Protein target profile

VK055_3709

shikimate kinase family protein

Genome: KpATCC43816 Gene: AIK82264.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GZE8
Length 173
Pocket druggability 0.984
Direct ligand evidence 0 60 total records
Functional annotation 1 EC 7 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 (%)
29.464 Lower values reduce human off-target concern.
Human E-value
1.81e-07
Gut microbiome similarity
3.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
96.532 Higher values support similarity to known essential genes.
DEG E-value
8.7e-123 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
93.06 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 0.984
Structure A0A0H3GZE8
Pocket Pocket 1
P2Rank 0.968
Structure A0A0H3GZE8
Pocket Pocket 1
ColabFold model
FPocket 0.391 · Pocket 10
P2Rank 0.892 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 170 / 4744 genomes with a hit
Prevalence 3.6%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MAEKRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQEIEKRTGADVGWVFDVEGEEGFRDREEKIINELTEKQGIVLATGGGSVKSRETRNRLSARGVVVYLETTIEKQLARTQRDKKRPLLQVDAPPREVLEALADERNPLYEEIADVTIRTDDQSAKVVANQIIHMLESN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0004765 Catalysis of the reaction: ATP + shikimate = 3-phosphoshikimate + ADP + 2 H+.
  • GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
  • GO:0009073 The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
  • GO:0009423 The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
3 165 PANTHER PTHR21087 SHIKIMATE KINASE
6 158 CDD cd00464 SK
6 158 InterPro IPR000623 Shikimate kinase/Threonine synthase-like 1
4 171 Hamap MF_00109 Shikimate kinase [aroK].
4 171 InterPro IPR000623 Shikimate kinase/Threonine synthase-like 1
4 170 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
4 170 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 173 FunFam G3DSA:3.40.50.300:FF:000099 Shikimate kinase 1
59 67 PRINTS PR01100 Shikimate kinase family signature
98 115 PRINTS PR01100 Shikimate kinase family signature
7 22 PRINTS PR01100 Shikimate kinase family signature
31 44 PRINTS PR01100 Shikimate kinase family signature
77 86 PRINTS PR01100 Shikimate kinase family signature
60 85 ProSitePatterns PS01128 Shikimate kinase signature.
60 85 InterPro IPR023000 Shikimate kinase, conserved site
1 173 Gene3D G3DSA:3.40.50.300 -
1 173 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
13 170 Pfam PF01202 Shikimate kinase
13 170 InterPro IPR031322 Shikimate kinase/gluconokinase

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 · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.984
Likely same site as P2Rank 1 4.9 Å 34 shared residues 87% 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
0.968
Likely same site as FPocket 1 4.9 Å 34 shared residues 87% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.027
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:108-108
UniProt: Binding site:128-128
UniProt: Binding site:145-145
UniProt: Binding site:2-7
UniProt: Binding site:24-24
UniProt: Binding site:48-48
UniProt: Binding site:6-6
UniProt: Binding site:70-70
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_A0A0H3GZE8
AlphaFold DB full sequence Viewing
ColabFold VK055_3709
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.

60 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 3 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3DS PDB via homolog 172.1 Da · LogP -1.31 · TPSA 94.8 Open detail RCSB PDB
ACP PDB via homolog Detail RCSB PDB
K2Q PDB via homolog Detail RCSB PDB
OSA PDB via homolog Detail RCSB PDB
S3P 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
3DS RCSB PDB G0S061 172.1 Da LogP -1.31 TPSA 94.8 ✓ Ro5 ✓ Clean C1[C@H]([C@@H](C(=O)C=C1C(=O)O)O)O
ACP RCSB PDB P9WPY3 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
K2Q RCSB PDB P9WPY3 212.2 Da LogP -0.55 TPSA 87.0 ✓ Ro5 ✓ Clean C1C=C[C@]2(C=C(C[C@H]([C@@H]2O)O1)C(=O)O)O
OSA RCSB PDB P56073 489.5 Da LogP 3.90 TPSA 199.9 ✓ Ro5 Alert c1cc2c(cc1N)cc(c(c2O)/N=N/c3ccc4c(c3)cc(cc4O)S(…
S3P RCSB PDB P9WPY3 254.1 Da LogP -1.40 TPSA 144.5 ✓ Ro5 ✓ Clean C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)OP(=O)(O)O)O)O
SKM RCSB PDB A0A0M3KL09 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
TLA RCSB PDB P56073 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=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.