Protein target profile

VK055_2490

acetolactate synthase, large subunit, biosynthetic type

Genome: KpATCC43816 Gene: ilvB AIK81087.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GMJ8
Length 574
Pocket druggability 0.959
Metabolic reactions 2
Chokepoint Yes
Direct ligand evidence 0 123 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 (%)
41.667 Lower values reduce human off-target concern.
Human E-value
3.34e-19
Gut microbiome similarity
5.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
63.778 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
97.07 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 0.959
Structure A0A0H3GMJ8
Pocket Pocket 1
P2Rank 0.933
Structure A0A0H3GMJ8
Pocket Pocket 1
ColabFold model
FPocket 0.998 · Pocket 1
P2Rank 0.946 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 254 / 4744 genomes with a hit
Prevalence 5.4%

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.

MEMLSGAEMVVQSLVDQGVKQVFGYPGGAVLDIYDALHTLGGIDHVLVRHEQAAVHMADGLARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVILSGQVATSLIGYDAFQECDMVGISRPVVKHSFLVKQTEDIPGVLKKAFWLAASGRPGPVVVDLPKDILNPAKKLPYVWPDAVSMRSYNPTTSGHKGQIKRALQTLVAASKPVVYVGGGAINAHCEPQLRELVEKLKLPVASSLMGLGAFPATHSQALGMLGMHGTYEANMTMHHSDVIFAVGVRFDDRTTNNLAKYCPNATVLHIDIDPTSISKTVPADVPIVGDARLVLEQMLELLEQEEAQQPLDDIRDWWQQIEQWRARHCLRYDDQSDKIKPQAVIETIWRLTQGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGLGTMGFGLPAALGVKMALPDEMVVCVTGDGSIQMNIQELSTALQYELPVLVLNLNNRYLGMVKQWQDMLYSGRHSQSYMESLPDFVRLAEAYGHVGIRISEPQELETKLAEALEQVRQRRLVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT

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: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:0000287 Binding to a magnesium (Mg) ion.
  • GO:0009082 The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
  • 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: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.

28 records
Show feature table
Start End DB Term Name
394 545 Pfam PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
394 545 InterPro IPR011766 Thiamine pyrophosphate enzyme, TPP-binding
370 567 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
370 567 InterPro IPR029061 Thiamin diphosphate-binding fold
196 363 Gene3D G3DSA:3.40.50.1220 -
364 554 FunFam G3DSA:3.40.50.970:FF:000016 Acetolactate synthase
5 167 Pfam PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
5 167 InterPro IPR012001 Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain
4 558 PANTHER PTHR18968 THIAMINE PYROPHOSPHATE ENZYMES
4 558 InterPro IPR045229 Thiamine pyrophosphate enzyme
372 556 CDD cd02015 TPP_AHAS
372 556 InterPro IPR039368 Acetolactate synthase large subunit, TPP binding domain
8 163 CDD cd07035 TPP_PYR_POX_like
2 178 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
2 178 InterPro IPR029061 Thiamin diphosphate-binding fold
2 176 Gene3D G3DSA:3.40.50.970 -
190 363 FunFam G3DSA:3.40.50.1220:FF:000008 Acetolactate synthase
189 362 SUPERFAMILY SSF52467 DHS-like NAD/FAD-binding domain
189 362 InterPro IPR029035 DHS-like NAD/FAD-binding domain superfamily
321 341 Coils Coil Coil
364 534 Gene3D G3DSA:3.40.50.970 -
431 450 ProSitePatterns PS00187 Thiamine pyrophosphate enzymes signature.
431 450 InterPro IPR000399 TPP-binding enzyme, conserved site
196 330 Pfam PF00205 Thiamine pyrophosphate enzyme, central domain
196 330 InterPro IPR012000 Thiamine pyrophosphate enzyme, central domain
4 569 NCBIfam TIGR00118 biosynthetic-type acetolactate synthase large subunit
4 569 InterPro IPR012846 Acetolactate synthase, large subunit, biosynthetic
1 183 FunFam G3DSA:3.40.50.970:FF:000007 Acetolactate synthase

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
0.959
Likely same site as P2Rank 1 1.0 Å 38 shared residues 95% 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
0.933
Likely same site as FPocket 1 1.0 Å 38 shared residues 95% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.456
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.239
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.208
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.047
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_A0A0H3GMJ8
AlphaFold DB full sequence Viewing
ColabFold VK055_2490
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.

