KpKP13 Protein target profile

dTDP-4-dehydrorhamnose 3,5-epimerase in cps region

Accession: KP13_03795

Gene: AHE43667.1 rmlC 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSI9
Length 184
Pocket druggability (P2Rank · AlphaFold DB model) 0.641
Direct ligand evidence 0 60 total records
Functional annotation 1 EC 4 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
No hit
Gut microbiome similarity
32.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
64.481 Higher values support similarity to known essential genes.
DEG E-value
1.24e-82 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.83 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) 0.641
Structure A0A0H3GSI9
Pocket Pocket 1
Druggability (FPocket) 0.188
Structure A0A0H3GSI9
Pocket Pocket 2
ColabFold model
P2Rank 0.738 · Pocket 1
FPocket 0.291 · Pocket 6
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 1559 / 4744 genomes with a hit
Prevalence 32.9%

Sequence

Primary amino-acid sequence viewer.

MNIIKTDIPDVLIFEPRVFGDARGFFFESFSSKVFNEAVGRQVDFVQDNHSQSQKGVLRGLHYQLDPHAQGKLVRCVEGEVFDVAVDIRRSSPTFGKWVGAVLSAENKRQLWIPEGFAHGFMALSDTVQFVYKATNYYAPQSERSIIWNDPEIGIDWPALGDCALSLSEKDLQAHTLATAEVYK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0008830 Catalysis of the reaction: dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0019305 The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate.
  • GO:0000271 The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
5 178 Pfam PF00908 dTDP-4-dehydrorhamnose 3,5-epimerase
5 178 InterPro IPR000888 dTDP-4-dehydrorhamnose 3,5-epimerase-related
2 180 NCBIfam TIGR01221 dTDP-4-dehydrorhamnose 3,5-epimerase
2 180 InterPro IPR000888 dTDP-4-dehydrorhamnose 3,5-epimerase-related
2 178 PANTHER PTHR21047 DTDP-6-DEOXY-D-GLUCOSE-3,5 EPIMERASE
2 178 InterPro IPR000888 dTDP-4-dehydrorhamnose 3,5-epimerase-related
1 184 Gene3D G3DSA:2.60.120.10 Jelly Rolls
1 184 InterPro IPR014710 RmlC-like jelly roll fold
3 174 CDD cd00438 cupin_RmlC
3 174 InterPro IPR000888 dTDP-4-dehydrorhamnose 3,5-epimerase-related
1 181 SUPERFAMILY SSF51182 RmlC-like cupins
1 181 InterPro IPR011051 RmlC-like cupin domain superfamily

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
0.641
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.011
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_A0A0H3GSI9
AlphaFold DB full sequence Viewing
ColabFold KP13_03795
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.

60 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 5 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ATY PDB via homolog 444.2 Da · LogP -0.71 · TPSA 203.7 Open detail RCSB PDB
SRT PDB via homolog Detail RCSB PDB
TDO PDB via homolog Detail RCSB PDB
TPE PDB via homolog Detail RCSB PDB
TYD 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
ATY RCSB PDB P26394 444.2 Da LogP -0.71 TPSA 203.7 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@…
SRT RCSB PDB Q9HU21 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@H]([C@H](C(=O)O)O)(C(=O)O)O
TDO RCSB PDB Q5ZXH5 546.3 Da LogP -2.22 TPSA 253.4 3 viol. ✓ Clean C[C@H]1C(=O)[C@H]([C@H]([C@H](O1)O[P@@](=O)(O)O…
TPE RCSB PDB P26394 520.3 Da LogP 1.38 TPSA 192.7 2 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@…
TYD RCSB PDB O27818 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.

Cross-references

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