KpATCC43816 Protein target profile

thiamine pyrophosphate enzyme, C-terminal TPP binding domain protein

Accession: VK055_4429

Gene: AIK82972.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GUE2
Length 569
Pocket druggability (P2Rank · AlphaFold DB model) 0.614
Direct ligand evidence 0 89 total records
Functional annotation 0 EC 8 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
No hit
Gut microbiome similarity
0.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
95.54 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.614
Structure A0A0H3GUE2
Pocket Pocket 1
Druggability (FPocket) 0.852
Structure A0A0H3GUE2
Pocket Pocket 26
ColabFold model
P2Rank 0.534 · Pocket 1
FPocket 0.785 · Pocket 10
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 6 / 4744 genomes with a hit
Prevalence 0.1%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MASITLSAAELLLHRLQALDVAYIFINSGTDYPPVIEAWAKARATGQKVPELVICPHENAAIGMAHGYYLGTGKVQAVMVHTNVGLANAACGVINLANSNIPVLIFGGRTPISEHSHFGCRNTPIGYGQEMRDQAALIRESVKWDFELRLADQIGEHVDRAWAIASSLPKGPVYLSLPREPLCETFAVDEAALQAGPSQQPVRYAPVREDIARAAEAIACARHPVIFAQRGARTAEGFARLDSLVREWAIPLVEYWGTEVTLSADNPLLAGADPSVWLADADVILVVDSQAPWMIAEGDCRQDSTVIQMGPDPLFSRYPVRGYRADINLAGETDEVFSLLEEALRPLQAARQQHVAERAAYTQNRIQQQKNQRDALLHASQSGAITKPWLSYCLGHLANQHRGRIVSELTTLPQFAGLTHAESYYQEALAGGLGEALPIALGLQLARREELIIAAVGDGSYLFANPAVCHHIAEVMKLPVLVVVGNNGGWGAVAGGTKALYPDGYAARAETIPATAFTTSPDFAAIAASSRAAALSVSRAEDLPGVLEEAVSLIRTRRQSVLVDVQLAR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

8
  • 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:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
  • 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: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: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.

24 records
Show feature table
Start End DB Term Name
1 18 SignalP_EUK SignalP-noTM SignalP-noTM
10 179 CDD cd07035 TPP_PYR_POX_like
1 18 Phobius SIGNAL_PEPTIDE Signal peptide region
415 567 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
415 567 InterPro IPR029061 Thiamin diphosphate-binding fold
19 569 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
3 196 Gene3D G3DSA:3.40.50.970 -
7 187 Pfam PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
7 187 InterPro IPR012001 Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain
414 565 Pfam PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
414 565 InterPro IPR011766 Thiamine pyrophosphate enzyme, TPP-binding
207 379 Gene3D G3DSA:3.40.50.1220 -
2 13 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
14 18 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
7 186 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
7 186 InterPro IPR029061 Thiamin diphosphate-binding fold
380 569 Gene3D G3DSA:3.40.50.970 -
211 314 Pfam PF00205 Thiamine pyrophosphate enzyme, central domain
211 314 InterPro IPR012000 Thiamine pyrophosphate enzyme, central domain
172 360 SUPERFAMILY SSF52467 DHS-like NAD/FAD-binding domain
172 360 InterPro IPR029035 DHS-like NAD/FAD-binding domain superfamily
6 567 PANTHER PTHR18968 THIAMINE PYROPHOSPHATE ENZYMES
6 567 InterPro IPR045229 Thiamine pyrophosphate enzyme

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.614
Likely same site as FPocket 1 8.0 Å 14 shared residues 82% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.096
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Surrounding area
Pocket 3 P2Rank #3
0.07
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Surrounding area
Pocket 4 P2Rank #4
0.034
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Surrounding area
Pocket 5 P2Rank #5
0.028
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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #26
0.852
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Surrounding area
Pocket 2 FPocket #1
0.823 Unusual size
Likely same site as P2Rank 1 8.0 Å 14 shared residues 82% of smaller site
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Surrounding area
Pocket 3 FPocket #2
0.514
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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_A0A0H3GUE2
AlphaFold DB full sequence Viewing
ColabFold VK055_4429
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.

89 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 39 records from similar proteins
Structural ligands 34 0 loaded crystals
Measured bioactivity 5 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1MM PDB via homolog 381.4 Da · LogP 0.49 · TPSA 149.5 Open detail RCSB PDB
1PG PDB via homolog Detail RCSB PDB
1SM PDB via homolog Detail RCSB PDB
60G PDB via homolog Detail RCSB PDB
6R4 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
1MM RCSB PDB P07342 381.4 Da LogP 0.49 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1nc(nc(n1)OC)NC(=O)NS(=O)(=O)c2ccccc2C(=O)OC
1PG RCSB PDB P0CH62 252.3 Da LogP -0.31 TPSA 66.4 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCO
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
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
6R4 RCSB PDB A0A1D8PJF9 398.4 Da LogP 0.10 TPSA 138.6 ✓ Ro5 ✓ Clean CCCOC1=NN(C(=O)N1C)C(=O)NS(=O)(=O)c2ccccc2C(=O)…
8GF RCSB PDB Q96VZ6 109.1 Da LogP 0.37 TPSA 51.8 ✓ Ro5 ✓ Clean Cc1nccc(n1)N
8PA RCSB PDB P20906 558.5 Da LogP 1.98 TPSA 202.1 1 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](\C=C\c3cccnc3)…
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 P07342 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 P07342 44.0 Da LogP -0.58 TPSA 34.1 ✓ Ro5 ✓ Clean C(=O)=O
CXO RCSB PDB P0CH62 112.1 Da LogP 0.70 TPSA 34.1 ✓ Ro5 Alert C1CCC(=O)C(=O)C1
D7K RCSB PDB P20906 625.5 Da LogP 1.87 TPSA 235.7 3 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](c3ccccc3)(O)[P…
DPO RCSB PDB Q96VZ6 173.9 Da LogP -3.34 TPSA 135.6 ✓ Ro5 ✓ Clean [O-]P(=O)([O-])OP(=O)([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 P07342 76.1 Da LogP 0.02 TPSA 46.5 ✓ Ro5 ✓ Clean CC(=O)OO
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 P07342 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 P07342 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
RMN RCSB PDB P20906 152.1 Da LogP 0.80 TPSA 57.5 ✓ Ro5 ✓ Clean c1ccc(cc1)[C@H](C(=O)O)O
TP9 RCSB PDB P07342 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 P20906 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.

Cross-references

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