Protein profile

VK055_0280

phenylalanine--tRNA ligase, alpha subunit

Genome: KpATCC43816

Gene: pheS AIK78906.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GU78
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Amino acids 327
Annotations 10
Features 20
PDB binders 8
Druggability 0.595

Overview

Basic information about this protein and its source genome.

Accession
VK055_0280
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
pheS AIK78906.1
Status
annotated
Amino acids
327
Structure source
AlphaFold + ColabFold
EC
6.1.1.20
GO
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. 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. 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:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP. 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:0004826 Catalysis of the reaction: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe).

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
33.333
Human E-value
3.18e-10
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
97.248
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.05

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 0.595
Structure A0A0H3GU78
Pocket Pocket 1
P2Rank 0.933
Structure A0A0H3GU78
Pocket Pocket 1
ColabFold model
FPocket 0.304 · Pocket 19
P2Rank 0.9 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 985 / 4744 genomes with a hit
Normalized 0.208

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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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.
  • 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:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • 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:0004826 Catalysis of the reaction: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0000049 Binding to a transfer RNA.
  • GO:0000287 Binding to a magnesium (Mg) ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
20 87 Pfam PF02912 Aminoacyl tRNA synthetase class II, N-terminal domain
20 87 InterPro IPR004188 Phenylalanine-tRNA ligase, class II, N-terminal
116 317 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile.
116 317 InterPro IPR006195 Aminoacyl-tRNA synthetase, class II
61 81 Coils Coil Coil
8 327 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
8 327 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
8 327 FunFam G3DSA:3.30.930.10:FF:000003 Phenylalanine--tRNA ligase alpha subunit
107 321 CDD cd00496 PheRS_alpha_core
92 326 Pfam PF01409 tRNA synthetases class II core domain (F)
92 326 InterPro IPR002319 Phenylalanyl-tRNA synthetase
14 99 SUPERFAMILY SSF46589 tRNA-binding arm
14 99 InterPro IPR010978 Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm
38 327 NCBIfam TIGR00468 phenylalanine--tRNA ligase subunit alpha
38 327 InterPro IPR004529 Phenylalanyl-tRNA synthetase, class IIc, alpha subunit
8 326 Hamap MF_00281 Phenylalanine--tRNA ligase alpha subunit [pheS].
8 326 InterPro IPR022911 Phenylalanine-tRNA ligase alpha chain 1, bacterial
93 327 PANTHER PTHR11538 PHENYLALANYL-TRNA SYNTHETASE
92 327 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
92 327 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)

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_A0A0H3GU78
AlphaFold — — full sequence — Viewing
ColabFold VK055_0280
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
1 0.595
6 0.017
20 0.005
22 0.005

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 35.53 0.933
2 6.1 0.251
3 2.4 0.052
4 2.02 0.037
5 1.91 0.032

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.

59 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
2NL
4P72
Q9I0A3 291.7 Da LogP 2.60 TPSA 63.2 ✓ Ro5 ✓ Clean CNC(=O)COc1cccc(c1)Nc2cc(ccn2)Cl
2NM
4P75
Q9I0A3 242.2 Da LogP 3.10 TPSA 37.9 ✓ Ro5 ✓ Clean COc1cccc(c1)c2cc([nH]n2)C(F)(F)F
2U9
4P74
Q9I0A3 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
2RHQ
Q4L5E3 444.5 Da LogP 2.69 TPSA 107.5 ✓ Ro5 ✓ Clean c1ccnc(c1)N2CCN(CC2)S(=O)(=O)c3cccc(c3)NC(=O)Nc…
H2L
7DB7
P9WFU3 441.5 Da LogP 3.79 TPSA 116.0 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)CCNS(=O)(=O)c3cccc(c3)NC(=O…
H2R
7DB8
P9WFU3 456.5 Da LogP 5.77 TPSA 67.3 1 viol. ✓ Clean c1cc(cc(c1)Oc2ccc(cn2)C(F)(F)F)CC3CCN(CC3)C(=O)…
NO4
6P26
P08312 215.3 Da LogP 3.67 TPSA 12.0 ✓ Ro5 ✓ Clean c1ccc(cc1)CNCCC2=CCCCC2
VB3
6OZ5
P08312 247.4 Da LogP 3.84 TPSA 32.3 ✓ Ro5 Alert C[C@@H](CC1CCCCC1)NCc2ccccc2O

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.