Protein target profile

KP13_04672

Phenylalanyl-tRNA synthetase beta chain

Genome: KpKP13 Gene: AHE44068.1 pheT 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GUX6
Length 795
Pocket druggability 0.821
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 7 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 (%)
22.716 Lower values reduce human off-target concern.
Human E-value
5.5e-10
Gut microbiome similarity
3.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
92.453 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
95.58 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 0.821
Structure A0A0H3GUX6
Pocket Pocket 1
P2Rank 0.876
Structure A0A0H3GUX6
Pocket Pocket 1
ColabFold model
FPocket 0.566 · Pocket 2
P2Rank 0.799 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 153 / 4744 genomes with a hit
Prevalence 3.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKFSELWLREWVNPAIDSEALSDQITMAGLEVDGVEPVAGSFNGVVVGEVVECGQHPNADKLRVTKVNVGGERLLDIVCGAPNCRQGLKVAVATIGAVLPGDFKIKAAKLRGEPSEGMLCSFSELGISDDHSGIIELPADAPIGTDIREYLKLDDNTIEISVTPNRADCLGIIGVARDVAVLNKAPLNAPEITPVAATIDDVLPIQVDAPQACPRYLGRVVKGINVKAPTPLWMKEKLRRCGIRSIDAVVDVTNYVLLELGQPMHAFDRDRIEGGIVVRMAKEGETLVLLDGSEAKLDSDTLVIADHNKALAMGGIFGGEHSGVNDETQNVLLECAFFSPLSITGRARRHGLHTDASHRYERGVDPALQYKALERATRLLIDLCGGEAGPVIDVTSKENLPTRATITLRRSKLDRLIGHHIADAQVTDILQRLGCEVTVGEGEWQAVAPSWRFDMEIEEDLVEEVARVYGYNNIPDEPVQAGLIMGTHREADLSLKRVKTLLNDKGYQEVITYSFVDPKVQQLIHAGEEALILPSPISSEMSAMRLSLWTGLLGTVVYNQNRQQSRVRIFESGLRFVPDTNAPLGIRQDVMLAGAICGNRYEEHWTLAKETVDFYDLKGDLEAVLDLTGKLADIEFRAEATTALHPGQSAAIYLKGERIGFIGVVHPELERKLDLNGRTLVFELEWNKLADRVVPQARDISRFPANRRDIAVLVAENVAAADVLAECKKVGVNQVVGVNLFDVYRGKGVAEGYKSLAISLILQDTSRTLEEEEIAATVARCVEALKERFQASLRD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • 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:0000287 Binding to a magnesium (Mg) ion.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0009328 An enzyme complex that catalyzes the ligation of phenylalanine to tRNA(Phe), forming L-phenylalanyl-tRNA(Phe).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

