Protein target profile

VK055_0497

diguanylate cyclase domain protein

Genome: KpATCC43816 Gene: AIK79120.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GTN9
Length 453
Pocket druggability 0.565
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 5 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
0.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
41.509 Higher values support similarity to known essential genes.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
91.09 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 0.565
Structure A0A0H3GTN9
Pocket Pocket 7
P2Rank 0.391
Structure A0A0H3GTN9
Pocket Pocket 1
ColabFold model
FPocket 0.582 · Pocket 1
P2Rank 0.321 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 25 / 4744 genomes with a hit
Prevalence 0.5%

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

Attractive metabolic target: catalyzes a producing chokepoint reaction, more central than 89.0% of genes in this genome, no human homolog detected.

Relative network centrality 89.0% more central than 89.0% of genes in this genome
Chokepoint Chokepoint gene
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

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.

MPEHVHHIVKRLILYICICLLAGIGISGMTAFFHTSFSSTSSILFPLLTSFLMVFHITIACFMGMKYWSSKRRLYLTPVSFGFACSALLMLGTLSSYPDWLTCNPAPVVNQNDAVIYYFFRNIMMAVLFMSSIILYYFRQRIMHSWKAHVLTFTACILFTLTIIVLSWLYSSHSPWLSVNFIDDLSHTFTPLWQSIIGWLLMAVWFITLILLISLSKLRNIFWFSGAFFCSAYLFTLFQLLSTAGELDQTWYQARFFETLCTLFLILVLLVDVFILYRESNHKYVHSYQNSIRDPLTRLYNRSFFYDTLNQQLAKVNAQHPLSVLISDLDHFKRINDSYGHVAGDKVIQFAASVLESHSRVDDAAARIGGEEFALLLVNTGEKEAQAIAERIRLAVSAGESHLPERMTISMGVYTTYDNSVTAEACVQRADEAMYEAKNNGRNQVIVWHQQGG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • 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:0052621 Catalysis of the reaction: 2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate + 2 H+.
  • GO:0005525 Binding to GTP, guanosine triphosphate.
  • GO:0043709 The attachment of a cell to a solid substrate, via cell adhesion molecules, during the formation of a biofilm composed of microorganisms of the same species.
  • GO:1902201 Any process that stops, prevents or reduces the frequency, rate or extent of bacterial-type flagellum-dependent cell motility.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
221 241 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
74 95 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
242 255 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
63 73 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
192 214 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
279 450 Gene3D G3DSA:3.30.70.270 -
279 450 InterPro IPR043128 Reverse transcriptase/Diguanylate cyclase domain
292 444 Pfam PF00990 Diguanylate cyclase, GGDEF domain
292 444 InterPro IPR000160 GGDEF domain
96 114 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
286 449 PANTHER PTHR45138 REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEM
115 138 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
40 277 Pfam PF17158 Membrane-associated sensor, integral membrane domain
40 277 InterPro IPR033424 Membrane-associated sensor domain
74 96 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
255 277 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
286 449 FunFam G3DSA:3.30.70.270:FF:000001 Diguanylate cyclase domain protein
296 449 SUPERFAMILY SSF55073 Nucleotide cyclase
296 449 InterPro IPR029787 Nucleotide cyclase
150 171 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
116 138 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
278 448 SMART SM00267 duf1_3
278 448 InterPro IPR000160 GGDEF domain
12 37 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
139 149 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
290 447 NCBIfam TIGR00254 diguanylate cyclase (GGDEF) domain
290 447 InterPro IPR000160 GGDEF domain
278 453 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
12 33 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
293 446 CDD cd01949 GGDEF
293 446 InterPro IPR000160 GGDEF domain
172 190 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
150 172 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
191 214 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
215 220 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
320 450 ProSiteProfiles PS50887 GGDEF domain profile.
320 450 InterPro IPR000160 GGDEF domain
38 42 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
256 277 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
221 240 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
43 62 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
43 65 TMHMM TMhelix 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 · FPocket

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

Site 1 FPocket #7
0.565
Likely same site as P2Rank 2 2.5 Å 8 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #12
0.462
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Surrounding area
Site 3 FPocket #21
0.385
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Surrounding area
Site 4 FPocket #4
0.201
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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
0.391
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Surrounding area
Site 2 P2Rank #2
0.266
Likely same site as FPocket 7 2.5 Å 8 shared residues 100% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.225
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Surrounding area
Site 4 P2Rank #4
0.218
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Surrounding area
Site 5 P2Rank #5
0.148
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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_A0A0H3GTN9
AlphaFold DB full sequence Viewing
ColabFold VK055_0497
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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
BEF PDB via homolog 66.0 Da · LogP 0.88 · TPSA 0.0 Open detail RCSB PDB
C2E PDB via homolog Detail RCSB PDB
GAV PDB via homolog Detail RCSB PDB
TLA PDB via homolog Detail RCSB PDB
ZINC12501894 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
BEF RCSB PDB B8GZM2 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
C2E RCSB PDB A1U3W3 690.4 Da LogP -3.05 TPSA 349.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=O…
GAV RCSB PDB B8GZM2 539.2 Da LogP -1.40 TPSA 278.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
TLA RCSB PDB Q9HXT9 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.