Protein target profile

VK055_0407

acetolactate synthase, catabolic

Genome: KpATCC43816 Gene: AIK79033.1 alsS 3D evidence: Experimental + ColabFold model Metabolism 2 reactions UniProt P27696
Length 559
Pocket druggability 0.958
Metabolic reactions 2
Chokepoint Yes
Direct ligand evidence 6 126 total records
Functional annotation 1 EC 9 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 (%)
36.905 Lower values reduce human off-target concern.
Human E-value
1.59e-10
Gut microbiome similarity
1.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.25 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.958
Structure 1OZF
Pocket Pocket 3
P2Rank 0.534
Structure 1OZG
Pocket Pocket 1
ColabFold model
FPocket 0.508 · Pocket 18
P2Rank 0.392 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 90 / 4744 genomes with a hit
Prevalence 1.9%

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 producing chokepoint reaction in Butanoate metabolism, more central than 93.8% of genes in this genome.

Relative network centrality 93.8% more central than 93.8% 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.

MDKQYPVRQWAHGADLVVSQLEAQGVRQVFGIPGAKIDKVFDSLLDSSIRIIPVRHEANAAFMAAAVGRITGKAGVALVTSGPGCSNLITGMATANSEGDPVVALGGAVKRADKAKQVHQSMDTVAMFSPVTKYAVEVTAPDALAEVVSNAFRAAEQGRPGSAFVSLPQDVVDGPVSGKVLPASGAPQMGAAPDDAIDQVAKLIAQAKNPIFLLGLMASQPENSKALRRLLETSHIPVTSTYQAAGAVNQDNFSRFAGRVGLFNNQAGDRLLQLADLVICIGYSPVEYEPAMWNSGNATLVHIDVLPAYEERNYTPDVELVGDIAGTLNKLAQNIDHRLVLSPQAAEILRDRQHQRELLDRRGAQLNQFALHPLRIVRAMQDIVNSDVTLTVDMGSFHIWIARYLYSFRARQVMISNGQQTMGVALPWAIGAWLVNPERKVVSVSGDGGFLQSSMELETAVRLKANVLHLIWVDNGYNMVAIQEEKKYQRLSGVEFGPMDFKAYAESFGAKGFAVESAEALEPTLRAAMDVDGPAVVAIPVDYRDNPLLMGQLHLSQIL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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:0003984 Catalysis of the reaction: H+ + 2 pyruvate = (2S)-2-acetolactate + CO2. Can also convert 2-oxobutanoate and pyruvate to (S)-2-ethyl-2-hydroxy-3-oxobutanoate.
  • GO:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
  • GO:0034077 The chemical reactions and pathways involving butanediol; the biologically relevant isomer is 2,3-butanediol, CH3CH(OH)CH(OH)CH3.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0005948 A dimeric (a large and a small chain) or tetrameric (two large and two small chains) enzyme complex. Catalyzes the formation of acetolactate from pyruvate.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • GO:0009097 OBSOLETE. The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
  • GO:0009099 The chemical reactions and pathways resulting in the formation of valine, 2-amino-3-methylbutanoic acid.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
393 538 Pfam PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
393 538 InterPro IPR011766 Thiamine pyrophosphate enzyme, TPP-binding
191 338 Gene3D G3DSA:3.40.50.1220 -
1 188 Gene3D G3DSA:3.40.50.970 -
341 361 Gene3D G3DSA:1.20.5.740 Single helix bin
13 550 NCBIfam TIGR02418 acetolactate synthase AlsS
13 550 InterPro IPR012782 Acetolactate synthase, catabolic
6 188 FunFam G3DSA:3.40.50.970:FF:000007 Acetolactate synthase
362 559 Gene3D G3DSA:3.40.50.970 -
371 550 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
371 550 InterPro IPR029061 Thiamin diphosphate-binding fold
15 169 CDD cd07035 TPP_PYR_POX_like
12 176 Pfam PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
12 176 InterPro IPR012001 Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain
11 550 PANTHER PTHR18968 THIAMINE PYROPHOSPHATE ENZYMES
11 550 InterPro IPR045229 Thiamine pyrophosphate enzyme
190 360 SUPERFAMILY SSF52467 DHS-like NAD/FAD-binding domain
190 360 InterPro IPR029035 DHS-like NAD/FAD-binding domain superfamily
373 549 CDD cd02010 TPP_ALS
6 180 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
6 180 InterPro IPR029061 Thiamin diphosphate-binding fold
197 331 Pfam PF00205 Thiamine pyrophosphate enzyme, central domain
197 331 InterPro IPR012000 Thiamine pyrophosphate enzyme, central domain
430 449 ProSitePatterns PS00187 Thiamine pyrophosphate enzymes signature.
430 449 InterPro IPR000399 TPP-binding enzyme, conserved site

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 #66
0.848
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Surrounding area
Site 2 FPocket #1
0.843
Likely same site as P2Rank 1 0.7 Å 20 shared residues 100% of smaller site
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Surrounding area
Site 3 FPocket #2
0.508
Likely same site as P2Rank 3 3.7 Å 16 shared residues 94% of smaller site
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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
0.583
Likely same site as FPocket 1 0.7 Å 20 shared residues 100% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.3
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Surrounding area
Site 3 P2Rank #3
0.295
Likely same site as FPocket 2 3.7 Å 16 shared residues 94% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.209
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Surrounding area
Site 5 P2Rank #5
0.118
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Surrounding area
All structural evidence 6 experimental · 1 predicted

Structural evidence

6 + 1

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
PDB 5DX6
X-ray 1.75 Å A,B
100.0% 1-559
Viewing
PDB 1OZH
X-ray 2.00 Å A,B,C,D
100.0% 1-559
Loaded
PDB 5WDG
X-ray 2.12 Å A,B
100.0% 1-559
Loaded
PDB 5D6R
X-ray 2.28 Å B,M
100.0% 1-559
Loaded
PDB 1OZF
X-ray 2.30 Å A,B
100.0% 1-559
Loaded
PDB 1OZG
X-ray 2.30 Å A,B
100.0% 1-559
Loaded
ColabFold VK055_0407
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.

126 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 6 same-protein records
Transferred evidence 70 records from similar proteins
Structural ligands 39 6 loaded crystals
Measured bioactivity 37 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5GY PDB co-crystal 487.4 Da · LogP 0.84 · TPSA 189.2 Open detail RCSB PDB
65S PDB co-crystal Detail RCSB PDB
A4Y PDB co-crystal Detail RCSB PDB
EN0 PDB co-crystal Detail RCSB PDB
HE3 PDB co-crystal Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
5GY RCSB PDB 487.4 Da LogP 0.84 TPSA 189.2 ✓ Ro5 ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@H](CF)O)CCOP(=O)…
65S RCSB PDB 106.1 Da LogP -0.39 TPSA 54.4 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)F
A4Y RCSB PDB 558.4 Da LogP 0.37 TPSA 232.1 3 viol. ✓ Clean Cc1ncc2c(n1)N[C@]3(N(C2)[C@H]([C@H](S3)CCOP(=O)…
EN0 RCSB PDB 565.3 Da LogP 1.17 TPSA 246.7 2 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)/C(=C(\F)/P(=O)(O)O)…
HE3 RCSB PDB 468.4 Da LogP 1.64 TPSA 174.6 ✓ Ro5 ✓ Clean Cc1ncc2c(n1)N[C@]3([N@@](C2)C(=C(S3)CCO[P@](=O)…
PYR RCSB PDB 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=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.