Protein profile

PA2740

phenylalanine--tRNA ligase subunit alpha

Genome: NC_002516.2

Gene: pheS PA2740 Structure source: Experimental + AlphaFold UniProt Q9I0A3
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Amino acids 338
Annotations 10
Features 19
PDB binders 10
Druggability 0.767

Overview

Basic information about this protein and its source genome.

Accession
PA2740
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
pheS PA2740
Status
annotated
Amino acids
338
Structure source
Experimental + AlphaFold
EC
6.1.1.20
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0000287 Binding to a magnesium (Mg) ion. GO:0004826 Catalysis of the reaction: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe). GO:0000049 Binding to a transfer RNA. GO:0006432 The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. The phenylalanyl-tRNA synthetase is a class-II synthetase. However, unlike other class II enzymes, The activated amino acid is transferred to the 2'-OH group of a phenylalanine-accepting tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
32.857
Human E-value
6.21e-06
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 0.767
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0004826 Catalysis of the reaction: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe).
  • GO:0000049 Binding to a transfer RNA.
  • GO:0006432 The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. The phenylalanyl-tRNA synthetase is a class-II synthetase. However, unlike other class II enzymes, The activated amino acid is transferred to the 2'-OH group of a phenylalanine-accepting 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:0043039 The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is 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, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
92 337 Pfam PF01409 tRNA synthetases class II core domain (F)
92 337 InterPro IPR002319 Phenylalanyl-tRNA synthetase
89 337 PANTHER PTHR11538 PHENYLALANYL-TRNA SYNTHETASE
38 337 NCBIfam TIGR00468 phenylalanine--tRNA ligase subunit alpha
38 337 InterPro IPR004529 Phenylalanyl-tRNA synthetase, class IIc, alpha subunit
7 338 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
7 338 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
8 338 FunFam G3DSA:3.30.930.10:FF:000003 Phenylalanine--tRNA ligase alpha subunit
13 99 SUPERFAMILY SSF46589 tRNA-binding arm
13 99 InterPro IPR010978 Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm
122 328 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile.
122 328 InterPro IPR006195 Aminoacyl-tRNA synthetase, class II
107 332 CDD cd00496 PheRS_alpha_core
8 337 Hamap MF_00281 Phenylalanine--tRNA ligase alpha subunit [pheS].
8 337 InterPro IPR022911 Phenylalanine-tRNA ligase alpha chain 1, bacterial
92 338 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
92 338 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
20 87 Pfam PF02912 Aminoacyl tRNA synthetase class II, N-terminal domain
20 87 InterPro IPR004188 Phenylalanine-tRNA ligase, class II, N-terminal

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

5 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 4P72
X-ray 2.62 Å C,D
100.0% 1-338
PDBe RCSB PDBj File
Viewing
PDB 4P74
X-ray 2.70 Å C,D
100.0% 1-338
PDBe RCSB PDBj File
Loaded
PDB 4P71
X-ray 2.79 Å C,D
100.0% 1-338
PDBe RCSB PDBj File
Loaded
PDB 4P75
X-ray 2.96 Å C,D
100.0% 1-338
PDBe RCSB PDBj File
Loaded
PDB 4P73
X-ray 3.03 Å C,D
100.0% 1-338
PDBe RCSB PDBj File
Loaded
AlphaFold PA2740
AlphaFold — — 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
1 0.767

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 22.46 0.881
2 2.33 0.06

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.

61 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
2NL
4P72 2.62 Å Open crystal
291.7 Da LogP 2.60 TPSA 63.2 ✓ Ro5 ✓ Clean CNC(=O)COc1cccc(c1)Nc2cc(ccn2)Cl
2NM
4P75 2.96 Å Open crystal
242.2 Da LogP 3.10 TPSA 37.9 ✓ Ro5 ✓ Clean COc1cccc(c1)c2cc([nH]n2)C(F)(F)F
2U9
4P74 2.70 Å Open crystal
366.5 Da LogP 1.95 TPSA 85.4 ✓ Ro5 ✓ Clean Cc1ccc(cc1)OCc2nc(cs2)C(=O)N[C@H]3CCS(=O)(=O)C3
GAX
4P73 3.03 Å Open crystal
444.5 Da LogP 2.69 TPSA 107.5 ✓ Ro5 ✓ Clean c1ccnc(c1)N2CCN(CC2)S(=O)(=O)c3cccc(c3)NC(=O)Nc…

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.