Protein target profile

VK055_4575

diguanylate cyclase domain protein

Genome: KpATCC43816 Gene: AIK83113.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GTW8
Length 379
Pocket druggability 0.986
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 54 total records
Functional annotation 0 EC 2 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
1.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
88.53 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 0.986
Structure A0A0H3GTW8
Pocket Pocket 1
P2Rank 0.105
Structure A0A0H3GTW8
Pocket Pocket 1
ColabFold model
FPocket 0.882 · Pocket 2
P2Rank 0.108 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 51 / 4744 genomes with a hit
Prevalence 1.1%

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.

MTLVWLLLSTASIFTLKQYAQKNLELTAATMGRSLEAALVFGDSAAAEETLASLGKQGQISQAIVLNGQMQHFAAWRHEPLANKEQVSGLISKWLFPEPTVQPIWHQGKQIGELRLTALDELISHFLGISILVLTGSILLASFIALLLTHSLHRGIVAALQSITEVVHDIRENRHFSRRVPEERIEEFHLFAQDFNSLLGEMEDWQRQLQAKNAQLLRSSLHDPLTGLANRAAFRNALAELMQNEVDHQTSALLFLDGDNFKLINDNWGHAAGDKVLMEVASRLMTFAGKRHLAWRLGGDEFAVLLREVRSEAEVQALCQALTEQFLPPFNLHNGHSATLSLSVGYALAWEHATAESLQELADQNMYRMKNQRIQQTLK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0007165 The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
221 373 CDD cd01949 GGDEF
221 373 InterPro IPR000160 GGDEF domain
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
154 207 ProSiteProfiles PS50885 HAMP domain profile.
154 207 InterPro IPR003660 HAMP domain
122 148 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
3 16 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
221 373 Pfam PF00990 Diguanylate cyclase, GGDEF domain
17 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
16 116 Pfam PF17152 Periplasmic sensor domain
16 116 InterPro IPR033417 Periplasmic sensor domain CHASE8
117 208 Gene3D G3DSA:6.10.340.10 -
193 372 PANTHER PTHR46663 DIGUANYLATE CYCLASE DGCT-RELATED
126 148 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
209 377 SMART SM00267 duf1_3
209 377 InterPro IPR000160 GGDEF domain
218 373 NCBIfam TIGR00254 diguanylate cyclase (GGDEF) domain
218 373 InterPro IPR000160 GGDEF domain
21 121 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
149 379 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
195 215 Coils Coil Coil
209 377 Gene3D G3DSA:3.30.70.270 -
209 377 InterPro IPR043128 Reverse transcriptase/Diguanylate cyclase domain
209 378 FunFam G3DSA:3.30.70.270:FF:000017 Predicted diguanylate cyclase
1 20 SignalP_EUK SignalP-noTM SignalP-noTM
225 373 SUPERFAMILY SSF55073 Nucleotide cyclase
225 373 InterPro IPR029787 Nucleotide cyclase
249 379 ProSiteProfiles PS50887 GGDEF domain profile.
249 379 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.

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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 #1
0.986
Likely same site as P2Rank 5 4.0 Å 10 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.105
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.041
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.041
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.04
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Surrounding area
Site 5 P2Rank #5
0.032
Likely same site as FPocket 1 4.0 Å 10 shared residues 100% of smaller site
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_A0A0H3GTW8
AlphaFold DB full sequence Viewing
ColabFold VK055_4575
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
BEZ PDB via homolog 122.1 Da · LogP 1.38 · TPSA 37.3 Open detail RCSB PDB
C2E PDB via homolog Detail RCSB PDB
GAV PDB via homolog Detail RCSB PDB
TBU 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
BEZ RCSB PDB P0AA89 122.1 Da LogP 1.38 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)O
C2E RCSB PDB A0A0H3CAN8 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 P0AA89 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…
TBU RCSB PDB Q9I4L5 74.1 Da LogP 0.78 TPSA 20.2 ✓ Ro5 ✓ Clean CC(C)(C)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.