Protein target profile

VK055_0852

diguanylate cyclase domain protein

Genome: KpATCC43816 Gene: AIK79475.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GT98
Length 474
Pocket druggability 0.663
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 5 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
No hit
Gut microbiome similarity
0.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
86.73 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 0.663
Structure A0A0H3GT98
Pocket Pocket 14
P2Rank 0.911
Structure A0A0H3GT98
Pocket Pocket 1
ColabFold model
FPocket 0.929 · Pocket 1
P2Rank 0.926 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 42 / 4744 genomes with a hit
Prevalence 0.9%

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.

MSSLSIRSFTLFREEQPVRDALVLFTLTLLLHFLGAMLRLVQELSFFWPLNAVMAGIFARYVWLNRSYFYAVCFAAMLVYDGLTSRWGMGFASLLINFSNIVFIVTLAQLVLWDKRRADSMPGPINALNLFCFCLLAALLCAAVGALGSVDVERATFVPQLADWFSEQFSTAVLILPFILTLTLPSALSGFRFRQLLPVLALVLSIALGVAVGGAGSITFPLPALIWCAVRYPLPLTCLLTFLTGIGEILLVANSLIHFSPDARMQPWQLFSTRLGIAAMLISPVIVASSVEAINTLVKQLALRADFDFQTRVYSRSGLSEALKRQTLPADKLLTVMVLDIDGFKRVNDALGHEGGDCVLTQFAQQVRQLVGEQGMVARIGGEEFAVAAVVDSAQQGYLLAEKIRHGVESQPFGLGQNPIHLTISLGLETREVGHARITELFNQLLLAADDEMVKAKQSGRNQICMPTLTESAP

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
68 87 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
234 259 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
125 147 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
44 63 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
311 466 SUPERFAMILY SSF55073 Nucleotide cyclase
311 466 InterPro IPR029787 Nucleotide cyclase
149 167 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
64 67 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
305 466 NCBIfam TIGR00254 diguanylate cyclase (GGDEF) domain
305 466 InterPro IPR000160 GGDEF domain
114 124 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
302 472 Gene3D G3DSA:3.30.70.270 -
302 472 InterPro IPR043128 Reverse transcriptase/Diguanylate cyclase domain
223 233 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
332 469 ProSiteProfiles PS50887 GGDEF domain profile.
332 469 InterPro IPR000160 GGDEF domain
271 291 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
68 88 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
125 148 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
200 222 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
189 199 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
233 255 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
305 463 Pfam PF00990 Diguanylate cyclase, GGDEF domain
305 463 InterPro IPR000160 GGDEF domain
46 63 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
199 466 PANTHER PTHR45138 REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEM
21 40 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
169 191 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
196 218 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
294 467 SMART SM00267 duf1_3
294 467 InterPro IPR000160 GGDEF domain
275 297 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
41 45 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
21 40 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
292 474 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
91 113 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
260 270 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
168 188 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
311 465 CDD cd01949 GGDEF
311 465 InterPro IPR000160 GGDEF domain
94 113 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
89 93 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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 #14
0.663
Likely same site as P2Rank 2 6.6 Å 7 shared residues 78% of smaller site
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Surrounding area
Site 2 FPocket #8
0.3
Likely same site as P2Rank 1 4.5 Å 11 shared residues 92% of smaller site
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Surrounding area
Site 3 FPocket #12
0.271
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Surrounding area
Site 4 FPocket #41
0.234
Likely same site as P2Rank 1 3.9 Å 17 shared residues 85% of smaller site
Unusual size
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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
0.911
Likely same site as FPocket 41 3.9 Å 17 shared residues 85% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.233
Likely same site as FPocket 14 6.6 Å 7 shared residues 78% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.01
Show in viewer
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_A0A0H3GT98
AlphaFold DB full sequence Viewing
ColabFold VK055_0852
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.