Protein target profile

HT085_RS00335

tyrosine--tRNA ligase

Genome: NZ_AP023069.1 Gene: TUM19854C_00560 NCTC11421_02832 tyrS 3D evidence: AlphaFold DB model UniProt A0A1D3GBP6
Length 431
Direct ligand evidence 0 65 total records
Functional annotation 1 EC 6 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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
Gut microbiome off-target
Hit

Essentiality

Essential (DEG)
Y

Localization

Localization
Cytoplasmic

Binding-site evidence

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 Medium
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MSVIQDLQSRGLIAQTTDIEALDALLNEQKIALYCGFDPTADSLHIGHLLPVLALRRFQQAGHTPIALVGGATGMIGDPSFKAAERSLNSAETVAGWVGSIRSQLTPFLSFEGGNAAIMANNADWFGSMNCLDFLRDIGKHFSVNAMLNKESVKQRIDRDGAGISFTEFAYSLLQGYDFAELNKRHGAVLEIGGSDQWGNITAGIDLTRRLNQKQVFGLTLPLVTKSDGTKFGKTEGGAVWLNAKKTSPYQFYQFWLKVADADVYKFLKYFTFLSIEEIGVIEAKDKASGSKPEAQRILAEEMTRLIHGEEALAAAQRISESLFAEDQSRLTESDFEQLALDGLPAFEVSDGINAVEALVKTGLAASNKEARGFVNAKAVLLNGKPAEANNPNHAAERPDDAYLLIGEYKRFGKYTILRRGKRNHALLVWK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0004831 Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H+.
  • GO:0006437 The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-tRNA synthetase. The tyrosyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tyrosine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0042803 Binding to an identical protein to form a homodimer.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
359 388 CDD cd00165 S4
1 430 Hamap MF_02006 Tyrosine--tRNA ligase [tyrS].
1 430 InterPro IPR024107 Tyrosine-tRNA ligase, bacterial-type, type 1
224 327 FunFam G3DSA:1.10.240.10:FF:000001 Tyrosine--tRNA ligase
39 49 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
39 49 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
324 430 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif
1 223 Gene3D G3DSA:3.40.50.620 HUPs
1 223 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
2 324 SUPERFAMILY SSF52374 Nucleotidylyl transferase
2 429 PANTHER PTHR11766 TYROSYL-TRNA SYNTHETASE
2 429 InterPro IPR024088 Tyrosine-tRNA ligase, bacterial-type
331 431 FunFam G3DSA:3.10.290.10:FF:000027 Tyrosine--tRNA ligase
4 430 NCBIfam TIGR00234 tyrosine--tRNA ligase
4 430 InterPro IPR002307 Tyrosine-tRNA ligase
224 330 Gene3D G3DSA:1.10.240.10 -
331 431 Gene3D G3DSA:3.10.290.10 -
331 431 InterPro IPR036986 RNA-binding S4 domain superfamily
1 223 FunFam G3DSA:3.40.50.620:FF:000008 Tyrosine--tRNA ligase
28 324 Pfam PF00579 tRNA synthetases class I (W and Y)
28 324 InterPro IPR002305 Aminoacyl-tRNA synthetase, class Ic
31 306 CDD cd00805 TyrRS_core
31 306 InterPro IPR002307 Tyrosine-tRNA ligase
353 422 ProSiteProfiles PS50889 S4 RNA-binding domain profile.
217 229 PRINTS PR01040 Tyrosyl-tRNA synthetase signature
217 229 InterPro IPR002307 Tyrosine-tRNA ligase
184 206 PRINTS PR01040 Tyrosyl-tRNA synthetase signature
184 206 InterPro IPR002307 Tyrosine-tRNA ligase
43 65 PRINTS PR01040 Tyrosyl-tRNA synthetase signature
43 65 InterPro IPR002307 Tyrosine-tRNA ligase
163 178 PRINTS PR01040 Tyrosyl-tRNA synthetase signature
163 178 InterPro IPR002307 Tyrosine-tRNA ligase

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.

Loading 3D structure...

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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 #4
0.535
Likely same site as P2Rank 2 3.4 Å 8 shared residues 73% of smaller site
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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
0.891
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Surrounding area
Site 2 P2Rank #2
0.207
Likely same site as FPocket 4 3.4 Å 8 shared residues 73% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.019
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Surrounding area
Site 4 P2Rank #4
0.015
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Surrounding area
Site 5 P2Rank #5
0.012
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Surrounding area
All structural evidence 0 experimental · 1 predicted

Structural evidence

0 + 1

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 HT085_RS00335
AlphaFold DB full sequence Viewing

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.

65 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 15 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 7 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AZY PDB via homolog 222.2 Da · LogP 1.29 · TPSA 132.3 Open detail RCSB PDB
IYR PDB via homolog Detail RCSB PDB
TYE PDB via homolog Detail RCSB PDB
TYS PDB via homolog Detail RCSB PDB
Y3U 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
AZY RCSB PDB P0AGJ9 222.2 Da LogP 1.29 TPSA 132.3 ✓ Ro5 Alert c1cc(c(cc1C[C@@H](C(=O)O)N)N=[N+]=[N-])O
IYR RCSB PDB P0AGJ9 307.1 Da LogP 0.95 TPSA 83.5 ✓ Ro5 ✓ Clean c1cc(c(cc1C[C@@H](C(=O)O)N)I)O
TYE RCSB PDB P83453 167.2 Da LogP 0.25 TPSA 66.5 ✓ Ro5 ✓ Clean c1cc(ccc1C[C@@H](CO)N)O
TYS RCSB PDB P0AGJ9 261.3 Da LogP -0.18 TPSA 126.9 ✓ Ro5 ✓ Clean c1cc(ccc1C[C@@H](C(=O)O)N)OS(=O)(=O)O
Y3U RCSB PDB P0AGJ9 500.5 Da LogP -3.18 TPSA 212.4 2 viol. ✓ Clean CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
YSA RCSB PDB P0AGJ9 509.5 Da LogP -2.32 TPSA 238.0 3 viol. ✓ Clean c1cc(ccc1C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@H](…
YSC RCSB PDB P0AGJ9 485.5 Da LogP -2.90 TPSA 229.3 2 viol. ✓ Clean c1cc(ccc1C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@H](…
YSU RCSB PDB P0AGJ9 486.5 Da LogP -3.19 TPSA 223.3 2 viol. ✓ Clean c1cc(ccc1C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@H](…

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.