Protein target profile

VK055_5034

UDP-galactopyranose mutase

Genome: KpATCC43816 Gene: AIK83560.1 glf 3D evidence: Experimental + ColabFold model Metabolism 1 reaction UniProt Q48485
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Length 384
Pocket druggability 0.902
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 3 58 total records
Functional annotation 1 EC 4 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.

Main supporting evidence

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.90, P2Rank 0.99). Use the 3D pocket comparison to verify whether they identify the same site. Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Direct ligand evidence 3 direct ligand records. Strong known ligand: co-crystal structure 3 PDB record(s) show a ligand actually co-crystallized with this exact protein - real experimental evidence, not a computational prediction. Review the complete evidence below

Risks to review

Microbiome similarity 21 of 4744 screened genomes (0.4%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.90) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant.

Evidence coverage

Core evidence streams are available for this target.
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
0.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
43.959 Higher values support similarity to known essential genes.
DEG E-value
5.96e-102 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.32 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 0.902
Structure 3INR
Pocket Pocket 4
P2Rank 0.988
Structure 3INR
Pocket Pocket 1
ColabFold model
FPocket 0.828 · Pocket 3
P2Rank 0.991 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 21 / 4744 genomes with a hit
Prevalence 0.4%

Cross-references

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

Sequence

UniProt Q48485

Structure

PDB 2BI7 PDB 3KYB PDB 1WAM PDB 2BI8 PDB 3GF4 PDB 3INT PDB 3INR

Pathways

KEGG R00505 BioCyc GALPMUT-RXN

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways
Amino sugar and nucleotide sugar metabolism Galactose metabolism
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MKSKKILIVGAGFSGAVIGRQLAEQGHQVHIIDQRDHIGGNSYDARDAETNVMVHVYGPHIFHTDNETVWNYVNEHAEMMPYVNRVKATVNGQVFSLPINLHTINQFFSKTCSPDEARALIAEKGDSTIADPQTFEEQALCFIGKELYEAFFKGYTIKQWGMQPSELPASILKRLPVRFNYDDNYFNHKFQGMPKCGYTQMIKSILNHENIKVDLQREFIVEERTHYDHVFYSGPLDAFYGYQYGRLGYRTLDFKKFTYQGDYQGCAVMNYCSVDVPYTRITEHKYFSPWEQHDGSVCYKEYSRACEENDIPYYPIRQMGEMALLEKYLSLAENEINITFVGRLGTYRYLDMDVTIAEALKTAEVYLNSLTENQPMPVFTVSVR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0008767 Catalysis of the reaction: UDP-D-galactopyranose = UDP-D-galacto-1,4-furanose.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • 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.

16 records
Show feature table
Start End DB Term Name
270 376 Gene3D G3DSA:3.40.50.720 -
1 23 Phobius SIGNAL_PEPTIDE Signal peptide region
248 316 SUPERFAMILY SSF54373 FAD-linked reductases, C-terminal domain
2 373 SUPERFAMILY SSF51971 Nucleotide-binding domain
137 265 Gene3D G3DSA:3.40.50.720 -
1 116 Gene3D G3DSA:3.40.50.720 -
150 349 Pfam PF03275 UDP-galactopyranose mutase
150 349 InterPro IPR015899 UDP-galactopyranose mutase, C-terminal
19 23 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
8 75 Pfam PF13450 NAD(P)-binding Rossmann-like domain
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
5 365 NCBIfam TIGR00031 UDP-galactopyranose mutase
5 365 InterPro IPR004379 UDP-galactopyranose mutase
7 18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
24 384 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
2 373 PANTHER PTHR21197 UDP-GALACTOPYRANOSE MUTASE

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 #7
0.416
Likely same site as P2Rank 2 4.3 Å 10 shared residues 91% of smaller site
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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
0.952
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Surrounding area
Site 2 P2Rank #2
0.497
Likely same site as FPocket 7 4.3 Å 10 shared residues 91% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.009
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Surrounding area
Site 4 P2Rank #4
0.001
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Surrounding area
All structural evidence 7 experimental · 1 predicted

Structural evidence

7 + 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 2BI7
X-ray 2.00 Å A
100.0% 1-384
PDBe RCSB PDBj File
Viewing
PDB 3KYB
X-ray 2.30 Å A,B
100.0% 1-384
PDBe RCSB PDBj File
Loaded
PDB 1WAM
X-ray 2.35 Å A
100.0% 1-384
PDBe RCSB PDBj File
Loaded
PDB 2BI8
X-ray 2.35 Å A
100.0% 1-384
PDBe RCSB PDBj File
Loaded
PDB 3GF4
X-ray 2.45 Å A,B
100.0% 1-384
PDBe RCSB PDBj File
Loaded
PDB 3INT
X-ray 2.51 Å A,B
100.0% 1-384
PDBe RCSB PDBj File
Loaded
PDB 3INR
X-ray 2.30 Å A,B
99.7% 1-383
PDBe RCSB PDBj File
Loaded
ColabFold VK055_5034
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.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 3 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 8 3 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
FDA PDB co-crystal 787.6 Da · LogP -1.75 · TPSA 363.3 Open detail RCSB PDB
GDU PDB co-crystal Detail RCSB PDB
UPG PDB co-crystal Detail RCSB PDB
3UA PDB via homolog Detail RCSB PDB
3UC 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
FDA RCSB PDB
3INT 2.51 Å Open crystal
787.6 Da LogP -1.75 TPSA 363.3 3 viol. ✓ Clean Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…
GDU RCSB PDB
3INR 2.30 Å Open crystal
566.3 Da LogP -4.79 TPSA 297.0 3 viol. ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
UPG RCSB PDB
3GF4 2.45 Å Open crystal
566.3 Da LogP -4.79 TPSA 297.0 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.