Protein target profile

KP13_31833

Isoleucyl-tRNA synthetase

Genome: KpKP13 Gene: AHE46413.1 ileS 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRH0
Length 938
Pocket druggability 0.944
Direct ligand evidence 0 87 total records
Functional annotation 1 EC 10 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 (%)
36.66 Lower values reduce human off-target concern.
Human E-value
0.0
Gut microbiome similarity
4.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
92.111 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
93.83 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 0.944
Structure A0A0H3GRH0
Pocket Pocket 36
P2Rank 0.953
Structure A0A0H3GRH0
Pocket Pocket 1
ColabFold model
FPocket 0.809 · Pocket 12
P2Rank 0.912 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 207 / 4744 genomes with a hit
Prevalence 4.4%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSDYKSTLNLPETGFPMRGDLAKREPGMLARWTDDDLYGIIRAAKKGKKTFILHDGPPYANGSIHIGHSVNKILKDIIVKSKGLTGYDSPYVPGWDCHGLPIELKVEQEYGKPGEKFTAAEFRAKCREYAAEQIDGQRKDFIRLGVLGDWSHPYLTMDFKTEANIIRALGKIIGNGHLHKGAKPVHWCVDCRSALAEAEVEYYDKTSPSIDVAFHAVDKAAVLAKFGVADVNGPVSLVIWTTTPWTLPANRAISLSPEFDYALVQVDGQALILAKDLVESVMKRVGATDYTILAAVQGSELELMRFKHPFLDFDVPAILGDHVTLDAGTGAVHTAGGHGPDDYTISQKYGLEIANPVGPDGAYLPGTWPSLDGINVFKANDIIVEMLRERGALLHVEKLQHSYPCCWRHKSPIIFRATPQWFVSMDQKGLRAQSLKEIKGVQWIPDWGQARIESMVANRPDWCISRQRTWGVPMSLFVHKETHELHPRTLELMEEVAKRVEVDGIQAWWDLDSRDILGDDADSYEKVPDTLDVWFDSGSTHSSVVDVRPEFAGHAADMYLEGSDQHRGWFMSSLMISTAMKGKAPYRQVLTHGFTVDGQGRKMSKSIGNTVSPQDVMNKLGADILRLWVASTDYTGEMAVSDEILKRAADSYRRIRNTARFLLANLNGFDPAKDMVKPEEMVVLDRWAVGCAQAAQEDILKAYESYDFHEVVQRLMRFCSIEMGSFYLDIIKDRQYTAKADSVARRSCQTALFHIVEALVRWMAPIMSFTADEIWGYLPGEREKYVFTGEWYEGLFGLADDEAMNDDFWDELLKVRGEVNKVIEQARADKKVGGSLEAAVTLYADADLAAKLNALGDELRFVLLTSGANVADYASASADAQQSELLKGLKVALSKAEGEKCPRCWHYTTDIGKVAEHAEICGRCVSNVAGDGEQRKFA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • GO:0004822 Catalysis of the reaction: L-isoleucine + ATP + tRNA(Ile) = L-isoleucyl-tRNA(Ile) + AMP + diphosphate + 2 H+.
  • GO:0002161 The hydrolysis of an incorrectly aminoacylated tRNA.
  • GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • GO:0000049 Binding to a transfer RNA.
  • GO:0006418 The synthesis of aminoacyl tRNA 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, to be used in ribosome-mediated polypeptide synthesis.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0006428 The process of coupling isoleucine to isoleucyl-tRNA, catalyzed by isoleucyl-tRNA synthetase. The isoleucyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a isoleucine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008270 Binding to a zinc ion (Zn).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