53 records
Show feature table
Start End DB Term Name
45 145 Pfam PF01588 Putative tRNA binding domain
45 145 InterPro IPR002547 tRNA-binding domain
1 788 Hamap MF_00283 Phenylalanine--tRNA ligase beta subunit [pheT].
1 788 InterPro IPR004532 Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type
696 794 SUPERFAMILY SSF54991 Anticodon-binding domain of PheRS
696 794 InterPro IPR036690 Ferrodoxin-fold anticodon-binding domain superfamily
401 476 ProSiteProfiles PS51483 B5 domain profile.
401 476 InterPro IPR005147 tRNA synthetase, B5-domain
53 147 CDD cd02796 tRNA_bind_bactPheRS
53 147 InterPro IPR033714 Phenylalanly tRNA synthetase, tRNA-binding-domain
196 397 FunFam G3DSA:3.50.40.10:FF:000001 Phenylalanine--tRNA ligase beta subunit
475 685 Pfam PF17759 Phenylalanyl tRNA synthetase beta chain CLM domain
475 685 InterPro IPR041616 Phenylalanyl tRNA synthetase beta chain, core domain
404 475 SUPERFAMILY SSF46955 Putative DNA-binding domain
404 475 InterPro IPR009061 Putative DNA-binding domain superfamily
701 794 Pfam PF03147 Ferredoxin-fold anticodon binding domain
701 794 InterPro IPR005121 Ferrodoxin-fold anticodon-binding domain
403 471 SMART SM00874 B5_2
403 471 InterPro IPR005147 tRNA synthetase, B5-domain
212 385 SMART SM00873 B3_4_2
212 385 InterPro IPR005146 B3/B4 tRNA-binding domain
401 475 Gene3D G3DSA:3.30.56.10 -
702 795 Gene3D G3DSA:3.30.70.380 -
702 795 InterPro IPR036690 Ferrodoxin-fold anticodon-binding domain superfamily
485 693 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
485 693 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
1 794 NCBIfam TIGR00472 phenylalanine--tRNA ligase subunit beta
1 794 InterPro IPR004532 Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type
702 795 FunFam G3DSA:3.30.70.380:FF:000001 Phenylalanine--tRNA ligase beta subunit
4 686 PANTHER PTHR10947 PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN AND LEUCINE-RICH REPEAT-CONTAINING PROTEIN 47
4 686 InterPro IPR045060 Phenylalanine-tRNA ligase, class IIc, beta subunit
487 692 FunFam G3DSA:3.30.930.10:FF:000022 Phenylalanine--tRNA ligase beta subunit
467 690 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
467 690 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
39 148 ProSiteProfiles PS50886 tRNA-binding domain profile.
39 148 InterPro IPR002547 tRNA-binding domain
7 180 Gene3D G3DSA:3.30.56.10 -
39 154 Gene3D G3DSA:2.40.50.140 -
39 154 InterPro IPR012340 Nucleic acid-binding, OB-fold
197 395 Gene3D G3DSA:3.50.40.10 -
197 395 InterPro IPR020825 Phenylalanyl-tRNA synthetase-like, B3/B4
39 154 FunFam G3DSA:2.40.50.140:FF:000045 Phenylalanine--tRNA ligase beta subunit
35 197 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
35 197 InterPro IPR012340 Nucleic acid-binding, OB-fold
195 396 SUPERFAMILY SSF56037 PheT/TilS domain
701 794 SMART SM00896 FDX_ACB_2
402 475 FunFam G3DSA:3.30.56.10:FF:000002 Phenylalanine--tRNA ligase beta subunit
212 385 Pfam PF03483 B3/4 domain
406 471 Pfam PF03484 tRNA synthetase B5 domain
406 471 InterPro IPR005147 tRNA synthetase, B5-domain
701 794 ProSiteProfiles PS51447 Ferredoxin-fold anticodon binding (FDX-ACB) domain profile.
495 689 CDD cd00769 PheRS_beta_core
495 689 InterPro IPR041616 Phenylalanyl tRNA synthetase beta chain, core domain

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
0.821
Likely same site as P2Rank 5 6.8 Å 6 shared residues 67% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #3
0.475
Likely same site as P2Rank 1 0.8 Å 22 shared residues 96% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 3 FPocket #32
0.232
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Surrounding area
Site 4 FPocket #6
0.227
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.876
Likely same site as FPocket 3 0.8 Å 22 shared residues 96% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.473
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Surrounding area
Site 3 P2Rank #3
0.15
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.098
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.097
Likely same site as FPocket 1 6.8 Å 6 shared residues 67% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:454-454
UniProt: Binding site:460-460
UniProt: Binding site:463-463
UniProt: Binding site:464-464
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_A0A0H3GUX6
AlphaFold DB full sequence Viewing
ColabFold KP13_04672
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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
DAH PDB via homolog 197.2 Da · LogP 0.05 · TPSA 103.8 Open detail RCSB PDB
MTY PDB via homolog Detail RCSB PDB
PUY PDB via homolog Detail RCSB PDB
TAM PDB via homolog Detail RCSB PDB
ZINC53147178 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
DAH RCSB PDB P27002 197.2 Da LogP 0.05 TPSA 103.8 ✓ Ro5 Alert c1cc(c(cc1C[C@@H](C(=O)O)N)O)O
MTY RCSB PDB Q5SGX1 181.2 Da LogP 0.35 TPSA 83.5 ✓ Ro5 ✓ Clean c1cc(cc(c1)O)C[C@@H](C(=O)O)N
PUY RCSB PDB Q5SGX1 471.5 Da LogP -0.79 TPSA 160.9 1 viol. ✓ Clean CN(C)c1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H]…
TAM RCSB PDB Q7MXR4 163.2 Da LogP -1.17 TPSA 86.7 ✓ Ro5 ✓ Clean C(CO)C(CCO)(CCO)N

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.