Protein target profile

KP13_04673

phenylalanyl-tRNA synthetase alpha subunit

Genome: KpKP13 Gene: pheS AHE44067.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GU78
Length 331
Pocket druggability 0.595
Direct ligand evidence 0 59 total records
Functional annotation 1 EC 9 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
33.333 Lower values reduce human off-target concern.
Human E-value
3.03e-10
Gut microbiome similarity
20.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
96.979 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
93.98 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.595
Structure A0A0H3GU78
Pocket Pocket 1
P2Rank 0.933
Structure A0A0H3GU78
Pocket Pocket 1
ColabFold model
FPocket 0.591 · Pocket 7
P2Rank 0.871 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 975 / 4744 genomes with a hit
Prevalence 20.6%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

Primary amino-acid sequence viewer.

MRKTMSHLAELVASAKAAINEASDVAALDNVRVEYLGKKGHLTLQMTTLRELPPEERPAAGAVINEAKEQVQQALNARKAELEGAALNARLAAETIDVSLPGRRIENGGLHPVTRTIDRIESFFGELGFTVATGPEIEDDYHNFDALNIPGHHPARADHDTFWFDATRLLRTQTSGVQIRTMENQQPPIRIIAPGRVYRNDYDQTHTPMFHQMEGLIVDKNISFTNLKGTLHDFLNNFFEEDLQVRFRPSYFPFTEPSAEVDVMGKNGKWLEVLGCGMVHPNVLRNVGIDPEVYSGFAFGMGMERLTMLRYGVTDLRAFFENDLRFLKQFK

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:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • 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: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: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:0000287 Binding to a magnesium (Mg) ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
12 331 FunFam G3DSA:3.30.930.10:FF:000003 Phenylalanine--tRNA ligase alpha subunit
111 325 CDD cd00496 PheRS_alpha_core
18 103 SUPERFAMILY SSF46589 tRNA-binding arm
18 103 InterPro IPR010978 Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm
96 330 Pfam PF01409 tRNA synthetases class II core domain (F)
96 330 InterPro IPR002319 Phenylalanyl-tRNA synthetase
42 331 NCBIfam TIGR00468 phenylalanine--tRNA ligase subunit alpha
42 331 InterPro IPR004529 Phenylalanyl-tRNA synthetase, class IIc, alpha subunit
96 331 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
96 331 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
65 85 Coils Coil Coil
12 331 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
12 331 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
120 321 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile.
120 321 InterPro IPR006195 Aminoacyl-tRNA synthetase, class II
24 91 Pfam PF02912 Aminoacyl tRNA synthetase class II, N-terminal domain
24 91 InterPro IPR004188 Phenylalanine-tRNA ligase, class II, N-terminal
12 330 Hamap MF_00281 Phenylalanine--tRNA ligase alpha subunit [pheS].
12 330 InterPro IPR022911 Phenylalanine-tRNA ligase alpha chain 1, bacterial
327 331 Coils Coil Coil
97 331 PANTHER PTHR11538 PHENYLALANYL-TRNA SYNTHETASE

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.595
Likely same site as P2Rank 1 0.7 Å 34 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.933
Likely same site as FPocket 1 0.7 Å 34 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.251
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.052
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.037
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.032
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:252-252
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GU78
AlphaFold DB full sequence Viewing
ColabFold KP13_04673
ColabFold full sequence Loaded

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
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 9 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2NL PDB via homolog 291.7 Da · LogP 2.60 · TPSA 63.2 Open detail RCSB PDB
2NM PDB via homolog Detail RCSB PDB
2U9 PDB via homolog Detail RCSB PDB
GAX PDB via homolog Detail RCSB PDB
H2L PDB via homolog Detail RCSB PDB

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 RCSB PDB Q9I0A3 291.7 Da LogP 2.60 TPSA 63.2 ✓ Ro5 ✓ Clean CNC(=O)COc1cccc(c1)Nc2cc(ccn2)Cl
2NM RCSB PDB Q9I0A3 242.2 Da LogP 3.10 TPSA 37.9 ✓ Ro5 ✓ Clean COc1cccc(c1)c2cc([nH]n2)C(F)(F)F
2U9 RCSB PDB 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 RCSB PDB 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 RCSB PDB 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 RCSB PDB 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 RCSB PDB P08312 215.3 Da LogP 3.67 TPSA 12.0 ✓ Ro5 ✓ Clean c1ccc(cc1)CNCCC2=CCCCC2
VB3 RCSB PDB 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.