Protein target profile

HT085_RS00030

leucine--tRNA ligase

Genome: NZ_AP023069.1 Gene: NGK_0009 TUM19854C_00060 E8M63_03515 leuS 3D evidence: Experimental + AlphaFold DB model UniProt B4RNT1 UniProt A0AAX2TSV3
Length 876
Direct ligand evidence 0 92 total records
Functional annotation 1 EC 5 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.

MQEHYQPAAIEPAAQKKWDDARISNVSEDASKPKYYCLSMFPYPSGKLHMGHVRNYTIGDVLSRFKLLNGFNVMQPMGWDAFGMPAENAAMKNNVAPAAWTYDNIEYMKTQLKSLGFAVDWEREVATCKPEYYRWEQWLFTKLFEKGIVYRKNGTVNWDPVDQTVLANEQVIDGRGWRSGALIEKREIPMYYFKITDYAEELLNDLDKLEHWPEQVKTMQRNWIGKSRGMTVRFAVSDDSKQGLEGDYAKFLQVYTTRPDTLMGATYVAVAAEHPLATAAAADKPELQAFIAECKAGSVAEADMATMEKKGVPTGRYVVNPLNGDKLEVWIANYVLWGYGDGAVMAVPAHDERDFEFAAKYNLPKKQVIAVGDNAFDANRWQEWYGDKENGVLVNSGDLDGLDFQTAFDAVAAKLQSQGAGEPKTQYRLRDWGISRQRYWGCPIPIVHCEKCGDVPVPADQLPVVLPENVVPDGMGSPLAKMPEFYETSCPCCGGAAKRETDTMDTFMESSWYFFRYMSPKFSDGMVSAESAKYWGAVDQYIGGIEHAILHLLYARFFTKLMRDEGLVNVDEPFERLLTQGMVVCETYYRENDKGGKDWINPADVELTFDDKGRPVSAVLKADGLPVVISGTEKMSKSKNNGVDPQELINAYGADTARLFMMFAAPPEQSLEWSDSGVEGAHRFLRRLWRTVYEYLKQGGAVKAFAGNQDGLSKELKDLRHKLHSTTAKVSDDYGRRQQFNTAIAAVMELLNQYDKTDTGSEQGRAVAQEVLEAAVRLLWPIVPHICETLWSELNGAKLWEAGWPTVDEAALVKSEIEVMVQVNGKLRGKITVAADASKADLEAAALANEGAVKFMEGKPAKKIIVVPGRLVNIVV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0004823 Catalysis of the reaction: leucine + ATP + tRNA(Leu) = AMP + diphosphate + 2 H+ + Leu-tRNA(Leu).
  • GO:0006429 The process of coupling leucine to leucyl-tRNA, catalyzed by leucyl-tRNA synthetase. The leucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a leucine-accetping 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:0002161 The hydrolysis of an incorrectly aminoacylated tRNA.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

