 171 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
15 171 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
618 652 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
618 652 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
485 503 PRINTS PR00985 Leucyl-tRNA synthetase signature
485 503 InterPro IPR002302 Leucine-tRNA ligase
127 144 PRINTS PR00985 Leucyl-tRNA synthetase signature
127 144 InterPro IPR002302 Leucine-tRNA ligase
215 234 PRINTS PR00985 Leucyl-tRNA synthetase signature
215 234 InterPro IPR002302 Leucine-tRNA ligase
557 567 PRINTS PR00985 Leucyl-tRNA synthetase signature
557 567 InterPro IPR002302 Leucine-tRNA ligase
185 198 PRINTS PR00985 Leucyl-tRNA synthetase signature
185 198 InterPro IPR002302 Leucine-tRNA ligase
153 169 PRINTS PR00985 Leucyl-tRNA synthetase signature
153 169 InterPro IPR002302 Leucine-tRNA ligase
524 546 PRINTS PR00985 Leucyl-tRNA synthetase signature
524 546 InterPro IPR002302 Leucine-tRNA ligase
42 53 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
42 53 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
235 409 FunFam G3DSA:3.90.740.10:FF:000012 Leucine--tRNA ligase
5 668 SUPERFAMILY SSF52374 Nucleotidylyl transferase
34 658 CDD cd00812 LeuRS_core
32 234 Gene3D G3DSA:3.40.50.620 HUPs
32 234 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
662 859 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
662 859 InterPro IPR009080 Aminoacyl-tRNA synthetase, class Ia, anticodon-binding
226 415 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain
226 415 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
235 408 Gene3D G3DSA:3.90.740.10 -
235 408 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
5 859 NCBIfam TIGR00396 bacterial-type leucine--tRNA ligase
5 859 InterPro IPR002302 Leucine-tRNA ligase
409 570 Gene3D G3DSA:3.40.50.620 HUPs
409 570 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
221 403 Pfam PF13603 Leucyl-tRNA synthetase, Domain 2
221 403 InterPro IPR025709 Leucyl-tRNA synthetase, editing domain
700 821 Pfam PF08264 Anticodon-binding domain of tRNA ligase
700 821 InterPro IPR013155 Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding
625 797 Gene3D G3DSA:1.10.730.10 -
3 859 PANTHER PTHR43740 LEUCYL-TRNA SYNTHETASE
3 859 InterPro IPR002302 Leucine-tRNA ligase
798 860 FunFam G3DSA:3.10.20.590:FF:000001 Leucine--tRNA ligase
613 798 FunFam G3DSA:1.10.730.10:FF:000002 Leucine--tRNA ligase
571 624 Gene3D G3DSA:2.20.28.290 -
799 860 Gene3D G3DSA:3.10.20.590 -
569 624 FunFam G3DSA:2.20.28.290:FF:000001 Leucine--tRNA ligase
4 859 Hamap MF_00049_B Leucine--tRNA ligase [leuS].
4 859 InterPro IPR002302 Leucine-tRNA ligase
658 776 CDD cd07958 Anticodon_Ia_Leu_BEm
32 249 FunFam G3DSA:3.40.50.620:FF:000003 Leucine--tRNA ligase
1 43 FunFam G3DSA:1.10.730.10:FF:000002 Leucine--tRNA ligase

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

Loading 3D structure...

Legend High Medium Low

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 VK055_1858
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.