Protein target profile

VK055_1836

asparagine synthase

Genome: KpATCC43816 Gene: AIK80449.1 asnB 3D evidence: AlphaFold DB model + ColabFold model Metabolism 3 reactions UniProt A0A0H3GQ75
Length 554
Pocket druggability 0.995
Metabolic reactions 3
Chokepoint No
Direct ligand evidence 0 62 total records
Functional annotation 1 EC 4 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 (%)
37.5 Lower values reduce human off-target concern.
Human E-value
1.28e-102
Gut microbiome similarity
8.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
30.839 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.22 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 0.995
Structure A0A0H3GQ75
Pocket Pocket 1
P2Rank 0.973
Structure A0A0H3GQ75
Pocket Pocket 1
ColabFold model
FPocket 0.995 · Pocket 1
P2Rank 0.983 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 396 / 4744 genomes with a hit
Prevalence 8.3%

Cross-references

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

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: more central than 92.4% of genes in this genome.

Relative network centrality 92.4% more central than 92.4% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reactions

3 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MCSIFGVLDIKTDAGELRKKALELSRLMRHRGPDWSGVYASDKAILAHERLSIVDVNAGAQPLYNAEKTHALAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQGMFAFALYDSEKDAYLIGRDHIGIIPLYMGHDEHGNFYVASEMKALVPVCRTIKEFPAGSYLWSKDGEIRQYYQRDWFDYDAVKDNVTDKNELRQALEESVKSHLMSDVPYGVLLSGGLDSSVISAITKKFAARRVEDQERSEAWWPQLHSFAVGLEGSPDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHKAPNAKELHEETVRKLQALHMFDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFESYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAKQISDQQLETASFRFPYNTPTSKEGYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKTMNDPSGRAVGVHQSAYK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0006529 OBSOLETE. The chemical reactions and pathways resulting in the formation of asparagine, 2-amino-3-carbamoylpropanoic acid.
  • GO:0004066 Catalysis of the reaction: ATP + L-aspartate + L-glutamine = AMP + diphosphate + L-asparagine + L-glutamate.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
2 193 CDD cd00712 AsnB
2 193 InterPro IPR033738 Asparagine synthase, N-terminal domain
194 514 FunFam G3DSA:3.40.50.620:FF:000031 Asparagine synthase B
194 514 Gene3D G3DSA:3.40.50.620 HUPs
194 514 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
210 479 SUPERFAMILY SSF52402 Adenine nucleotide alpha hydrolases-like
2 193 FunFam G3DSA:3.60.20.10:FF:000037 Asparagine synthetase B
48 166 Pfam PF13537 Glutamine amidotransferase domain
48 166 InterPro IPR017932 Glutamine amidotransferase type 2 domain
2 373 NCBIfam TIGR01536 asparagine synthase (glutamine-hydrolyzing)
2 373 InterPro IPR006426 Asparagine synthase, glutamine-hydrolyzing
1 368 PIRSF PIRSF001589 Asn_synthetase_glu-h
1 368 InterPro IPR006426 Asparagine synthase, glutamine-hydrolyzing
361 507 PIRSF PIRSF001589 Asn_synthetase_glu-h
361 507 InterPro IPR006426 Asparagine synthase, glutamine-hydrolyzing
2 193 Gene3D G3DSA:3.60.20.10 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
2 193 InterPro IPR029055 Nucleophile aminohydrolases, N-terminal
1 196 SUPERFAMILY SSF56235 N-terminal nucleophile aminohydrolases (Ntn hydrolases)
1 196 InterPro IPR029055 Nucleophile aminohydrolases, N-terminal
213 456 CDD cd01991 Asn_Synthase_B_C
213 456 InterPro IPR001962 Asparagine synthase
211 366 Pfam PF00733 Asparagine synthase
211 366 InterPro IPR001962 Asparagine synthase
2 186 ProSiteProfiles PS51278 Glutamine amidotransferase type 2 domain profile.
2 186 InterPro IPR017932 Glutamine amidotransferase type 2 domain
1 554 PANTHER PTHR11772 ASPARAGINE SYNTHETASE

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
0.995
Likely same site as P2Rank 1 4.5 Å 41 shared residues 85% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #28
0.271
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Surrounding area
Site 3 FPocket #2
0.268
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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
0.973
Likely same site as FPocket 1 4.5 Å 41 shared residues 85% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.106
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Surrounding area
Site 3 P2Rank #3
0.099
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Surrounding area
Site 4 P2Rank #4
0.088
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Surrounding area
Site 5 P2Rank #5
0.05
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Surrounding area
Residue sets
UniProt: Active site:2-2 For GATase activity
UniProt: Binding site:233-233
UniProt: Binding site:273-273
UniProt: Binding site:347-348
UniProt: Binding site:99-99
UniProt: Site:349-349 Important for beta-aspartyl-AMP intermediate formation
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_A0A0H3GQ75
AlphaFold DB full sequence Viewing
ColabFold VK055_1836
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.

62 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 12 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 4 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
APC PDB via homolog 505.2 Da · LogP -1.52 · TPSA 269.9 Open detail RCSB PDB
CMA PDB via homolog Detail RCSB PDB
IOT PDB via homolog Detail RCSB PDB
IUM PDB via homolog Detail RCSB PDB
ONL 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
APC RCSB PDB P0DJQ7 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)…
CMA RCSB PDB P0DJQ7 246.3 Da LogP -1.23 TPSA 148.5 1 viol. ✓ Clean C(C[C@@H](C(=O)O)NCCC(=O)O)CNC(=N)N
IOT RCSB PDB P0DJQ7 561.4 Da LogP -3.01 TPSA 303.4 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
IUM RCSB PDB P22106 270.0 Da LogP -2.38 TPSA 46.1 ✓ Ro5 ✓ Clean [O-][U+4][O-]
ONL RCSB PDB P08243 145.2 Da LogP -0.23 TPSA 80.4 ✓ Ro5 ✓ Clean CC(=O)CC[C@@H](C(=O)O)N
PCX RCSB PDB P0DJQ7 228.3 Da LogP -1.06 TPSA 119.5 ✓ Ro5 ✓ Clean [H]/N=C(/N)\NCCC[C@@H](C(=O)O)N1CCC1=O
POP RCSB PDB P0DJQ7 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
SSC RCSB PDB Q9XB61 173.2 Da LogP -0.33 TPSA 86.6 ✓ Ro5 ✓ Clean C1C[C@H](N[C@@H]1CC(=O)O)C(=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.