KpKP13 Protein target profile

Threonine dehydratase biosynthetic

Accession: KP13_31507

Gene: AHE47014.1 ilvA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GKB0
Length 514
Pocket druggability (P2Rank · AlphaFold DB model) 0.91
Direct ligand evidence 0 55 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.

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 (%)
51.562 Lower values reduce human off-target concern.
Human E-value
2.26e-14
Gut microbiome similarity
5.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
52.456 Higher values support similarity to known essential genes.
DEG E-value
2.46e-180 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
91.42 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) 0.91
Structure A0A0H3GKB0
Pocket Pocket 1
Druggability (FPocket) 0.343
Structure A0A0H3GKB0
Pocket Pocket 5
ColabFold model
P2Rank 0.883 · Pocket 1
FPocket 0.243 · Pocket 6
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 263 / 4744 genomes with a hit
Prevalence 5.5%

Sequence

Primary amino-acid sequence viewer.

MADSQPLSGAPEGAEYLRAVLRAPVYEAVQKTPLQKMDKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMSSLTAEQKSHGVITASAGNHAQGVAFSASRLGVKALIVMPVATADIKVDAVRGFGGEVLLHGANFDEAKARAIELAQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHIDRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIAQHNIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADAKDACIFVGVRLSRGLEERKEILQLLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSKALQERLFSFEFPESPGALLKFLHTLGTHWNISLFHYRSHGTDYGRVLAAFELGEHEPDFETRLNELGYECHDETHNPAFRFFLAG

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:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
  • 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:0003941 Catalysis of the reaction: L-serine = pyruvate + NH4+.
  • 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.

32 records
Show feature table
Start End DB Term Name
425 512 Pfam PF00585 C-terminal regulatory domain of Threonine dehydratase
425 512 InterPro IPR001721 Threonine dehydratase, ACT-like domain
329 419 Pfam PF00585 C-terminal regulatory domain of Threonine dehydratase
329 419 InterPro IPR001721 Threonine dehydratase, ACT-like domain
17 320 CDD cd01562 Thr-dehyd
336 423 SUPERFAMILY SSF55021 ACT-like
336 423 InterPro IPR045865 ACT-like domain
65 156 Gene3D G3DSA:3.40.50.1100 -
65 156 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
15 512 NCBIfam TIGR01124 threonine ammonia-lyase, biosynthetic
15 512 InterPro IPR005787 Threonine dehydratase, biosynthetic
25 511 PANTHER PTHR48078 THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED
14 365 SUPERFAMILY SSF53686 Tryptophan synthase beta subunit-like PLP-dependent enzymes
14 365 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
32 310 Gene3D G3DSA:3.40.50.1100 -
32 310 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
434 504 ProSiteProfiles PS51672 ACT-like domain profile.
434 504 InterPro IPR001721 Threonine dehydratase, ACT-like domain
28 316 Pfam PF00291 Pyridoxal-phosphate dependent enzyme
28 316 InterPro IPR001926 Tryptophan synthase beta chain-like, PALP domain
433 512 CDD cd04907 ACT_ThrD-I_2
420 512 SUPERFAMILY SSF55021 ACT-like
420 512 InterPro IPR045865 ACT-like domain
339 411 ProSiteProfiles PS51672 ACT-like domain profile.
339 411 InterPro IPR001721 Threonine dehydratase, ACT-like domain
338 514 FunFam G3DSA:3.40.1020.10:FF:000001 L-threonine dehydratase
338 422 CDD cd04906 ACT_ThrD-I_1
338 514 Gene3D G3DSA:3.40.1020.10 Biosynthetic Threonine Deaminase; Domain 3
338 514 InterPro IPR038110 Threonine dehydratase, ACT-like domain superfamily
145 310 FunFam G3DSA:3.40.50.1100:FF:000008 L-threonine dehydratase
53 66 ProSitePatterns PS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.
53 66 InterPro IPR000634 Serine/threonine dehydratase, pyridoxal-phosphate-binding 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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.91
Likely same site as FPocket 24 4.2 Å 37 shared residues 97% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.111
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.041
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.038
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.035
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #5
0.343 Unusual size
Show in viewer
Surrounding area
Pocket 2 FPocket #24
0.224 Unusual size
Likely same site as P2Rank 1 4.2 Å 37 shared residues 97% 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_A0A0H3GKB0
AlphaFold DB full sequence Viewing
ColabFold KP13_31507
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.

55 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 1 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
SD4 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 P25306 1529.8 Da LogP 0.17 TPSA 334.1 2 viol. ✓ Clean COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO…
ACP RCSB PDB 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 Q76EQ0 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PDD RCSB PDB 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.