Protein target profile

VK055_3227

argininosuccinate lyase

Genome: KpATCC43816 Gene: AIK81788.1 argH 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GGE5
Length 457
Pocket druggability 0.592
Metabolic reactions 2
Chokepoint Yes
Direct ligand evidence 0 57 total records
Functional annotation 1 EC 4 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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 (%)
70.0 Lower values reduce human off-target concern.
Human E-value
9.84e-18
Gut microbiome similarity
5.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
73.742 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
97.4 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 0.592
Structure A0A0H3GGE5
Pocket Pocket 6
P2Rank 0.499
Structure A0A0H3GGE5
Pocket Pocket 1
ColabFold model
FPocket 0.567 · Pocket 13
P2Rank 0.323 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 245 / 4744 genomes with a hit
Prevalence 5.2%

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

Attractive metabolic target: catalyzes a consuming chokepoint reaction in Alanine, aspartate and glutamate metabolism, no isoenzyme backup detected, more central than 98.6% of genes in this genome.

Relative network centrality 98.6% more central than 98.6% of genes in this genome
Chokepoint Chokepoint gene
Catalyzed reactions

2 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.

MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLSAAEQQQLEEALNVLLEEVRANPQQILASDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLWCKDTVVELLSANRQLQSALVETAQQNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDESRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLSDAAIGMVHLSRFAEDLIFFNSGEANFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQGALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCAEAAQQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIAQGKPLEALTLADLQKFSPVIADDVYPILSLQSCLEKRAAKGGVSPQQVAQAINEAKARLS

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:0042450 OBSOLETE. The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound ornithine.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0004056 Catalysis of the reaction: N-(L-arginino)succinate = fumarate + L-arginine.
  • 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.

37 records
Show feature table
Start End DB Term Name
108 370 FunFam G3DSA:1.20.200.10:FF:000006 Argininosuccinate lyase
6 301 Pfam PF00206 Lyase
6 301 InterPro IPR022761 Fumarate lyase, N-terminal
364 431 Pfam PF14698 Argininosuccinate lyase C-terminal
364 431 InterPro IPR029419 Argininosuccinate lyase, C-terminal
276 285 ProSitePatterns PS00163 Fumarate lyases signature.
276 285 InterPro IPR020557 Fumarate lyase, conserved site
103 121 PRINTS PR00149 Fumarate lyase superfamily signature
103 121 InterPro IPR000362 Fumarate lyase family
232 259 PRINTS PR00149 Fumarate lyase superfamily signature
232 259 InterPro IPR000362 Fumarate lyase family
148 166 PRINTS PR00149 Fumarate lyase superfamily signature
148 166 InterPro IPR000362 Fumarate lyase family
276 292 PRINTS PR00149 Fumarate lyase superfamily signature
276 292 InterPro IPR000362 Fumarate lyase family
2 454 Hamap MF_00006 Argininosuccinate lyase [argH].
2 454 InterPro IPR009049 Argininosuccinate lyase
3 456 SUPERFAMILY SSF48557 L-aspartase-like
3 456 InterPro IPR008948 L-Aspartase-like
2 456 PANTHER PTHR43814 ARGININOSUCCINATE LYASE
2 456 InterPro IPR009049 Argininosuccinate lyase
3 456 NCBIfam TIGR00838 argininosuccinate lyase
3 456 InterPro IPR009049 Argininosuccinate lyase
143 163 PRINTS PR00145 Argininosuccinate lyase family signature
232 256 PRINTS PR00145 Argininosuccinate lyase family signature
102 124 PRINTS PR00145 Argininosuccinate lyase family signature
311 330 PRINTS PR00145 Argininosuccinate lyase family signature
194 210 PRINTS PR00145 Argininosuccinate lyase family signature
276 292 PRINTS PR00145 Argininosuccinate lyase family signature
1 107 FunFam G3DSA:1.10.275.10:FF:000004 Argininosuccinate lyase
1 107 Gene3D G3DSA:1.10.275.10 -
1 107 InterPro IPR024083 Fumarase/histidase, N-terminal
108 445 Gene3D G3DSA:1.20.200.10 Fumarase/aspartase (Central domain)
363 433 Gene3D G3DSA:1.10.40.30 -
22 456 CDD cd01359 Argininosuccinate_lyase
22 456 InterPro IPR009049 Argininosuccinate lyase
361 433 FunFam G3DSA:1.10.40.30:FF:000001 Argininosuccinate lyase

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 #6
0.592
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Surrounding area
Site 2 FPocket #2
0.342
Likely same site as P2Rank 5 3.5 Å 7 shared residues 100% of smaller site
Unusual size
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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
0.499
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Surrounding area
Site 2 P2Rank #2
0.294
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Surrounding area
Site 3 P2Rank #3
0.106
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Surrounding area
Site 4 P2Rank #4
0.028
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Surrounding area
Site 5 P2Rank #5
0.017
Likely same site as FPocket 2 3.5 Å 7 shared residues 100% of smaller site
Show in viewer
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_A0A0H3GGE5
AlphaFold DB full sequence Viewing
ColabFold VK055_3227
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
DTT PDB via homolog 154.3 Da · LogP -0.43 · TPSA 40.5 Open detail RCSB PDB
EKN PDB via homolog Detail RCSB PDB
EKQ PDB via homolog Detail RCSB PDB
FUM PDB via homolog Detail RCSB PDB
LMR 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
DTT RCSB PDB Q88N37 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
EKN RCSB PDB Q11KV9 176.2 Da LogP -1.54 TPSA 112.7 ✓ Ro5 ✓ Clean C(CN[C@@H](CC(=O)O)C(=O)O)N
EKQ RCSB PDB Q11KV9 292.2 Da LogP -1.98 TPSA 173.3 1 viol. ✓ Clean C(CN[C@@H](CC(=O)O)C(=O)O)N[C@@H](CC(=O)O)C(=O)O
FUM RCSB PDB Q11KV9 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\C(=O)O
LMR RCSB PDB Q65UJ3 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)O)C(=O)O
OXL RCSB PDB Q7A0G9 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
SIN RCSB PDB Q11KV9 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=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.