KpKP13 Protein target profile

aspartyl-tRNA synthetase

Accession: KP13_31936

Gene: aspS AHE43852.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H058
Length 595
Pocket druggability (P2Rank · AlphaFold DB model) 0.903
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 9 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
Human identity (%)
62.963 Lower values reduce human off-target concern.
Human E-value
1.23e-06
Gut microbiome similarity
19.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
95.64 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.903
Structure A0A0H3H058
Pocket Pocket 1
Druggability (FPocket) 0.348
Structure A0A0H3H058
Pocket Pocket 1
ColabFold model
P2Rank 0.905 · Pocket 1
FPocket 0.579 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 907 / 4744 genomes with a hit
Prevalence 19.1%

Sequence

Primary amino-acid sequence viewer.

MRTEYCGQLRQSHVGQQVTLCGWVNRRRDLGSLIFIDMRDREGIVQVFFDPDRADALKLASELRNEFCIQVTGTVRAREEKNINADMATGAIEVLASDLTIINRSESLPLDSNHVNTEEARLKYRYLDLRRPEMAQRLKTRAKITSFVRRFMDDHGFLDIETPMLTKATPEGARDYLVPSRVHKGKFYALPQSPQLFKQLLMMSGFDRYYQIVKCFRDEDLRADRQPEFTQIDVETSFMTAPQVREIMEAMVRQLWLEVKGVDLGEFPIMTFAEAERRYGSDKPDLRNPMELVDVADLLKSVEFAVFAGPANDPKGRVAALRVPGGASLTRKLIDEYGNFVKIYGAKGLAYIKVTERAKGMDGINSPVAKFLTAEIVEAILDRTGAQDGDMIFFGADNKKVVADALGALRLKLGKDLSLTDESKWAPLWVIDFPMFEDDGEGGLTAMHHPFTSPKDMTADELKAAPEEAVANAYDMVINGYEVGGGSVRIHRGEMQQTVFGILGINEQEQREKFGFLLDALKYGTPPHAGLAFGLDRLTMLLTGTDNIRDVIAFPKTTAAACLMTEAPSFANPAALGELGIQVVEKEAKASLENK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
Cytoplasmic

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:0003676 Binding to a nucleic acid.
  • GO:0016874 Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.
  • 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: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:0004815 Catalysis of the reaction: ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp).
  • GO:0006422 The process of coupling aspartate to aspartyl-tRNA, catalyzed by aspartyl-tRNA synthetase. The aspartyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an aspartic acid accetping tRNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

39 records
Show feature table
Start End DB Term Name
18 102 Pfam PF01336 OB-fold nucleic acid binding domain
18 102 InterPro IPR004365 OB-fold nucleic acid binding domain, AA-tRNA synthetase-type
190 202 PRINTS PR01042 Aspartyl-tRNA synthetase signature
190 202 InterPro IPR002312 Aspartyl/Asparaginyl-tRNA synthetase, class IIb
518 532 PRINTS PR01042 Aspartyl-tRNA synthetase signature
518 532 InterPro IPR002312 Aspartyl/Asparaginyl-tRNA synthetase, class IIb
207 220 PRINTS PR01042 Aspartyl-tRNA synthetase signature
207 220 InterPro IPR002312 Aspartyl/Asparaginyl-tRNA synthetase, class IIb
474 490 PRINTS PR01042 Aspartyl-tRNA synthetase signature
474 490 InterPro IPR002312 Aspartyl/Asparaginyl-tRNA synthetase, class IIb
1 584 Hamap MF_00044 Aspartate--tRNA(Asp/Asn) ligase [aspS].
1 584 InterPro IPR004524 Aspartate-tRNA ligase, type 1
271 420 Gene3D G3DSA:3.30.1360.30 -
271 420 InterPro IPR004115 GAD-like domain superfamily
108 584 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
108 584 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
307 406 Pfam PF02938 GAD domain
307 406 InterPro IPR029351 GAD domain
1 106 FunFam G3DSA:2.40.50.140:FF:000080 Aspartate--tRNA ligase
1 585 NCBIfam TIGR00459 aspartate--tRNA ligase
1 585 InterPro IPR004524 Aspartate-tRNA ligase, type 1
1 105 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
1 105 InterPro IPR012340 Nucleic acid-binding, OB-fold
4 560 PANTHER PTHR22594 ASPARTYL/LYSYL-TRNA SYNTHETASE
1 106 Gene3D G3DSA:2.40.50.140 -
1 106 InterPro IPR012340 Nucleic acid-binding, OB-fold
271 420 FunFam G3DSA:3.30.1360.30:FF:000001 Aspartate--tRNA ligase
118 558 Pfam PF00152 tRNA synthetases class II (D, K and N)
118 558 InterPro IPR004364 Aminoacyl-tRNA synthetase, class II (D/K/N)
138 558 CDD cd00777 AspRS_core
138 558 InterPro IPR047090 Aspartate-tRNA ligase, type 1, core domain
118 579 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
118 579 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
138 555 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile.
138 555 InterPro IPR006195 Aminoacyl-tRNA synthetase, class II
288 419 SUPERFAMILY SSF55261 GAD domain-like
288 419 InterPro IPR004115 GAD-like domain superfamily
2 134 CDD cd04317 EcAspRS_like_N
2 134 InterPro IPR047089 Aspartate-tRNA ligase, type 1, anticodon recognition 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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.903
Likely same site as FPocket 1 5.6 Å 14 shared residues 82% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.17
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Surrounding area
Pocket 3 P2Rank #3
0.136
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Surrounding area
Pocket 4 P2Rank #4
0.057
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Surrounding area
Pocket 5 P2Rank #5
0.033
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.348
Likely same site as P2Rank 1 5.6 Å 14 shared residues 82% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:171-171
UniProt: Binding site:217-217
UniProt: Binding site:217-219
UniProt: Binding site:226-226
UniProt: Binding site:448-448
UniProt: Binding site:482-482
UniProt: Binding site:489-489
UniProt: Binding site:534-537
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_A0A0H3H058
AlphaFold DB full sequence Viewing
ColabFold KP13_31936
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.

55 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 2 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3SY PDB via homolog 136.1 Da · LogP -2.06 · TPSA 80.9 Open detail RCSB PDB
AMO PDB via homolog Detail RCSB PDB
BUA PDB via homolog Detail RCSB PDB
DSZ ChEMBL via homolog · pchembl 10.28 (~0.1 nM) Detail ChEMBL
CHEMBL4203761 ChEMBL via homolog · pchembl 7.60 (~25.1 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
3SY RCSB PDB A0QWN3 136.1 Da LogP -2.06 TPSA 80.9 ✓ Ro5 ✓ Clean C(C(CO)(CO)CO)O
AMO RCSB PDB P21889 462.3 Da LogP -2.51 TPSA 255.5 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BUA RCSB PDB P56459 88.1 Da LogP 0.87 TPSA 37.3 ✓ Ro5 ✓ Clean CCCC(=O)O

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.

Cross-references

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