Protein target profile

VK055_5071

diguanylate cyclase domain protein

Genome: KpATCC43816 Gene: AIK83597.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GVP9
Length 323
Pocket druggability 0.608
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 55 total records
Functional annotation 1 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
0.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
93.75 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 0.608
Structure A0A0H3GVP9
Pocket Pocket 14
P2Rank 0.699
Structure A0A0H3GVP9
Pocket Pocket 1
ColabFold model
FPocket 0.816 · Pocket 1
P2Rank 0.658 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 31 / 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.

MKLAGLHPDEQRRLQSLRSSGLLNSGKEERFDRLTRLARSLYNLPVASISLVGEDLLHIKSCAGLDVDTVPRDISFCAHTILQTDPLIVNDMQQDERFHDNPLVIEAPFIRFYAGYPVQLPDGATVGSFCLMDHQPRSFSAHEMQILSDLAAIVEDEFKVLDAATSDELTGLFNRRGFLTLAEYALLTAQRRHEPVSLAFVDLDRFKHINDTWGHEEGDRALIAIADLMKAAFRESDILARQGGDEFIILFANTSRHDAAAAMETLSHNVARFNQQAAHPWQLAFSWGCVEYDPAHHPSLNALVATADRLMYQAKQKQGRERR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

2
  • GO:0005515 Binding to a protein.
  • GO:0052621 Catalysis of the reaction: 2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate + 2 H+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
163 321 NCBIfam TIGR00254 diguanylate cyclase (GGDEF) domain
163 321 InterPro IPR000160 GGDEF domain
10 153 Gene3D G3DSA:3.30.450.40 -
10 153 InterPro IPR029016 GAF-like domain superfamily
194 323 ProSiteProfiles PS50887 GGDEF domain profile.
194 323 InterPro IPR000160 GGDEF domain
154 322 Gene3D G3DSA:3.30.70.270 -
154 322 InterPro IPR043128 Reverse transcriptase/Diguanylate cyclase domain
154 322 SMART SM00267 duf1_3
154 322 InterPro IPR000160 GGDEF domain
159 323 FunFam G3DSA:3.30.70.270:FF:000001 Diguanylate cyclase domain protein
26 168 SMART SM00065 gaf_1
26 168 InterPro IPR003018 GAF domain
28 155 Pfam PF01590 GAF domain
28 155 InterPro IPR003018 GAF domain
167 322 CDD cd01949 GGDEF
167 322 InterPro IPR000160 GGDEF domain
164 318 Pfam PF00990 Diguanylate cyclase, GGDEF domain
164 318 InterPro IPR000160 GGDEF domain
28 154 SUPERFAMILY SSF55781 GAF domain-like
169 318 SUPERFAMILY SSF55073 Nucleotide cyclase
169 318 InterPro IPR029787 Nucleotide cyclase
16 322 PANTHER PTHR45138 REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEM

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
0.608
Likely same site as P2Rank 1 3.8 Å 9 shared residues 69% of smaller site
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Surrounding area
Site 2 FPocket #3
0.431
Likely same site as P2Rank 2 6.1 Å 12 shared residues 67% 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
0.699
Likely same site as FPocket 14 3.8 Å 9 shared residues 69% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.236
Likely same site as FPocket 3 6.1 Å 12 shared residues 67% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.107
Likely same site as FPocket 3 6.9 Å 17 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.06
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Surrounding area
Site 5 P2Rank #5
0.018
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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_A0A0H3GVP9
AlphaFold DB full sequence Viewing
ColabFold VK055_5071
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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 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
CYC PDB via homolog Detail RCSB PDB
GAV PDB via homolog Detail RCSB PDB
POP 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
BEZ RCSB PDB P0AA89 122.1 Da LogP 1.38 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)O
C2E RCSB PDB Q886S7 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…
CYC RCSB PDB Q55434 588.7 Da LogP 5.19 TPSA 160.9 2 viol. ✓ Clean CC[C@@H]\1[C@H](C(=O)N/C1=C\c2c(c(c([nH]2)/C=C\…
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…
POP RCSB PDB Q39UD1 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=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.