123 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 73 records from similar proteins
Structural ligands 37 0 loaded crystals
Measured bioactivity 36 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1CS PDB via homolog 357.8 Da · LogP 1.35 · TPSA 123.2 Open detail RCSB PDB
1IQ PDB via homolog Detail RCSB PDB
1MM PDB via homolog Detail RCSB PDB
1MS PDB via homolog Detail RCSB PDB
1SM 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
1CS RCSB PDB P17597 357.8 Da LogP 1.35 TPSA 123.2 ✓ Ro5 ✓ Clean Cc1nc(nc(n1)OC)NC(=O)NS(=O)(=O)c2ccccc2Cl
1IQ RCSB PDB P17597 311.3 Da LogP 2.22 TPSA 91.7 ✓ Ro5 ✓ Clean CC(C)[C@@]1(C(=O)NC(=N1)c2c(cc3ccccc3n2)C(=O)O)C
1MM RCSB PDB P17597 381.4 Da LogP 0.49 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1nc(nc(n1)OC)NC(=O)NS(=O)(=O)c2ccccc2C(=O)OC
1MS RCSB PDB P17597 337.3 Da LogP 1.20 TPSA 144.2 ✓ Ro5 ✓ Clean Cc1ccnc(n1)NC(=O)NS(=O)(=O)c2ccccc2[N+](=O)[O-]
1SM RCSB PDB A0A1D8PJF9 364.4 Da LogP 1.39 TPSA 127.3 ✓ Ro5 ✓ Clean Cc1cc(nc(n1)NC(=O)NS(=O)(=O)c2ccccc2C(=O)OC)C
1TB RCSB PDB P17597 395.4 Da LogP 0.51 TPSA 140.7 ✓ Ro5 ✓ Clean Cc1nc(nc(n1)OC)N(C)C(=O)NS(=O)(=O)c2ccccc2C(=O)…
2SM RCSB PDB P17597 350.4 Da LogP 1.08 TPSA 127.3 ✓ Ro5 ✓ Clean Cc1ccnc(n1)NC(=O)NS(=O)(=O)c2ccccc2C(=O)OC
60G RCSB PDB A0A1D8PJF9 410.4 Da LogP 0.93 TPSA 145.8 ✓ Ro5 ✓ Clean COc1cc(nc(n1)NC(=O)NS(=O)(=O)Cc2ccccc2C(=O)OC)OC
6QK RCSB PDB P17597 326.8 Da LogP 3.00 TPSA 81.5 ✓ Ro5 ✓ Clean COc1cc(nc(n1)Sc2cccc(c2C(=O)O)Cl)OC
6QL RCSB PDB P17597 430.4 Da LogP 2.58 TPSA 144.2 1 viol. ✓ Clean COc1cc(nc(n1)Oc2cccc(c2C(=O)O)Oc3nc(cc(n3)OC)OC…
6R4 RCSB PDB P17597 398.4 Da LogP 0.10 TPSA 138.6 ✓ Ro5 ✓ Clean CCCOC1=NN(C(=O)N1C)C(=O)NS(=O)(=O)c2ccccc2C(=O)…
6R5 RCSB PDB P17597 390.4 Da LogP -0.31 TPSA 138.6 1 viol. ✓ Clean Cc1c(c(cs1)C(=O)OC)S(=O)(=O)NC(=O)N2C(=O)N(C(=N…
AUJ RCSB PDB P07342 Cc1ncc(c(n1)N)C[N]2=C(SC(=C2C)CCOP(=O)(O)OP(=O)…
AYD RCSB PDB P07342 382.3 Da LogP 0.98 TPSA 177.1 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN/C(=C/CCO[P@@](=O)(O)OP(=O)(O)O…
CIE RCSB PDB P17597 414.8 Da LogP 1.83 TPSA 136.6 ✓ Ro5 ✓ Clean CCOC(=O)c1ccccc1S(=O)(=O)NC(=O)Nc2nc(cc(n2)Cl)OC
CO2 RCSB PDB A0A1D8PJF9 44.0 Da LogP -0.58 TPSA 34.1 ✓ Ro5 ✓ Clean C(=O)=O
