KpATCC43816 Protein target profile

acetate kinase

Accession: VK055_4828

Gene: ackA3 AIK83355.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GVR4
Length 400
Pocket druggability (P2Rank · AlphaFold DB model) 0.834
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 60 total records
Functional annotation 1 EC 10 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
3.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
96.26 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.834
Structure A0A0H3GVR4
Pocket Pocket 1
Druggability (FPocket) 0.434
Structure A0A0H3GVR4
Pocket Pocket 9
ColabFold model
P2Rank 0.754 · Pocket 1
FPocket 0.384 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 156 / 4744 genomes with a hit
Prevalence 3.3%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 89.4% of genes in this genome, no human homolog detected.

Relative network centrality 89.4% more central than 89.4% of genes in this genome
Chokepoint Not a chokepoint
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.

MSSKLVLVLNCGSSSLKFAILDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAELGAGAAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDAASFAPLHNPAHLIGIAEALKSFPHLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYGAHGTSHFYVTQEAAKILNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVMGTRSGDIDPAIIFHLHDTLGMSVDAINKMLTKESGLLGLTEVTSDCRYVEDNYQEKADAKRAMDVYCHRLAKYIGSYTALMDGRLDAVIFTGGIGENAAMVRELSLGKLGVLGFEVDHERNLAARFGKSGFINKEGTRPAVVIPTNEELVIAQDASRLTA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • GO:0016774 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a carboxyl group (acceptor).
  • GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
  • GO:0006082 The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
  • GO:0016310 The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008776 Catalysis of the reaction: ATP + acetate = ADP + acetyl phosphate.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0006083 The chemical reactions and pathways involving acetate, the anion of acetic acid.
  • GO:0006085 The chemical reactions and pathways resulting in the formation of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

34 records
Show feature table
Start End DB Term Name
2 400 PIRSF PIRSF000722 Acetate_prop_kin
2 400 InterPro IPR004372 Acetate/propionate kinase
5 393 Pfam PF00871 Acetokinase family
5 393 InterPro IPR000890 Aliphatic acid kinase, short-chain
199 400 Gene3D G3DSA:3.30.420.40 -
1 399 NCBIfam TIGR00016 acetate/propionate family kinase
1 399 InterPro IPR004372 Acetate/propionate kinase
1 398 PANTHER PTHR21060 ACETATE KINASE
1 398 InterPro IPR000890 Aliphatic acid kinase, short-chain
199 400 FunFam G3DSA:3.30.420.40:FF:000042 Acetate kinase
1 400 Hamap MF_00020 Acetate kinase [ackA].
1 400 InterPro IPR004372 Acetate/propionate kinase
3 198 Gene3D G3DSA:3.30.420.40 -
3 198 FunFam G3DSA:3.30.420.40:FF:000041 Acetate kinase
206 223 ProSitePatterns PS01076 Acetate and butyrate kinases family signature 2.
206 223 InterPro IPR023865 Aliphatic acid kinase, short-chain, conserved site
160 398 SUPERFAMILY SSF53067 Actin-like ATPase domain
160 398 InterPro IPR043129 ATPase, nucleotide binding domain
4 199 SUPERFAMILY SSF53067 Actin-like ATPase domain
4 199 InterPro IPR043129 ATPase, nucleotide binding domain
6 17 ProSitePatterns PS01075 Acetate and butyrate kinases family signature 1.
6 17 InterPro IPR023865 Aliphatic acid kinase, short-chain, conserved site
6 17 PRINTS PR00471 Acetate kinase family signature
6 17 InterPro IPR000890 Aliphatic acid kinase, short-chain
325 341 PRINTS PR00471 Acetate kinase family signature
325 341 InterPro IPR000890 Aliphatic acid kinase, short-chain
302 315 PRINTS PR00471 Acetate kinase family signature
302 315 InterPro IPR000890 Aliphatic acid kinase, short-chain
176 189 PRINTS PR00471 Acetate kinase family signature
176 189 InterPro IPR000890 Aliphatic acid kinase, short-chain
206 227 PRINTS PR00471 Acetate kinase family signature
206 227 InterPro IPR000890 Aliphatic acid kinase, short-chain
380 392 PRINTS PR00471 Acetate kinase family signature
380 392 InterPro IPR000890 Aliphatic acid kinase, short-chain

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.834
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.352
Likely same site as FPocket 9 1.3 Å 15 shared residues 94% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.062
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.052
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.007
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #9
0.434
Likely same site as P2Rank 2 1.3 Å 15 shared residues 94% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:150-150 Proton donor/acceptor
UniProt: Binding site:10-10
UniProt: Binding site:17-17
UniProt: Binding site:210-214
UniProt: Binding site:285-287
UniProt: Binding site:333-337
UniProt: Binding site:387-387
UniProt: Binding site:91-91
UniProt: Site:182-182 Transition state stabilizer
UniProt: Site:243-243 Transition state stabilizer
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_A0A0H3GVR4
AlphaFold DB full sequence Viewing
ColabFold VK055_4828
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 ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 10 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5GP PDB via homolog 363.2 Da · LogP -2.57 · TPSA 206.0 Open detail RCSB PDB
ACP PDB via homolog Detail RCSB PDB
AF3 PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
APC 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
5GP RCSB PDB O06961 363.2 Da LogP -2.57 TPSA 206.0 1 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
ACP RCSB PDB Q9X278 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)…
AF3 RCSB PDB P38502 84.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean F[Al](F)F
ANP RCSB PDB O06961 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)…
APC RCSB PDB A0QLU8 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)…
AQP RCSB PDB O06961 587.2 Da LogP -1.51 TPSA 325.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
B4P RCSB PDB O06961 836.4 Da LogP -2.45 TPSA 434.0 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
PIS RCSB PDB P38502 193.0 Da LogP -0.26 TPSA 104.1 ✓ Ro5 ✓ Clean OP(=O)(O)O[P@](=O)(O)[S-]
PPI RCSB PDB O06961 74.1 Da LogP 0.48 TPSA 37.3 ✓ Ro5 ✓ Clean CCC(=O)O
SIN RCSB PDB A0QLU8 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=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.

Cross-references

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