KpATCC43816 Protein target profile

tdcB

Accession: VK055_0161

Gene: tdcB AIK78789.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GPX2
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Length 329
Pocket druggability (P2Rank · AlphaFold DB model) 0.919
Direct ligand evidence 0 57 total records
Functional annotation 1 EC 7 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.92. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 4 structural and 3 bioactivity records.

Risks to review

Human similarity Top human hit identity: 47.541%. This target also has a predicted binding pocket (P2Rank 0.92) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 108 of 4744 screened genomes (2.3%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.92) — check the ligand evidence before deprioritizing on off-target risk alone. Weak predicted binding pocket FPocket selected-pocket score 0.26.

Evidence coverage

Core evidence streams are available for this target.
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 (%)
47.541 Lower values reduce human off-target concern.
Human E-value
9.61e-15
Gut microbiome similarity
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
95.68 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) 0.919
Structure A0A0H3GPX2
Pocket Pocket 1
Druggability (FPocket) 0.264
Structure A0A0H3GPX2
Pocket Pocket 12
ColabFold model
P2Rank 0.862 · Pocket 1
FPocket 0.302 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 108 / 4744 genomes with a hit
Prevalence 2.3%

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.

MHITYDLPVSIDDILEAKQRLAGKIYKTGMPRSNYFSERCQGEIFLKFENMQRTGSFKIRGAFNKLCGLTAAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVLHGDNFNDTLAKASDIVELEGRIFIPPYDDPQVIAGQGTIGLEILEDLYDVDNVIVPIGGGGLIAGIAIAIKSINPTIRIIGVQSENVHGMAASWYAGEITSHRHAGTLADGCDVARPGKLTYEIARQLVDDIVLVSEDDIRQSMVALIQRNKVITEGAGALACAALLSGKLDSYIQNRKTVSLISGGNIDLSRVSQITGFVDA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0003941 Catalysis of the reaction: L-serine = pyruvate + NH4+.
  • GO:0004794 Catalysis of the reaction: L-threonine = 2-oxobutanoate + NH4.
  • GO:0009097 OBSOLETE. The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
  • GO:0006565 The chemical reactions and pathways resulting in the breakdown of L-serine.
  • GO:0006567 The chemical reactions and pathways resulting in the breakdown of L-threonine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
11 316 CDD cd01562 Thr-dehyd
57 153 Gene3D G3DSA:3.40.50.1100 -
57 153 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
49 62 ProSitePatterns PS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.
49 62 InterPro IPR000634 Serine/threonine dehydratase, pyridoxal-phosphate-binding site
154 316 FunFam G3DSA:3.40.50.1100:FF:000007 L-threonine dehydratase catabolic TdcB
57 153 FunFam G3DSA:3.40.50.1100:FF:000005 Threonine dehydratase catabolic
10 320 SUPERFAMILY SSF53686 Tryptophan synthase beta subunit-like PLP-dependent enzymes
10 320 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
12 324 PANTHER PTHR48078 THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED
20 316 Gene3D G3DSA:3.40.50.1100 -
20 316 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
24 312 Pfam PF00291 Pyridoxal-phosphate dependent enzyme
24 312 InterPro IPR001926 Tryptophan synthase beta chain-like, PALP 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
0.919
Likely same site as FPocket 12 2.4 Å 27 shared residues 96% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.006
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #12
0.264 Unusual size
Likely same site as P2Rank 1 2.4 Å 27 shared residues 96% 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_A0A0H3GPX2
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0161
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 and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 3 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
15P PDB via homolog 1529.8 Da · LogP 0.17 · TPSA 334.1 Open detail RCSB PDB
ACP PDB via homolog Detail RCSB PDB
MLI PDB via homolog Detail RCSB PDB
PDD PDB via homolog Detail RCSB PDB
CHEMBL566071 ChEMBL via homolog Detail ChEMBL

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
15P RCSB PDB
3IAU
P25306 1529.8 Da LogP 0.17 TPSA 334.1 2 viol. ✓ Clean COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO…
ACP RCSB PDB
1WTC
O59791 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
MLI RCSB PDB
3L6C
Q76EQ0 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PDD RCSB PDB
2ZPU
O59791 320.2 Da LogP 0.27 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](C)C(=O)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.

Sequence

UniProt A0A0H3GPX2

Chemistry

ChEMBL CHEMBL566071 ChEMBL CHEMBL569435 ChEMBL SD4