Protein target profile

KP13_04176

Asparaginyl-tRNA synthetase

Genome: KpKP13 Gene: asnS AHE45407.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A377WK68
Length 441
Pocket druggability 0.973
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 8 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 (%)
57.143 Lower values reduce human off-target concern.
Human E-value
7.69e-11
Gut microbiome similarity
60.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
95.465 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
96.17 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 0.973
Structure A0A377WK68
Pocket Pocket 1
P2Rank 0.905
Structure A0A377WK68
Pocket Pocket 1
ColabFold model
FPocket 0.971 · Pocket 2
P2Rank 0.878 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 2853 / 4744 genomes with a hit
Prevalence 60.1%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MRTRRDSKAGFSFLAVYDGSCFDPVQAVINNSLPNYNQEVLRLTTGCSVIVTGKVVASQGQGQSFEIQATSVEVTGWVEDPDTYPMAAKRHSIEYLREVAHLRPRTNLIGAVARVRHTLAQALHRFFNEQGFFWVSTPLITASDTEGAGEMFRVSTLDLENLPRNDQGKVDFDKDFFGKESFLTVSGQLNGETYACALSKIYTFGPTFRAENSNTSRHLAEFWMLEPEVAFANLNDVAGLAEAMLKYVFKAVLEERADDMQFFAERVDKDAIDRLQRFITADFAQVDYTDAVTILENCGKQFENPVYWGVDLSSEHERYLAEEHFKAPVVVKNYPKDIKAFYMRLNEDGKTVAAMDVLAPGIGEIIGGSQREERLDVLDARMAEMGLNKEDYWWYRDLRRYGTVPHSGFGLGFERLIAYVTGVQNVRDVIPFPRTPRNATF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0004816 Catalysis of the reaction: L-asparagine + ATP + tRNA(Asn) = AMP + Asn-tRNA(Asn) + diphosphate + 2 H+.
  • GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • GO:0003676 Binding to a nucleic acid.
  • 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:0006421 The process of coupling asparagine to asparaginyl-tRNA, catalyzed by asparaginyl-tRNA synthetase. The asparaginyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an asparagine-accetping tRNA.
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
94 435 Pfam PF00152 tRNA synthetases class II (D, K and N)
94 435 InterPro IPR004364 Aminoacyl-tRNA synthetase, class II (D/K/N)
22 441 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 80 Gene3D G3DSA:2.40.50.140 -
1 80 InterPro IPR012340 Nucleic acid-binding, OB-fold
1 441 Hamap MF_00534 Asparagine--tRNA ligase [asnS].
1 441 InterPro IPR004522 Asparagine-tRNA ligase
90 437 CDD cd00776 AsxRS_core
4 74 Pfam PF01336 OB-fold nucleic acid binding domain
4 74 InterPro IPR004365 OB-fold nucleic acid binding domain, AA-tRNA synthetase-type
17 21 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
85 440 FunFam G3DSA:3.30.930.10:FF:000016 Asparagine--tRNA ligase
1 21 Phobius SIGNAL_PEPTIDE Signal peptide region
85 440 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
85 440 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
2 77 CDD cd04318 EcAsnRS_like_N
114 431 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile.
114 431 InterPro IPR006195 Aminoacyl-tRNA synthetase, class II
2 441 NCBIfam TIGR00457 asparagine--tRNA ligase
2 441 InterPro IPR004522 Asparagine-tRNA ligase
2 76 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
2 76 InterPro IPR012340 Nucleic acid-binding, OB-fold
9 16 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
74 440 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
74 440 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
2 438 PANTHER PTHR22594 ASPARTYL/LYSYL-TRNA SYNTHETASE
396 410 PRINTS PR01042 Aspartyl-tRNA synthetase signature
396 410 InterPro IPR002312 Aspartyl/Asparaginyl-tRNA synthetase, class IIb
183 195 PRINTS PR01042 Aspartyl-tRNA synthetase signature
183 195 InterPro IPR002312 Aspartyl/Asparaginyl-tRNA synthetase, class IIb
199 212 PRINTS PR01042 Aspartyl-tRNA synthetase signature
199 212 InterPro IPR002312 Aspartyl/Asparaginyl-tRNA synthetase, class IIb
356 372 PRINTS PR01042 Aspartyl-tRNA synthetase signature
356 372 InterPro IPR002312 Aspartyl/Asparaginyl-tRNA synthetase, class IIb

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
0.973
Likely same site as P2Rank 3 2.9 Å 9 shared residues 90% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #16
0.471
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Surrounding area
Site 3 FPocket #3
0.298
Likely same site as P2Rank 1 1.6 Å 25 shared residues 93% of smaller site
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
0.905
Likely same site as FPocket 3 1.6 Å 25 shared residues 93% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.114
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Surrounding area
Site 3 P2Rank #3
0.085
Likely same site as FPocket 1 2.9 Å 9 shared residues 90% of smaller site
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.031
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Surrounding area
Site 5 P2Rank #5
0.029
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Surrounding area
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_A0A377WK68
AlphaFold DB full sequence Viewing
ColabFold KP13_04176
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 ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
4AD PDB via homolog 462.3 Da · LogP -3.83 · TPSA 262.9 Open detail RCSB PDB
ACP PDB via homolog Detail RCSB PDB
AMO PDB via homolog Detail RCSB PDB
B4P PDB via homolog Detail RCSB PDB
NSS 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
4AD RCSB PDB C4LWW8 462.3 Da LogP -3.83 TPSA 262.9 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ACP RCSB PDB P0A8N5 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AMO RCSB PDB Q52428 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)…
B4P RCSB PDB P0A8N5 836.4 Da LogP -2.45 TPSA 434.0 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
NSS RCSB PDB O57980 461.4 Da LogP -5.11 TPSA 262.5 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.