Protein target profile

VK055_4383

glucarate dehydratase

Genome: KpATCC43816 Gene: AIK82926.1 gudD 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GXH9
Length 435
Pocket druggability 0.944
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 57 total records
Functional annotation 0 EC 3 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
No hit
Gut microbiome similarity
3.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
22.762 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
98.25 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 0.944
Structure A0A0H3GXH9
Pocket Pocket 1
P2Rank 0.941
Structure A0A0H3GXH9
Pocket Pocket 1
ColabFold model
FPocket 0.867 · Pocket 22
P2Rank 0.936 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 182 / 4744 genomes with a hit
Prevalence 3.8%

Cross-references

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

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
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.

MKVIPVTGHDSMLLNIGGAHNAWFTRNIVVLTDNAGHTGVGEAPGGEVIYQTLLAAIPQVVGQEVARLNRVVQQVHKGNQAADFDTFGKGAWTFELKVNAVAALEAALLDLLGQVLNVPVCELLGPGKQRDAVTVLGYLFYIGDRQNTDLGYLDHTPGDHEWYRLRHQQALSSEAVVRLAEAAQDRYGFKDFKLKGGVLPGEQEIDTARALKKRFPDARITVDPNGAWLLDEAIALCKGLQDVLTYAEDPCGAEQGFSGREVMAEFRRATGLPVATNMIATNWREMGHAVMLNAVDIPLADPHFWTLSGAVRVAQLCDDWGLTWGCHSNNHFDISLAMFTHVGAAAPGNPTAIDTHWIWQEGDARLTKNPLQIINGSIAVPDAPGLGVELDWEQVRRAHEAYKALPGGARNDAGPMQYLIPGWTFDRKRPVFGRH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0009063 The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
  • GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
100 125 ProSitePatterns PS00908 Mandelate racemase / muconate lactonizing enzyme family signature 1.
100 125 InterPro IPR018110 Mandelate racemase/muconate lactonizing enzyme, conserved site
126 386 FunFam G3DSA:3.20.20.120:FF:000003 Glucarate dehydratase
19 401 PANTHER PTHR48080 D-GALACTONATE DEHYDRATASE-RELATED
19 401 InterPro IPR034593 D-galactonate dehydratase DgoD-like
127 403 SUPERFAMILY SSF51604 Enolase C-terminal domain-like
127 403 InterPro IPR036849 Enolase-like, C-terminal domain superfamily
1 402 Gene3D G3DSA:3.30.390.10 -
1 402 InterPro IPR029017 Enolase-like, N-terminal
173 273 SMART SM00922 MR_MLE_2
173 273 InterPro IPR013342 Mandelate racemase/muconate lactonizing enzyme, C-terminal
1 434 SFLD SFLDF00005 glucarate dehydratase
1 434 InterPro IPR034598 D-Glucarate dehydratase-like
28 125 Pfam PF02746 Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
28 125 InterPro IPR013341 Mandelate racemase/muconate lactonizing enzyme, N-terminal domain
1 405 CDD cd03323 D-glucarate_dehydratase
1 405 InterPro IPR034598 D-Glucarate dehydratase-like
126 386 Gene3D G3DSA:3.20.20.120 -
126 386 InterPro IPR036849 Enolase-like, C-terminal domain superfamily
1 434 SFLD SFLDS00001 Enolase
1 125 SUPERFAMILY SSF54826 Enolase N-terminal domain-like
1 125 InterPro IPR029017 Enolase-like, N-terminal
177 394 Pfam PF13378 Enolase C-terminal domain-like
177 394 InterPro IPR029065 Enolase C-terminal domain-like

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
0.944
Likely same site as P2Rank 2 0.2 Å 20 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #5
0.918
Likely same site as P2Rank 1 2.4 Å 19 shared residues 90% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 3 FPocket #2
0.688
Likely same site as P2Rank 3 4.1 Å 10 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.941
Likely same site as FPocket 5 2.4 Å 19 shared residues 90% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.693
Likely same site as FPocket 1 0.2 Å 20 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.116
Likely same site as FPocket 2 4.1 Å 10 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.059
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:206-206 Proton acceptor
UniProt: Active site:338-338 Proton acceptor
UniProt: Binding site:104-104
UniProt: Binding site:149-149
UniProt: Binding site:204-204
UniProt: Binding site:234-234
UniProt: Binding site:234-236
UniProt: Binding site:265-265
UniProt: Binding site:288-288
UniProt: Binding site:31-31
UniProt: Binding site:338-340
UniProt: Binding site:367-367
UniProt: Binding site:421-421
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_A0A0H3GXH9
AlphaFold DB full sequence Viewing
ColabFold VK055_4383
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
DTT PDB via homolog 154.3 Da · LogP -0.43 · TPSA 40.5 Open detail RCSB PDB
DTU PDB via homolog Detail RCSB PDB
DXG PDB via homolog Detail RCSB PDB
GKR PDB via homolog Detail RCSB PDB
GLR 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
DTT RCSB PDB A6VQF1 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
DTU RCSB PDB A6VQF1 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@H]([C@H](CS)O)O)S
DXG RCSB PDB P0AES2 192.1 Da LogP -5.04 TPSA 140.9 ✓ Ro5 ✓ Clean C([C@@H]([C@H](C(=O)[O-])O)O)[C@@H](C(=O)[O-])O
GKR RCSB PDB A6VQF6 208.1 Da LogP -6.07 TPSA 161.2 ✓ Ro5 ✓ Clean [C@H]([C@@H]([C@@H](C(=O)[O-])O)O)([C@H](C(=O)[…
GLR RCSB PDB P0AES2 190.1 Da LogP -4.83 TPSA 137.8 ✓ Ro5 ✓ Clean C([C@@H]([C@H](C(=O)[O-])O)O)C(=O)C(=O)[O-]
TLA RCSB PDB Q3KB33 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O
XYH RCSB PDB P0AES2 194.1 Da LogP -4.68 TPSA 150.1 ✓ Ro5 ✓ Clean [C@H]([C@@H](C(=O)NO)O)([C@H](C(=O)[O-])O)O

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.