Protein target profile

KP13_03794

UDP-glucose 6-dehydrogenase in cps region

Genome: KpKP13 Gene: AHE43668.1 ugd 3D evidence: Experimental + ColabFold model UniProt A0A0J9WZA6
Length 388
Pocket druggability 0.951
Direct ligand evidence 2 55 total records
Functional annotation 1 EC 6 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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 (%)
31.737 Lower values reduce human off-target concern.
Human E-value
4.92e-06
Gut microbiome similarity
23.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
74.485 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
95.84 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 0.951
Structure 3PLR
Pocket Pocket 1
P2Rank 0.674
Structure 3PLR
Pocket Pocket 1
ColabFold model
FPocket 0.798 · Pocket 20
P2Rank 0.811 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 1128 / 4744 genomes with a hit
Prevalence 23.8%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKITISGTGYVGLSNGVLIAQNHEVVALDIVQAKVDMLNQKISPIVDKEIQEYLAEKPLNFRATTDKHDAYRNADYVIIATPTDYDPKTNYFNTSTVEAVIRDVTEINPNAVMIIKSTIPVGFTRDIKERLGIDNVIFSPEFLREGRALYDNLHPSRIVIGERSARAERFADLLKEGAIKQDIPTLFTDSTEAEAIKLFANTYLALRVAYFNELDSYAESQGLNSKQIIEGVCLDPRIGNHYNNPSFGYGGYCLPKDTKQLLANYESVPNNIIAAIVDANRTRKDFIADSILARKPKVVGVYRLIMKSGSDNFRASSIQGIMKRIKAKGIPVIIYEPVMQEDEFFNSRVVRDLAAFKQEADVIISNRMAEELADVADKVYTRDLFGND

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
  • 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.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
  • GO:0003979 Catalysis of the reaction: H2O + 2 NAD+ + UDP-alpha-D-glucose = 3 H+ + 2 NADH + UDP-alpha-D-glucuronate.
  • GO:0006065 The chemical reactions and pathways resulting in the formation of UDP-glucuronate, a substance composed of glucuronic acid in glycosidic linkage with uridine diphosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
192 281 Pfam PF00984 UDP-glucose/GDP-mannose dehydrogenase family, central domain
192 281 InterPro IPR014026 UDP-glucose/GDP-mannose dehydrogenase, dimerisation
191 287 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like
191 287 InterPro IPR008927 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
288 388 Gene3D G3DSA:3.40.50.720 -
1 197 FunFam G3DSA:3.40.50.720:FF:000400 UDP-glucose 6-dehydrogenase
283 388 SUPERFAMILY SSF52413 UDP-glucose/GDP-mannose dehydrogenase C-terminal domain
283 388 InterPro IPR036220 UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily
198 287 FunFam G3DSA:1.10.1040.10:FF:000026 UDP-glucose 6-dehydrogenase
1 378 NCBIfam TIGR03026 nucleotide sugar dehydrogenase
1 378 InterPro IPR017476 UDP-glucose/GDP-mannose dehydrogenase
300 387 SMART SM00984 UDPG_MGDP_dh_C_a_2_a
300 387 InterPro IPR014027 UDP-glucose/GDP-mannose dehydrogenase, C-terminal
198 287 Gene3D G3DSA:1.10.1040.10 -
198 287 InterPro IPR013328 6-phosphogluconate dehydrogenase, domain 2
288 388 FunFam G3DSA:3.40.50.720:FF:000297 UDP-glucose 6-dehydrogenase
1 168 Pfam PF03721 UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
1 168 InterPro IPR001732 UDP-glucose/GDP-mannose dehydrogenase, N-terminal
1 386 PANTHER PTHR43750 UDP-GLUCOSE 6-DEHYDROGENASE TUAD
338 388 PIRSF PIRSF500134 UDPglc_DH_bac
338 388 InterPro IPR028357 UDP-glucose 6-dehydrogenase, bacterial type
1 342 PIRSF PIRSF500134 UDPglc_DH_bac
1 342 InterPro IPR028357 UDP-glucose 6-dehydrogenase, bacterial type
1 194 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
1 194 InterPro IPR036291 NAD(P)-binding domain superfamily
1 388 PIRSF PIRSF000124 UDPglc_GDPman_dh
1 388 InterPro IPR017476 UDP-glucose/GDP-mannose dehydrogenase
1 197 Gene3D G3DSA:3.40.50.720 -

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 #22
0.358
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Surrounding area
Site 2 FPocket #9
0.293
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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
0.555
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Surrounding area
Site 2 P2Rank #2
0.432
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Surrounding area
Site 3 P2Rank #3
0.287
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Surrounding area
Site 4 P2Rank #4
0.256
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Surrounding area
Site 5 P2Rank #5
0.047
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Surrounding area
All structural evidence 5 experimental · 1 predicted

Structural evidence

5 + 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 3PID
X-ray 1.40 Å A
100.0% 1-388
Viewing
PDB 3PLN
X-ray 1.50 Å A
100.0% 1-388
Loaded
PDB 3PLR
X-ray 1.70 Å A
100.0% 1-388
Loaded
PDB 3PHL
X-ray 1.90 Å A
100.0% 1-388
Loaded
PDB 3PJG
X-ray 2.70 Å A
100.0% 1-388
Loaded
ColabFold KP13_03794
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 ligand evidence is available for this target.

Direct evidence 2 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 5 2 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CXS PDB co-crystal 221.3 Da · LogP 1.19 · TPSA 66.4 Open detail RCSB PDB
UGA PDB co-crystal Detail RCSB PDB
GDX PDB via homolog Detail RCSB PDB
UDX PDB via homolog Detail RCSB PDB
UPG PDB via homolog Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
CXS RCSB PDB 221.3 Da LogP 1.19 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCCS(=O)(=O)O
UGA RCSB PDB 580.3 Da LogP -4.70 TPSA 314.1 3 viol. ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…

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.