Protein target profile

KP13_03796

dTDP-4-dehydrorhamnose reductase in cps region

Genome: KpKP13 Gene: AHE43666.1 rmlD 3D evidence: Experimental + ColabFold model UniProt C9K1F1
Length 296
Pocket druggability 0.895
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 5 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 (%)
34.188 Lower values reduce human off-target concern.
Human E-value
7.45e-15
Gut microbiome similarity
1.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
61.905 Higher values support similarity to known essential genes.
DEG E-value
1.8e-132 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
98.35 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.895
Structure 8CTR
Pocket Pocket 1
P2Rank 0.917
Structure 8CTR
Pocket Pocket 1
ColabFold model
FPocket 0.262 · Pocket 7
P2Rank 0.935 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 53 / 4744 genomes with a hit
Prevalence 1.1%

Cross-references

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

Structure

Sequence

Primary amino-acid sequence viewer.

MKILLIGKNGQVGWELQRSLSTLGDVVAVDYFDKLLCGDLTNLEGIAQTVRTVRPDVVVNAAAHTAVDKAESERELSDLLNDKGVAVLAAESAKLGALMVHYSTDYVFDGAGSHYRREDEATGPLNVYGETKRAGELALEQGNPRHLIFRTSWVYATRGANFAKTMLRLAGEKETLSIIDDQHGAPTGAELLADCTATAIRETLRNPALAGTYHLVASGETSWCDYARYVFEVARAHGAELAVQEVKGIPTTAYPTPAKRPLNSRLSNEKFQQAFGVTLPDWRQGVARVVTEVLGK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008831 Catalysis of the reaction: dTDP-6-deoxy-L-mannose + NADP+ = dTDP-4-dehydro-6-deoxy-L-mannose + H+ + NADPH.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • 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:0009243 The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
3 280 Gene3D G3DSA:3.40.50.720 -
162 287 Gene3D G3DSA:3.90.25.10 -
2 293 PANTHER PTHR10491 DTDP-4-DEHYDRORHAMNOSE REDUCTASE
2 293 InterPro IPR005913 dTDP-4-dehydrorhamnose reductase family
2 292 NCBIfam TIGR01214 dTDP-4-dehydrorhamnose reductase
2 292 InterPro IPR005913 dTDP-4-dehydrorhamnose reductase family
1 293 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
1 293 InterPro IPR036291 NAD(P)-binding domain superfamily
1 293 Pfam PF04321 RmlD substrate binding domain
1 293 InterPro IPR029903 RmlD-like substrate binding domain
2 287 CDD cd05254 dTDP_HR_like_SDR_e

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
0.895
Likely same site as P2Rank 1 6.8 Å 23 shared residues 72% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #9
0.47
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.917
Likely same site as FPocket 1 6.8 Å 23 shared residues 72% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.099
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Surrounding area
Site 3 P2Rank #3
0.029
Likely same site as FPocket 1 7.6 Å 11 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.016
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Surrounding area
Site 5 P2Rank #5
0.002
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Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 8CTR
X-ray 1.65 Å A,B,C,D
100.0% 1-296
Viewing
ColabFold KP13_03796
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 3 0 loaded crystals
Measured bioactivity 2 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
STL PDB via homolog 228.2 Da · LogP 2.97 · TPSA 60.7 Open detail RCSB PDB
TRH PDB via homolog Detail RCSB PDB
TXP PDB via homolog Detail RCSB PDB
DWT ChEMBL via homolog · pchembl 7.28 (~52.5 nM) Detail ChEMBL
CHEMBL375328 ChEMBL via homolog · pchembl 6.05 (~891.3 nM) 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
STL RCSB PDB Q9NZL9 228.2 Da LogP 2.97 TPSA 60.7 ✓ Ro5 ✓ Clean c1cc(ccc1\C=C\c2cc(cc(c2)O)O)O
TRH RCSB PDB P26392 548.3 Da LogP -2.43 TPSA 256.5 3 viol. ✓ Clean C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O[P@](=O)(O)…
TXP RCSB PDB Q9NZL9 747.4 Da LogP -3.18 TPSA 364.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.