Protein target profile

VK055_3791

dehydroshikimate reductase

Genome: KpATCC43816 Gene: aroE AIK82346.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3H3T6
Length 272
Pocket druggability 0.042
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 54 total records
Functional annotation 0 EC 3 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
No hit
Gut microbiome similarity
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
55.311 Higher values support similarity to known essential genes.
DEG E-value
6.26e-90 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.75 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 0.042
Structure A0A0H3H3T6
Pocket Pocket 10
P2Rank 0.809
Structure A0A0H3H3T6
Pocket Pocket 1
ColabFold model
FPocket 0.026 · Pocket 9
P2Rank 0.711 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 140 / 4744 genomes with a hit
Prevalence 3.0%

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

Attractive metabolic target: catalyzes a producing chokepoint reaction in Phenylalanine, tyrosine and tryptophan biosynthesis, more central than 99.1% of genes in this genome, no human homolog detected.

Relative network centrality 99.1% more central than 99.1% of genes in this genome
Chokepoint Chokepoint gene
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.

METYAVFGNPIAHSKSPAIHQLFARQLGITHPYGRVLAPLDDFVSSLNQFFAEGGKGANVTVPFKEEAFARADELTERAALAGAVNTLKRLEDGRLLGDNTDGIGLLSDLERLGFIKPRQRILLVGAGGASRGVLLPLLSLGCAVTIVNRTYSRARELATLFAHTGSVSAREMDTLSGETFDLIVNATSSGIDGDVPAISASIVNADVYCYDMFYQKGPTPFLHWCQQYGAVHCADGLGMLVAQAAHAVLLWHGVLPAIAPVIETLQQELNA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0004764 Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
  • GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
  • GO:0019632 The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
2 101 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain
2 101 InterPro IPR046346 Aminoacid dehydrogenase-like, N-terminal domain superfamily
102 244 Gene3D G3DSA:3.40.50.720 -
119 190 Pfam PF01488 Shikimate / quinate 5-dehydrogenase
119 190 InterPro IPR006151 Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase
1 269 Hamap MF_00222 Shikimate dehydrogenase (NADP(+)) [aroE].
1 269 InterPro IPR022893 Shikimate dehydrogenase family
2 259 PANTHER PTHR21089 SHIKIMATE DEHYDROGENASE
2 259 InterPro IPR022893 Shikimate dehydrogenase family
5 117 FunFam G3DSA:3.40.50.10860:FF:000006 Shikimate dehydrogenase (NADP(+))
237 267 Pfam PF18317 Shikimate 5'-dehydrogenase C-terminal domain
237 267 InterPro IPR041121 SDH, C-terminal
101 254 CDD cd01065 NAD_bind_Shikimate_DH
5 254 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase, chain A, domain 1
3 270 NCBIfam TIGR00507 shikimate dehydrogenase
3 270 InterPro IPR011342 Shikimate dehydrogenase
6 88 Pfam PF08501 Shikimate dehydrogenase substrate binding domain
6 88 InterPro IPR013708 Shikimate dehydrogenase substrate binding, N-terminal
102 269 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
102 269 InterPro IPR036291 NAD(P)-binding domain superfamily
102 244 FunFam G3DSA:3.40.50.720:FF:000104 Shikimate dehydrogenase (NADP(+))

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.

Download VMD script Full viewer

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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

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

Site 1 P2Rank #1
0.809
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.108
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.024
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:65-65 Proton acceptor
UniProt: Binding site:102-102
UniProt: Binding site:126-130
UniProt: Binding site:14-16
UniProt: Binding site:149-154
UniProt: Binding site:213-213
UniProt: Binding site:215-215
UniProt: Binding site:237-237
UniProt: Binding site:244-244
UniProt: Binding site:61-61
UniProt: Binding site:77-77
UniProt: Binding site:86-86
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_A0A0H3H3T6
AlphaFold DB full sequence Viewing
ColabFold VK055_3791
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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ATR PDB via homolog 507.2 Da · LogP -1.63 · TPSA 279.1 Open detail RCSB PDB
DHK PDB via homolog Detail RCSB PDB
DTV PDB via homolog Detail RCSB PDB
SKM PDB via homolog Detail RCSB PDB
ZINC3871401 ZINC proposed compound · Tanimoto 0.860 Detail ZINC

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
ATR RCSB PDB O67049 507.2 Da LogP -1.63 TPSA 279.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DHK RCSB PDB P56119 174.2 Da LogP -0.75 TPSA 98.0 ✓ Ro5 ✓ Clean C1[C@@H](C=C([C@H]([C@@H]1O)O)O)C(=O)O
DTV RCSB PDB P15770 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@H]([C@@H](CS)O)O)S
SKM RCSB PDB O67049 174.2 Da LogP -1.52 TPSA 98.0 ✓ Ro5 ✓ Clean C1[C@H]([C@@H]([C@@H](C=C1C(=O)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.