54 records
Show feature table
Start End DB Term Name
583 639 FunFam G3DSA:2.20.28.290:FF:000001 Leucine--tRNA ligase
718 838 Pfam PF08264 Anticodon-binding domain of tRNA ligase
718 838 InterPro IPR013155 Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding
632 673 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
632 673 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
430 586 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
430 586 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
673 794 CDD cd07958 Anticodon_Ia_Leu_BEm
815 876 FunFam G3DSA:3.10.20.590:FF:000001 Leucine--tRNA ligase
241 422 Gene3D G3DSA:3.90.740.10 -
241 422 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
677 876 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
677 876 InterPro IPR009080 Aminoacyl-tRNA synthetase, class Ia, anticodon-binding
585 639 Gene3D G3DSA:2.20.28.290 -
226 427 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain
226 427 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
42 53 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
42 53 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
244 421 FunFam G3DSA:3.90.740.10:FF:000012 Leucine--tRNA ligase
538 560 PRINTS PR00985 Leucyl-tRNA synthetase signature
538 560 InterPro IPR002302 Leucine-tRNA ligase
215 234 PRINTS PR00985 Leucyl-tRNA synthetase signature
215 234 InterPro IPR002302 Leucine-tRNA ligase
499 517 PRINTS PR00985 Leucyl-tRNA synthetase signature
499 517 InterPro IPR002302 Leucine-tRNA ligase
153 169 PRINTS PR00985 Leucyl-tRNA synthetase signature
153 169 InterPro IPR002302 Leucine-tRNA ligase
185 198 PRINTS PR00985 Leucyl-tRNA synthetase signature
185 198 InterPro IPR002302 Leucine-tRNA ligase
127 144 PRINTS PR00985 Leucyl-tRNA synthetase signature
127 144 InterPro IPR002302 Leucine-tRNA ligase
571 581 PRINTS PR00985 Leucyl-tRNA synthetase signature
571 581 InterPro IPR002302 Leucine-tRNA ligase
3 875 PANTHER PTHR43740 LEUCYL-TRNA SYNTHETASE
3 875 InterPro IPR002302 Leucine-tRNA ligase
221 415 Pfam PF13603 Leucyl-tRNA synthetase, Domain 2
221 415 InterPro IPR025709 Leucyl-tRNA synthetase, editing domain
34 228 CDD cd00812 LeuRS_core
39 171 Pfam PF09334 tRNA synthetases class I (M)
39 171 InterPro IPR015413 Methionyl/Leucyl tRNA synthetase
4 876 Hamap MF_00049_B Leucine--tRNA ligase [leuS].
4 876 InterPro IPR002302 Leucine-tRNA ligase
640 814 Gene3D G3DSA:1.10.730.10 -
32 240 Gene3D G3DSA:3.40.50.620 HUPs
32 240 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
5 876 NCBIfam TIGR00396 bacterial-type leucine--tRNA ligase
5 876 InterPro IPR002302 Leucine-tRNA ligase
640 814 FunFam G3DSA:1.10.730.10:FF:000003 Leucine--tRNA ligase
815 876 Gene3D G3DSA:3.10.20.590 -
4 683 SUPERFAMILY SSF52374 Nucleotidylyl transferase
32 254 FunFam G3DSA:3.40.50.620:FF:000003 Leucine--tRNA ligase
370 585 FunFam G3DSA:3.40.50.620:FF:000124 Leucine--tRNA ligase
423 584 Gene3D G3DSA:3.40.50.620 HUPs
423 584 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
All structural evidence 17 experimental · 1 predicted

Structural evidence

17 + 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
PDB 7NU0
X-ray 1.89 Å A
100.0% 1-876
Viewing
PDB 7NTZ
X-ray 2.10 Å A
100.0% 1-876
Loaded
PDB 7NU2
X-ray 2.10 Å A
100.0% 1-876
Loaded
PDB 7YP8
X-ray 2.10 Å A
100.0% 1-876
Loaded
PDB 6Q8A
X-ray 2.11 Å A
100.0% 1-876
Loaded
PDB 7NU8
X-ray 2.11 Å A
100.0% 1-876
Loaded
PDB 7NU9
X-ray 2.17 Å A
100.0% 1-876
Loaded
PDB 7NU4
X-ray 2.18 Å A
100.0% 1-876
Loaded
PDB 7NU6
X-ray 2.20 Å A
100.0% 1-876
Loaded
PDB 7NU3
X-ray 2.27 Å A
100.0% 1-876
Loaded
PDB 7NU7
X-ray 2.31 Å A
100.0% 1-876
Loaded
PDB 7NTY
X-ray 2.39 Å A
100.0% 1-876
Loaded
PDB 7NU1
X-ray 2.51 Å A
100.0% 1-876
Loaded
PDB 7NU5
X-ray 2.58 Å A
100.0% 1-876
Loaded
PDB 7NUC
X-ray 2.77 Å A
100.0% 1-876
Loaded
PDB 7NUB
X-ray 3.02 Å A
100.0% 1-876
Loaded
PDB 7NUA
X-ray 3.09 Å A
100.0% 1-876
Loaded
AlphaFold DB HT085_RS00030
AlphaFold DB 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.