42 records
Show feature table
Start End DB Term Name
2 933 PANTHER PTHR42765 SOLEUCYL-TRNA SYNTHETASE
898 926 Pfam PF06827 Zinc finger found in FPG and IleRS
898 926 InterPro IPR010663 Zinc finger, FPG/IleRS-type
640 820 CDD cd07960 Anticodon_Ia_Ile_BEm
640 820 InterPro IPR033708 Isoleucyl tRNA synthetase type 1, anticodon-binding domain
641 930 FunFam G3DSA:1.10.730.20:FF:000001 Isoleucine--tRNA ligase
204 403 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain
204 403 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
58 69 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
58 69 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
381 638 Gene3D G3DSA:3.40.50.620 HUPs
381 638 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
3 648 SUPERFAMILY SSF52374 Nucleotidylyl transferase
526 539 PRINTS PR00984 Isoleucyl-tRNA synthetase signature
526 539 InterPro IPR002301 Isoleucine-tRNA ligase
51 62 PRINTS PR00984 Isoleucyl-tRNA synthetase signature
51 62 InterPro IPR002301 Isoleucine-tRNA ligase
238 261 PRINTS PR00984 Isoleucyl-tRNA synthetase signature
238 261 InterPro IPR002301 Isoleucine-tRNA ligase
401 416 PRINTS PR00984 Isoleucyl-tRNA synthetase signature
401 416 InterPro IPR002301 Isoleucine-tRNA ligase
561 570 PRINTS PR00984 Isoleucyl-tRNA synthetase signature
561 570 InterPro IPR002301 Isoleucine-tRNA ligase
379 638 FunFam G3DSA:3.40.50.620:FF:000048 Isoleucine--tRNA ligase
685 840 Pfam PF08264 Anticodon-binding domain of tRNA ligase
685 840 InterPro IPR013155 Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding
2 929 Hamap MF_02002 Isoleucine--tRNA ligase [ileS].
2 929 InterPro IPR023585 Isoleucine-tRNA ligase, type 1
49 640 CDD cd00818 IleRS_core
19 216 Gene3D G3DSA:3.40.50.620 HUPs
19 216 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
28 640 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
28 640 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
15 843 NCBIfam TIGR00392 isoleucine--tRNA ligase
15 843 InterPro IPR002301 Isoleucine-tRNA ligase
652 929 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
652 929 InterPro IPR009080 Aminoacyl-tRNA synthetase, class Ia, anticodon-binding
18 214 FunFam G3DSA:3.40.50.620:FF:000042 Isoleucine--tRNA ligase
640 930 Gene3D G3DSA:1.10.730.20 -
217 380 Gene3D G3DSA:3.90.740.10 -
217 380 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
215 375 FunFam G3DSA:3.90.740.10:FF:000002 Isoleucine--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.

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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 #36
0.944
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
0.953
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.754
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.513
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.231
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.113
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:573-573
UniProt: Binding site:617-617
UniProt: Binding site:913-913
UniProt: Binding site:916-916
UniProt: Binding site:933-933
UniProt: Binding site:936-936
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_A0A0H3GRH0
AlphaFold DB full sequence Viewing
ColabFold KP13_31833
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.

87 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 37 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 34 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
GV6 PDB via homolog 460.4 Da · LogP -0.94 · TPSA 218.2 Open detail RCSB PDB
GVU PDB via homolog Detail RCSB PDB
ILA PDB via homolog Detail RCSB PDB
CHEMBL4553017 ChEMBL via homolog · pchembl 8.92 (~1.2 nM) Detail ChEMBL
CHEMBL1163069 ChEMBL via homolog · pchembl 8.72 (~1.9 nM) Detail ChEMBL

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
GV6 RCSB PDB P09436 460.4 Da LogP -0.94 TPSA 218.2 1 viol. ✓ Clean CC[C@H](C)[C@@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([…
GVU RCSB PDB P09436 660.8 Da LogP 6.13 TPSA 176.9 2 viol. ✓ Clean CCCC[C@]1(CC[C@]2(CC[C@@H]([C@H](O2)C/C=C(\C)/C…
ILA RCSB PDB P56690 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](…

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.