Protein target profile

VK055_3457

glycerol kinase

Genome: KpATCC43816 Gene: glpK2 AIK82013.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GUW1
Length 503
Pocket druggability 0.891
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 64 total records
Functional annotation 1 EC 9 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
Hit
Human identity (%)
48.98 Lower values reduce human off-target concern.
Human E-value
2.45e-07
Gut microbiome similarity
55.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
63.232 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.53 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 0.891
Structure A0A0H3GUW1
Pocket Pocket 2
P2Rank 0.943
Structure A0A0H3GUW1
Pocket Pocket 1
ColabFold model
FPocket 0.844 · Pocket 3
P2Rank 0.939 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 2643 / 4744 genomes with a hit
Prevalence 55.7%

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: more central than 95.3% of genes in this genome.

Relative network centrality 95.3% more central than 95.3% 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.

MTDKKYIVALDQGTTSSRAVVMDHDANIVSVSQREFEQIYPKPGWVEHDPMEIWASQSSTLVEALAKADINSDQIAAIGITNQRETVVVWERETGKPIYNAIVWQCRRTAEICEQLKRDGMEEYIRKATGLVVDPYFSGTKVKWILDHVEGSRERAKRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHDLDWDDKMLDALDIPRAMLPEVRKSSEVYGQTNIGGKGGTRIPIAGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVTSTHGLLTTIACGPRGEVNYALEGAVFMAGASIQWLRDEMKLISDAFDSEYFATKVKDTNGVYVVPAFTGLGAPYWDPYARGAIFGLTRGVNSNHIIRATLESIAFQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNYRYSGWKKAVKRALAWEEHDEA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0016773 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
  • GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0006072 The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
  • GO:0004370 Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H+.
  • 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:0046872 Binding to a metal ion.
  • GO:0019563 The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
255 497 FunFam G3DSA:3.30.420.40:FF:000007 Glycerol kinase
262 451 Pfam PF02782 FGGY family of carbohydrate kinases, C-terminal domain
262 451 InterPro IPR018485 Carbohydrate kinase, FGGY, C-terminal
5 497 NCBIfam TIGR01311 glycerol kinase GlpK
5 497 InterPro IPR005999 Glycerol kinase
5 256 SUPERFAMILY SSF53067 Actin-like ATPase domain
5 256 InterPro IPR043129 ATPase, nucleotide binding domain
136 148 ProSitePatterns PS00933 FGGY family of carbohydrate kinases signature 1.
136 148 InterPro IPR018483 Carbohydrate kinase, FGGY, conserved site
6 253 Pfam PF00370 FGGY family of carbohydrate kinases, N-terminal domain
6 253 InterPro IPR018484 Carbohydrate kinase, FGGY, N-terminal
1 254 Gene3D G3DSA:3.30.420.40 -
4 498 Hamap MF_00186 Glycerol kinase [glpK].
4 498 InterPro IPR005999 Glycerol kinase
6 492 CDD cd07786 FGGY_EcGK_like
255 501 Gene3D G3DSA:3.30.420.40 -
256 498 SUPERFAMILY SSF53067 Actin-like ATPase domain
256 498 InterPro IPR043129 ATPase, nucleotide binding domain
2 254 FunFam G3DSA:3.30.420.40:FF:000008 Glycerol kinase
363 383 ProSitePatterns PS00445 FGGY family of carbohydrate kinases signature 2.
363 383 InterPro IPR018483 Carbohydrate kinase, FGGY, conserved site
4 503 PIRSF PIRSF000538 GlpK
4 503 InterPro IPR000577 Carbohydrate kinase, FGGY
7 497 PANTHER PTHR10196 SUGAR KINASE

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 #2
0.891
Likely same site as P2Rank 1 6.7 Å 13 shared residues 76% 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
0.943
Likely same site as FPocket 2 6.7 Å 13 shared residues 76% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.222
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Surrounding area
Site 3 P2Rank #3
0.15
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Surrounding area
Site 4 P2Rank #4
0.051
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Surrounding area
Site 5 P2Rank #5
0.032
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Surrounding area
Residue sets
UniProt: Binding site:136-136
UniProt: Binding site:14-14
UniProt: Binding site:15-15
UniProt: Binding site:16-16
UniProt: Binding site:18-18
UniProt: Binding site:235-235
UniProt: Binding site:237-237
UniProt: Binding site:246-246
UniProt: Binding site:247-247
UniProt: Binding site:268-268
UniProt: Binding site:311-311
UniProt: Binding site:315-315
UniProt: Binding site:412-412
UniProt: Binding site:416-416
UniProt: Binding site:479-479
UniProt: Binding site:84-84
UniProt: Binding site:85-85
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_A0A0H3GUW1
AlphaFold DB full sequence Viewing
ColabFold VK055_3457
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.

64 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 14 records from similar proteins
Structural ligands 14 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
4NP PDB via homolog 219.1 Da · LogP 1.07 · TPSA 109.9 Open detail RCSB PDB
6XZ PDB via homolog Detail RCSB PDB
6Y0 PDB via homolog Detail RCSB PDB
ACP PDB via homolog Detail RCSB PDB
ANP 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
4NP RCSB PDB D3KVM3 219.1 Da LogP 1.07 TPSA 109.9 ✓ Ro5 ✓ Clean c1cc(ccc1[N+](=O)[O-])OP(=O)(O)O
6XZ RCSB PDB D3KVM3 382.4 Da LogP 2.54 TPSA 86.4 ✓ Ro5 Alert COc1ccc(cc1)N2CCN(CC2)CC3=CC(=O)Oc4c3ccc(c4O)O
6Y0 RCSB PDB D3KVM3 234.3 Da LogP 2.55 TPSA 70.7 ✓ Ro5 Alert CCCCC1=CC(=O)Oc2c1ccc(c2O)O
ACP RCSB PDB P0A6F3 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)…
ANP RCSB PDB O93623 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ATF RCSB PDB P0A6F3 541.2 Da LogP -0.93 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ATS RCSB PDB P0A6F3 549.2 Da LogP -2.76 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BTB RCSB PDB Q665C6 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
DXP RCSB PDB Q5FM28 214.1 Da LogP -1.59 TPSA 124.3 ✓ Ro5 ✓ Clean CC(=O)[C@H]([C@@H](COP(=O)(O)O)O)O
G3H RCSB PDB P0A6F3 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C([C@H](C=O)O)OP(=O)(O)O
G3P RCSB PDB D3KVM3 172.1 Da LogP -1.55 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@H](COP(=O)(O)O)O)O
NH4 RCSB PDB P09099 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
POP RCSB PDB D3KVM3 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
XUL RCSB PDB Q5FM28 150.1 Da LogP -2.74 TPSA 98.0 ✓ Ro5 ✓ Clean C([C@H]([C@@H](C(=O)CO)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.