92 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 42 records from similar proteins
Structural ligands 21 1 loaded crystals
Measured bioactivity 21 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2AD PDB via homolog 266.3 Da · LogP -2.01 · TPSA 145.3 Open detail RCSB PDB
84T PDB via homolog Detail RCSB PDB
9YN PDB via homolog Detail RCSB PDB
FGX PDB via homolog Detail RCSB PDB
HQ5 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
2AD RCSB PDB Q7SIE4 266.3 Da LogP -2.01 TPSA 145.3 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
84T RCSB PDB P07813 460.4 Da LogP -1.33 TPSA 215.2 2 viol. ✓ Clean CC(C)[C@H]([C@@H](C(=O)NP(=O)(O)OC[C@@H]1C[C@@H…
9YN RCSB PDB P07813 379.4 Da LogP -1.48 TPSA 174.4 ✓ Ro5 ✓ Clean CC(C)C[C@@H](C(=O)N[C@@H]1[C@@H]([C@H](O[C@H]1n…
FGX RCSB PDB B8ZKS5 655.4 Da LogP 1.43 TPSA 204.5 2 viol. ✓ Clean [B-]12(CCc3c1cc(cc3)[C@@H](c4ccc(cc4)SCC(=O)C)O…
HQ5 RCSB PDB B4RNT1 435.5 Da LogP -2.80 TPSA 209.1 1 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
ILA RCSB PDB P07813 458.5 Da LogP -2.65 TPSA 220.6 2 viol. ✓ Clean CC[C@H](C)[C@@H](C(=O)NS(=O)(=O)NC[C@@H]1[C@H](…
LMS RCSB PDB Q72GM3 346.3 Da LogP -2.75 TPSA 188.7 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
NVA RCSB PDB Q72GM3 117.1 Da LogP 0.20 TPSA 63.3 ✓ Ro5 ✓ Clean CCC[C@@H](C(=O)O)N
OV8 RCSB PDB Q5FAJ3 478.6 Da LogP -2.00 TPSA 204.9 1 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
OVB RCSB PDB Q5FAJ3 609.6 Da LogP 1.11 TPSA 188.1 2 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
OVH RCSB PDB Q5FAJ3 525.6 Da LogP 0.21 TPSA 178.9 2 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
OVK RCSB PDB Q5FAJ3 498.6 Da LogP -1.03 TPSA 191.8 1 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
OVN RCSB PDB Q5FAJ3 521.6 Da LogP -1.14 TPSA 199.1 2 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
OVQ RCSB PDB Q5FAJ3 526.6 Da LogP -0.39 TPSA 191.8 2 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
OVT RCSB PDB Q5FAJ3 553.7 Da LogP 0.33 TPSA 178.9 2 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
OVW RCSB PDB Q5FAJ3 561.7 Da LogP 1.45 TPSA 178.9 2 viol. ✓ Clean CCCCCCCCc1cn(nn1)CCC[C@@H]2CO[C@@H]([C@H]([C@H]…
OVZ RCSB PDB Q5FAJ3 568.7 Da LogP -0.16 TPSA 190.9 2 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
OW2 RCSB PDB Q5FAJ3 611.7 Da LogP -0.45 TPSA 220.0 3 viol. ✓ Clean CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…
OW5 RCSB PDB Q5FAJ3 595.8 Da LogP 1.95 TPSA 178.9 2 viol. ✓ Clean CCCCCc1ccc(cc1)c2cn(nn2)CCC[C@@H]3CO[C@@H]([C@H…
VRT RCSB PDB P07813 365.4 Da LogP -1.73 TPSA 174.4 ✓ Ro5 ✓ Clean CCCC(C(=O)N[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2n…
WMP RCSB PDB B8ZKS5 568.3 Da LogP 0.66 TPSA 193.5 2 viol. ✓ Clean [B-]12(c3cc(ccc3CO1)[C@@H](c4ccccc4)O)O[C@H]5[C…

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.