Protein target profile

VK055_0020

diguanylate cyclase domain protein

Genome: KpATCC43816 Gene: AIK78651.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A6A8EJI3
Length 559
Pocket druggability 0.595
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 7 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
0.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
87.5 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 0.595
Structure A0A6A8EJI3
Pocket Pocket 3
P2Rank 0.352
Structure A0A6A8EJI3
Pocket Pocket 1
ColabFold model
FPocket 0.705 · Pocket 1
P2Rank 0.241 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 35 / 4744 genomes with a hit
Prevalence 0.7%

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

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.

MDKPLRLKLKKCYHLARPAHVVNACFIAVLFFSTLLIWREINVLEEAYVANQRNNLANVAHEMDGLLQFNIDRMMFFRHGMQAALEQPLDIDVLRKASQRYLSQRHQQAWRVALPNRRTLPVFGISGSVAGHNPILLVDDPLAADELMATLELGYLLNLTQHDRDFAERMQYISRSGFFTSTLPLRDESQVITHYSQALGAPWFTRQTQRNNPGRGVIWQTFPDDDPQLEEQVVTASIPLDFAGYWRGVLAMDFSVSEIKAFLVSAMQGGQEGEYQLYDSHLNLLASSAPGNVLTLLSPREQELLSRAFVHDNQGGLRLLTRYISWAKLRNFDGVLLRIHTLREGVRGNFGTITIALTLMWVLFTLMLLLSWLVIRRMVRNMSVLQTSLEWQAWHDALTRLLNRGALFEQAMAVASDCQRSGRPLAVIQLDLDHFKHINDRYGHQAGDRVLSMVASTLSSAVRQGDLLGRVGGEEFCIVMPNTTLQEAAAVAERLRQRIQGREVFLHNNVTLRVSASLGVSASEERGEYQFEALQSVADGRLYLAKQNGRNQVCFRSAA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • 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:0046872 Binding to a metal ion.
  • 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:0030244 The chemical reactions and pathways resulting in the formation of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
  • 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.

25 records
Show feature table
Start End DB Term Name
350 375 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
353 375 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
21 38 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
389 554 NCBIfam TIGR00254 diguanylate cyclase (GGDEF) domain
389 554 InterPro IPR000160 GGDEF domain
21 38 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
395 554 CDD cd01949 GGDEF
395 554 InterPro IPR000160 GGDEF domain
393 552 Pfam PF00990 Diguanylate cyclase, GGDEF domain
393 552 InterPro IPR000160 GGDEF domain
254 555 PANTHER PTHR45138 REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEM
1 20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
388 557 FunFam G3DSA:3.30.70.270:FF:000001 Diguanylate cyclase domain protein
37 222 Pfam PF17151 Periplasmic sensor domain
37 222 InterPro IPR033416 Periplasmic sensor domain CHASE7
376 559 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
39 349 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
398 556 SUPERFAMILY SSF55073 Nucleotide cyclase
398 556 InterPro IPR029787 Nucleotide cyclase
423 558 ProSiteProfiles PS50887 GGDEF domain profile.
423 558 InterPro IPR000160 GGDEF domain
380 557 Gene3D G3DSA:3.30.70.270 -
380 557 InterPro IPR043128 Reverse transcriptase/Diguanylate cyclase domain
382 556 SMART SM00267 duf1_3
382 556 InterPro IPR000160 GGDEF domain

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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 #3
0.595
Likely same site as P2Rank 3 1.4 Å 13 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 2 FPocket #46
0.293
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.352
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.223
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.16
Likely same site as FPocket 3 1.4 Å 13 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.1
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.03
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_A0A6A8EJI3
AlphaFold DB full sequence Viewing
ColabFold VK055_0020
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
BEZ PDB via homolog Detail RCSB PDB
C2E PDB via homolog Detail RCSB PDB
GAV 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
BEZ RCSB PDB P0AA89 122.1 Da LogP 1.38 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)O
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…

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.