KpATCC43816 Protein target profile

thiamine biosynthesis protein ThiC

Accession: VK055_3098

Gene: thiC AIK81679.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GKP1
Length 631
Pocket druggability (P2Rank · AlphaFold DB model) 0.852
Direct ligand evidence 0 53 total records
Functional annotation 1 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
15.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
72.1 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
92.27 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) 0.852
Structure A0A0H3GKP1
Pocket Pocket 1
Druggability (FPocket) 0.903
Structure A0A0H3GKP1
Pocket Pocket 1
ColabFold model
P2Rank 0.89 · Pocket 1
FPocket 0.802 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 739 / 4744 genomes with a hit
Prevalence 15.6%

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.

MSTTKLTRREQREHAQRFIDTLAGTAFPNSRRIYVHGSQADIRVPMREIQLSPTLVGGDKDNPRYETNEPIPVYDTSGPYGDPDISIDVRQGLAKLRQPWIDARNDCAPLSERSSAYTKARLADDGLDELRFSGLLTPKRAVAGKCVTQLHYARQGIVTPEMEFIAIRENMGRERIRSEVLRQQHAGEGFGAHLPENITPEFVRDEVAAGRAIIPANINHPESEPMIIGRNFLVKVNANIGNSAVTSSIEEEVEKLVWSTRWGADTVMDLSTGRYIHETREWILRNSPVPIGTVPIYQALEKVNGIAENLTWQVFRDTLLEQAEQGVDYFTIHAGVLLRYVPMTAKRLTGIVSRGGSIMAKWCLSHHQENFLYQHFREICEICAAYDVSLSLGDGLRPGSIQDANDEAQFSELRTLGELTKIAWEYDVQVMIEGPGHVPMQMIRRNMTEQLEHCHEAPFYTLGPLTTDIAPGYDHFTSGIGAAMIGWFGCAMLCYVTPKEHLGLPNKEDVKQGLITYKIAAHAADLAKGHPGAQIRDNAMSKARFEFRWEDQFNLALDPFTARAYHDETLPQESGKVAHFCSMCGPKFCSMKITQEVRDYAAKQSIEAGMADMSNNFRARGGEIYLKQEEA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0009228 The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0016830 Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0070284 Catalysis of the reaction: 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + CO + 5'-deoxyadenosine + formate + L-methionine + 3 H+.
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0009229 The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
218 531 FunFam G3DSA:3.20.20.540:FF:000001 Phosphomethylpyrimidine synthase
23 625 SFLD SFLDG01114 phosphomethylpyrimidine synthase (ThiC)
6 620 PANTHER PTHR30557 THIAMINE BIOSYNTHESIS PROTEIN THIC
6 620 InterPro IPR002817 Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B
148 596 Pfam PF01964 Radical SAM ThiC family
148 596 InterPro IPR002817 Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B
147 599 NCBIfam TIGR00190 phosphomethylpyrimidine synthase
147 599 InterPro IPR002817 Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B
148 596 SFLD SFLDF00407 phosphomethylpyrimidine synthase (ThiC)
147 600 Hamap MF_00089 Phosphomethylpyrimidine synthase [thiC].
147 600 InterPro IPR037509 Phosphomethylpyrimidine synthase
532 566 Gene3D G3DSA:6.10.250.620 -
8 628 SFLD SFLDS00113 Radical SAM Phosphomethylpyrimidine Synthase
218 531 Gene3D G3DSA:3.20.20.540 Radical SAM ThiC family, central domain
218 531 InterPro IPR038521 ThiC/Bza, core domain
27 107 Pfam PF13667 ThiC-associated domain
27 107 InterPro IPR025747 ThiC-associated domain

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
0.852
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Surrounding area
Pocket 2 P2Rank #2
0.797
Likely same site as FPocket 1 3.1 Å 16 shared residues 80% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.313
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.184
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.085
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.903
Likely same site as P2Rank 2 3.1 Å 16 shared residues 80% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:239-239
UniProt: Binding site:268-268
UniProt: Binding site:297-297
UniProt: Binding site:333-333
UniProt: Binding site:353-355
UniProt: Binding site:394-397
UniProt: Binding site:433-433
UniProt: Binding site:437-437
UniProt: Binding site:460-460
UniProt: Binding site:501-501
UniProt: Binding site:581-581
UniProt: Binding site:584-584
UniProt: Binding site:589-589
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_A0A0H3GKP1
AlphaFold DB full sequence Viewing
ColabFold VK055_3098
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5AD PDB via homolog 251.2 Da · LogP -0.95 · TPSA 119.3 Open detail RCSB PDB
AIR PDB via homolog Detail RCSB PDB
IRN PDB via homolog Detail RCSB PDB
ZINC100352250 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1095430 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
5AD RCSB PDB O82392 251.2 Da LogP -0.95 TPSA 119.3 ✓ Ro5 ✓ Clean C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
AIR RCSB PDB O82392 295.2 Da LogP -1.81 TPSA 160.3 ✓ Ro5 ✓ Clean c1c(n(cn1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(…
IRN RCSB PDB O82392 280.2 Da LogP -1.39 TPSA 134.3 ✓ Ro5 ✓ Clean c1cn(cn1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=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.

Cross-references

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