Protein target profile

KP13_31530

dTDP-D-glucose 4,6-dehydratase in cps region

Genome: KpKP13 Gene: AHE43664.1 rmlB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVT8
Length 354
Pocket druggability 0.991
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 2 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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 (%)
35.0 Lower values reduce human off-target concern.
Human E-value
1.03e-65
Gut microbiome similarity
34.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
70.536 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
95.05 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 0.991
Structure A0A0H3GVT8
Pocket Pocket 1
P2Rank 0.99
Structure A0A0H3GVT8
Pocket Pocket 1
ColabFold model
FPocket 0.833 · Pocket 1
P2Rank 0.992 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 1656 / 4744 genomes with a hit
Prevalence 34.9%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKILVTGGAGFIGSAVVRHIIENTQDEVRVVDCLTYAGNLESLAPVAGSERYSFSQTDITDAAAVAAQFSEFRPDIVMHLAAESHVDRSIDGPAAFIQTNVIGTFTLLEAARHYWSGLGEAQKQAFRFHHISTDEVYGDLHGTDDLFTEETPYAPSSPYSASKAGSDHLVRAWNRTYGLPVVVTNCSNNYGPYHFPEKLIPLTILNALAGKPLPVYGNGEQIRDWLYVEDHARALYKVATEGKSGETYNIGGHNERKNIDVVRTICAILDKVVAQKPGNITHFADLITFVTDRPGHDLRYAIDAAKIQRDLGWVPQETFESGIEKTVHWYLNNQTWWQRVLDGSYAGERLGLNN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

2
  • GO:0008460 Catalysis of the reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O.
  • GO:0009225 The cellular chemical reactions and pathways involving nucleotide-sugars, any nucleotide-carbohydrate in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
2 339 NCBIfam TIGR01181 dTDP-glucose 4,6-dehydratase
2 339 InterPro IPR005888 dTDP-glucose 4,6-dehydratase
1 18 Phobius SIGNAL_PEPTIDE Signal peptide region
200 334 Gene3D G3DSA:3.90.25.10 -
19 354 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
2 324 Gene3D G3DSA:3.40.50.720 -
4 326 Pfam PF16363 GDP-mannose 4,6 dehydratase
4 326 InterPro IPR016040 NAD(P)-binding domain
1 334 CDD cd05246 dTDP_GD_SDR_e
1 334 InterPro IPR005888 dTDP-glucose 4,6-dehydratase
1 344 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
1 344 InterPro IPR036291 NAD(P)-binding domain superfamily
14 18 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
2 341 PANTHER PTHR43000 DTDP-D-GLUCOSE 4,6-DEHYDRATASE-RELATED
2 19 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
2 19 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
159 178 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
159 178 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
38 49 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
38 49 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
3 13 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.

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
0.991
Likely same site as P2Rank 1 2.3 Å 44 shared residues 90% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #5
0.503
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Surrounding area
Site 3 FPocket #3
0.218
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.99
Likely same site as FPocket 1 2.3 Å 44 shared residues 90% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.009
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.004
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_A0A0H3GVT8
AlphaFold DB full sequence Viewing
ColabFold KP13_31530
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
DAU PDB via homolog 564.3 Da · LogP -3.46 · TPSA 276.8 Open detail RCSB PDB
TDX PDB via homolog Detail RCSB PDB
TYD PDB via homolog Detail RCSB PDB
ZINC33979243 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC13507072 ZINC proposed compound · Tanimoto 0.754 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
DAU RCSB PDB P26391 564.3 Da LogP -3.46 TPSA 276.8 3 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…
TDX RCSB PDB Q8GIP9 534.3 Da LogP -2.82 TPSA 256.5 3 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…
TYD RCSB PDB P26391 402.2 Da LogP -1.28 TPSA 197.6 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…

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.