Protein target profile

VK055_4385

glycerate kinase I

Genome: KpATCC43816 Gene: AIK82928.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3H232
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Length 379
Pocket druggability 0.969
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 1 total records
Functional annotation 0 EC 2 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.

Main supporting evidence

Central metabolic position More central than 95.5% of genes in this genome. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.52. Review the complete evidence below

Risks to review

Microbiome similarity 273 of 4744 screened genomes (5.8%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.97) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.97, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

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
5.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
58.445 Higher values support similarity to known essential genes.
DEG E-value
1.05e-141 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.54 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 0.969
Structure A0A0H3H232
Pocket Pocket 1
P2Rank 0.523
Structure A0A0H3H232
Pocket Pocket 1
ColabFold model
FPocket 0.886 · Pocket 1
P2Rank 0.671 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 273 / 4744 genomes with a hit
Prevalence 5.8%

Cross-references

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

Sequence

UniProt A0A0H3H232

Chemistry

ChEMBL FOM

Pathways

KEGG R01514 BioCyc GLY3KIN-RXN KEGG R08572 BioCyc GKI-RXN

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 95.5% of genes in this genome, no human homolog detected.

Relative network centrality 95.5% more central than 95.5% of genes in this genome
Chokepoint Not a chokepoint
Pathways
Glycerolipid metabolism Glycine, serine and threonine metabolism Glyoxylate and dicarboxylate metabolism Methane metabolism Pentose phosphate pathway
Catalyzed reactions

2 reactions 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.

MKIVIAPDSWKESLSALEVASAIEQGFREIYPDAEYVKLPVADGGEGTVEAMVAATGGLLVPLTVTGPLGEPVEAFYGLSGDRQCAFIEMAAASGLESVPPAQRNPLLTTSWGTGELIRHALDAGVRQIIIGIGGSATNDGGAGMAQALGAKLLTAEGQQIASGGGALETLALIDLSELDSRLADCRIDVACDVTNPLTGPQGASAVFGPQKGATAQMIDRLDSGLRHYARIIARDLDIDVLSLEGGGAAGGMGAALYAFCGAQLRPGIEIVTDALQLAERVADADLVITGEGRIDSQTIHGKVPVGVARVAKRFNVPVIGIAGSLTADVGVVHQHGLDAVFSVLYTICTLDEALANAAANLRMTARNVAAVLQMGDRR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • GO:0031388 The process of introducing one or more phosphate groups into an organic acid.
  • GO:0008887 Catalysis of the reaction: D-glycerate + ATP = 3-phospho-D-glycerate + ADP + 2 H+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
2 375 NCBIfam TIGR00045 glycerate kinase
2 375 InterPro IPR004381 Glycerate kinase
42 276 Gene3D G3DSA:3.90.1510.10 Glycerate kinase, domain 2
42 276 InterPro IPR018193 Glycerate kinase, flavodoxin-like fold
1 376 PANTHER PTHR21599 GLYCERATE KINASE
1 376 InterPro IPR004381 Glycerate kinase
1 377 PIRSF PIRSF006078 GlxK
1 377 InterPro IPR004381 Glycerate kinase
3 373 Pfam PF02595 Glycerate kinase family
3 373 InterPro IPR004381 Glycerate kinase
1 375 SUPERFAMILY SSF110738 Glycerate kinase I
1 375 InterPro IPR036129 Glycerate kinase superfamily
1 363 Gene3D G3DSA:3.40.50.10350 Glycerate kinase; domain 1
1 363 InterPro IPR018197 Glycerate kinase, restriction-enzyme-like fold

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
0.969
Likely same site as P2Rank 4 3.9 Å 11 shared residues 100% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #16
0.298
Likely same site as P2Rank 1 7.2 Å 6 shared residues 55% 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
0.523
Likely same site as FPocket 16 7.2 Å 6 shared residues 55% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.227
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Surrounding area
Site 3 P2Rank #3
0.217
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Surrounding area
Site 4 P2Rank #4
0.119
Likely same site as FPocket 1 3.9 Å 11 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.046
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Surrounding area
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_A0A0H3H232
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4385
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.

1 records
Chemistry signal

Bioactivity evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 0 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 0 similarity-based ZINC candidates
Best available ligand signal
FOM ChEMBL via homolog 183.1 Da · LogP -0.60 · TPSA 98.1 Open detail ChEMBL

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

Show only:
Ligand UniProt (homolog) pchembl MW · LogP · TPSA Lipinski PAINS SMILES
FOM ChEMBL P77364 — 183.1 Da LogP -0.60 TPSA 98.1 ✓ Ro5 ✓ Clean C(CN(C=O)O)CP(=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.