DTT RCSB PDB P07342 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
F50 RCSB PDB P17597 76.1 Da LogP 0.02 TPSA 46.5 ✓ Ro5 ✓ Clean CC(=O)OO
FAB RCSB PDB P17597 855.6 Da LogP -2.87 TPSA 373.8 3 viol. Alert Cc1cc2c(cc1C)[N+](=C3C(=O)NC(=O)N=C3N2C[C@@H]([…
G87 RCSB PDB A0A1D8PJF9 418.3 Da LogP 2.56 TPSA 107.7 ✓ Ro5 ✓ Clean Cc1ccc(c(c1Cl)NS(=O)(=O)c2nc3nc(cc(n3n2)OC)OC)Cl
G8A RCSB PDB A0A1D8PJF9 506.3 Da LogP 1.78 TPSA 136.6 1 viol. ✓ Clean CCOC(=O)c1ccccc1S(=O)(=O)NC(=O)Nc2nc(cc(n2)I)OC
G8G RCSB PDB A0A1D8PJF9 442.3 Da LogP 1.10 TPSA 185.4 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN(C=O)/C(=C(/CCOP(=O)(O)OP(=O)(O…
H4V RCSB PDB A0A1D8PJF9 492.3 Da LogP 1.39 TPSA 136.6 ✓ Ro5 ✓ Clean COc1cc(nc(n1)NC(=O)NS(=O)(=O)c2ccccc2C(=O)OC)I
HTL RCSB PDB P07342 467.4 Da LogP 1.04 TPSA 186.0 ✓ Ro5 ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(=O)C)CCO[P@@](=O)(…
NSP RCSB PDB P07342 138.2 Da LogP -0.17 TPSA 77.8 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN
OXY RCSB PDB P07342 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean O=O
P22 RCSB PDB P17597 206.0 Da LogP 0.23 TPSA 113.3 ✓ Ro5 ✓ Clean CCO[P@](=O)(O)OP(=O)(O)O
P23 RCSB PDB P07342 220.1 Da LogP 0.62 TPSA 113.3 ✓ Ro5 ✓ Clean CCCO[P@@](=O)(O)OP(=O)(O)O
P25 RCSB PDB P07342 248.1 Da LogP 1.40 TPSA 113.3 ✓ Ro5 ✓ Clean CCCCCO[P@@](=O)(O)OP(=O)(O)O
PXD RCSB PDB P17597 483.4 Da LogP 2.61 TPSA 116.9 ✓ Ro5 ✓ Clean COc1cnc(n2c1nc(n2)NS(=O)(=O)c3c(cccc3OCC(F)F)C(…
PYD RCSB PDB P07342 123.2 Da LogP 0.68 TPSA 51.8 ✓ Ro5 ✓ Clean Cc1cnc(nc1N)C
PYR RCSB PDB P07342 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
TDM RCSB PDB P17597 468.4 Da LogP 2.51 TPSA 188.6 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN\2C(=C(S/C2=C(\C)/O)CCO[P@@](=O…
TP9 RCSB PDB P17597 412.3 Da LogP -0.03 TPSA 182.8 1 viol. ✓ Clean Cc1ncc(c(n1)N)CN/C(=C(/CCO[P@](=O)([O-])O[P@@](…
TZD RCSB PDB A0A1D8PJF9 440.3 Da LogP 0.72 TPSA 187.1 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN2C(=C(SC2=O)CCO[P@@](=O)(O)OP(=…
YF3 RCSB PDB P07342 212.3 Da LogP 0.78 TPSA 63.8 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CNC(C)CS
YF4 RCSB PDB P07342 180.3 Da LogP 0.82 TPSA 55.0 ✓ Ro5 ✓ Clean CCN(C)Cc1cnc(nc1N)C

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.