KpATCC43816 Protein target profile

dgkA

Accession: VK055_3043

Gene: dgkA AIK81628.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GHH5
Length 122
Pocket druggability (P2Rank · AlphaFold DB model) 0.179
Direct ligand evidence 0 57 total records
Functional annotation 1 EC 9 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
4.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
71.429 Higher values support similarity to known essential genes.
DEG E-value
6.22e-56 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
93.58 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) 0.179
Structure A0A0H3GHH5
Pocket Pocket 1
Druggability (FPocket) 0.837
Structure A0A0H3GHH5
Pocket Pocket 1
ColabFold model
P2Rank 0.102 · Pocket 1
FPocket 0.781 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 212 / 4744 genomes with a hit
Prevalence 4.5%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MANNTTGLTRIIKAAGYSWKGFRAAWINEAAFRQEGVAAIVAVAVACWLDVDAITRVLLIGSVLLVMIVEILNSAIEAVVDRIGSDFHELSGRAKDMGSAAVLLAIIIALITWGTLLWSHYH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0008654 The chemical reactions and pathways resulting in the formation of a phospholipid, a lipid containing phosphoric acid as a mono- or diester.
  • GO:0008610 The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
  • GO:0006654 The chemical reactions and pathways resulting in the formation of phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
  • GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0004143 Catalysis of the reaction: a 1,2-diacyl-sn-glycerol + ATP = a 1,2-diacyl-sn-glycero-3-phosphate + ADP + H+.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
1 29 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 122 Gene3D G3DSA:1.10.287.3610 -
1 122 InterPro IPR036945 Diacylglycerol kinase (DAGK) superfamily
1 122 FunFam G3DSA:1.10.287.3610:FF:000001 Diacylglycerol kinase
101 121 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
16 116 Pfam PF01219 Prokaryotic diacylglycerol kinase
16 116 InterPro IPR000829 DAGK family
9 117 CDD cd14264 DAGK_IM
9 117 InterPro IPR033718 Diacylglycerol kinase, prokaryotic
2 120 PANTHER PTHR34299 DIACYLGLYCEROL KINASE
2 120 InterPro IPR000829 DAGK family
52 56 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
70 81 ProSitePatterns PS01069 Prokaryotic diacylglycerol kinase signature.
70 81 InterPro IPR000829 DAGK family
57 79 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
81 100 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
99 121 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
122 122 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
30 51 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
57 80 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.

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
0.179
Likely same site as FPocket 2 1.9 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.096
Likely same site as FPocket 1 3.3 Å 8 shared residues 89% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.051
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.008
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.837 Unusual size
Likely same site as P2Rank 2 3.3 Å 8 shared residues 89% of smaller site
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Surrounding area
Pocket 2 FPocket #2
0.714
Likely same site as P2Rank 1 1.9 Å 9 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:70-70 Proton acceptor
UniProt: Binding site:10-10
UniProt: Binding site:113-118
UniProt: Binding site:14-19
UniProt: Binding site:17-17
UniProt: Binding site:23-26
UniProt: Binding site:29-29
UniProt: Binding site:31-35
UniProt: Binding site:48-51
UniProt: Binding site:56-56
UniProt: Binding site:70-70
UniProt: Binding site:77-77
UniProt: Binding site:95-96
UniProt: Binding site:99-99
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_A0A0H3GHH5
AlphaFold DB full sequence Viewing
ColabFold VK055_3043
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
78M PDB via homolog 314.5 Da · LogP 3.75 · TPSA 66.8 Open detail RCSB PDB
78N PDB via homolog Detail RCSB PDB
79M PDB via homolog Detail RCSB PDB
79N PDB via homolog Detail RCSB PDB
ACP 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
78M RCSB PDB P0ABN1 314.5 Da LogP 3.75 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCC/C=C\CCCCCC(=O)OC[C@H](CO)O
78N RCSB PDB P0ABN1 314.5 Da LogP 3.75 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCC/C=C\CCCCCC(=O)OC[C@@H](CO)O
79M RCSB PDB P0ABN1 328.5 Da LogP 4.14 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC/C=C\CCCCCC(=O)OC[C@@H](CO)O
79N RCSB PDB P0ABN1 328.5 Da LogP 4.14 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC/C=C\CCCCCC(=O)OC[C@H](CO)O
ACP RCSB PDB P0ABN1 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)…
FLC RCSB PDB P0ABN1 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
OLC RCSB PDB P0ABN1 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)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.