Protein profile

PA3987

leucine--tRNA ligase

Genome: NC_002516.2

Gene: PA3987 leuS Structure source: AlphaFold UniProt Q9HX33
Amino acids 873
Annotations 9
Features 54
PDB binders 13
Druggability 0.482

Overview

Basic information about this protein and its source genome.

Accession
PA3987
Gene
PA3987 leuS
Status
annotated
Amino acids
873
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
51.613
Human E-value
1.44e-12
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.482
Structure
Pocket

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • 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:0004823 Catalysis of the reaction: leucine + ATP + tRNA(Leu) = AMP + diphosphate + 2 H+ + Leu-tRNA(Leu).
  • 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:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

54 records
Show feature table
Start End DB Term Name
5 872 NCBIfam TIGR00396 bacterial-type leucine--tRNA ligase
5 872 InterPro IPR002302 Leucine-tRNA ligase
536 558 PRINTS PR00985 Leucyl-tRNA synthetase signature
536 558 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
215 234 PRINTS PR00985 Leucyl-tRNA synthetase signature
215 234 InterPro IPR002302 Leucine-tRNA ligase
497 515 PRINTS PR00985 Leucyl-tRNA synthetase signature
497 515 InterPro IPR002302 Leucine-tRNA ligase
127 144 PRINTS PR00985 Leucyl-tRNA synthetase signature
127 144 InterPro IPR002302 Leucine-tRNA ligase
569 579 PRINTS PR00985 Leucyl-tRNA synthetase signature
569 579 InterPro IPR002302 Leucine-tRNA ligase
221 413 Pfam PF13603 Leucyl-tRNA synthetase, Domain 2
221 413 InterPro IPR025709 Leucyl-tRNA synthetase, editing domain
239 419 FunFam G3DSA:3.90.740.10:FF:000012 Leucine--tRNA ligase
365 583 FunFam G3DSA:3.40.50.620:FF:000124 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
714 834 Pfam PF08264 Anticodon-binding domain of tRNA ligase
714 834 InterPro IPR013155 Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding
4 872 Hamap MF_00049_B Leucine--tRNA ligase [leuS].
4 872 InterPro IPR002302 Leucine-tRNA ligase
581 637 FunFam G3DSA:2.20.28.290:FF:000001 Leucine--tRNA ligase
226 424 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain
226 424 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
671 789 CDD cd07958 Anticodon_Ia_Leu_BEm
32 236 Gene3D G3DSA:3.40.50.620 HUPs
32 236 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
32 252 FunFam G3DSA:3.40.50.620:FF:000003 Leucine--tRNA ligase
39 171 Pfam PF09334 tRNA synthetases class I (M)
39 171 InterPro IPR015413 Methionyl/Leucyl tRNA synthetase
237 409 Gene3D G3DSA:3.90.740.10 -
237 409 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
811 873 Gene3D G3DSA:3.10.20.590 -
638 810 Gene3D G3DSA:1.10.730.10 -
638 810 FunFam G3DSA:1.10.730.10:FF:000003 Leucine--tRNA ligase
5 681 SUPERFAMILY SSF52374 Nucleotidylyl transferase
428 584 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
428 584 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
631 666 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
631 666 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
34 235 CDD cd00812 LeuRS_core
410 580 Gene3D G3DSA:3.40.50.620 HUPs
410 580 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
581 637 Gene3D G3DSA:2.20.28.290 -
811 873 FunFam G3DSA:3.10.20.590:FF:000001 Leucine--tRNA ligase
675 872 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
675 872 InterPro IPR009080 Aminoacyl-tRNA synthetase, class Ia, anticodon-binding
3 872 PANTHER PTHR43740 LEUCYL-TRNA SYNTHETASE
3 872 InterPro IPR002302 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

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Structural evidence

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA3987
AlphaFold full sequence Viewing
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
3 0.482
14 0.284
29 0.211

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.

90 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…
HQ5 B4RNT1 435.5 Da LogP -2.80 TPSA 209.1 1 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
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 Q72GM3 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)…
LSS P07813 459.5 Da LogP -2.22 TPSA 217.8 1 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
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…
OVB Q5FAJ3 609.6 Da LogP 1.11 TPSA 188.1 2 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
OVH Q5FAJ3 525.6 Da LogP 0.21 TPSA 178.9 2 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…

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.