KpATCC43816 Protein target profile

diguanylate cyclase domain protein

Accession: VK055_5065

Gene: AIK83591.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GSE6
Length 595
Pocket druggability (P2Rank · AlphaFold DB model) 0.798
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 51 total records
Functional annotation 0 EC 0 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 (%)
39.48 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
90.09 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.798
Structure A0A0H3GSE6
Pocket Pocket 1
Druggability (FPocket) 0.539
Structure A0A0H3GSE6
Pocket Pocket 1
ColabFold model
P2Rank 0.797 · Pocket 1
FPocket 0.794 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 31 / 4744 genomes with a hit
Prevalence 0.7%

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.

MSQMVSEYMRLESRLAGMAIGAEGADHDEVRLRLEIMMSQIELLQEGDLGKFISKSEQRKTVVATLIRNLHLLDKQVDTMTPEQVRQILPVLSELDGPLTSMAAATLTQDINIVNITHDKIQHLYYIYSVISILLIAMCITLGLLMLRQNNNLRRAHVRMKTLANDLQASKEKLQVQNRRLQYDAYHDSLTGMPNRLSFWQRLQEIVNQVRPYKGCAVVMLFDLDSFKDVNDTLGHDAGDKLLQDLASRLSFFRKTSETLYRLGGDEFAMLSYDLTEEMALERANVIREKISQPYQIYDAQLNIDACIGIVISDGESRTDYLYKCADLALYEAKKEGSGHVQIFRPGMLQRLQENKSFEDDLLQALAHDEFKVYYQPIADTVTREIYGYEALVRWFHPVRGAVPPTVFIPVAEKIGLINALGEWVLKTACAEAASWATPLKVSVNVSPIQLMNTSLTDTIIEVLHQTGLDPRRLDLEITESDVFNENTRSLEILSQLREQGIQISIDDFGTGYSSLSRLSYFPFDKIKIDRSFVINIPEQKDDLDIVRLIISMGKSLHMRIVAEGVETEEQLASLQALGCDLVQGYLIGKPSPLR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

Subcellular localization

Localization
CytoplasmicMembrane

No GO or EC annotations are currently loaded for this protein.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
215 346 ProSiteProfiles PS50887 GGDEF domain profile.
215 346 InterPro IPR000160 GGDEF domain
124 146 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
181 343 NCBIfam TIGR00254 diguanylate cyclase (GGDEF) domain
181 343 InterPro IPR000160 GGDEF domain
160 184 Coils Coil Coil
360 591 Pfam PF00563 EAL domain
360 591 InterPro IPR001633 EAL domain
361 594 CDD cd01948 EAL
361 594 InterPro IPR001633 EAL domain
174 344 SMART SM00267 duf1_3
174 344 InterPro IPR000160 GGDEF domain
125 147 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
345 595 Gene3D G3DSA:3.20.20.450 EAL domain
345 595 InterPro IPR035919 EAL domain superfamily
185 338 Pfam PF00990 Diguanylate cyclase, GGDEF domain
185 338 InterPro IPR000160 GGDEF domain
169 344 Gene3D G3DSA:3.30.70.270 -
169 344 InterPro IPR043128 Reverse transcriptase/Diguanylate cyclase domain
355 595 ProSiteProfiles PS50883 EAL domain profile.
355 595 InterPro IPR001633 EAL domain
186 342 CDD cd01949 GGDEF
186 342 InterPro IPR000160 GGDEF domain
148 595 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
190 346 SUPERFAMILY SSF55073 Nucleotide cyclase
190 346 InterPro IPR029787 Nucleotide cyclase
359 594 SUPERFAMILY SSF141868 EAL domain-like
359 594 InterPro IPR035919 EAL domain superfamily
1 124 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
354 595 SMART SM00052 duf2_2
354 595 InterPro IPR001633 EAL domain
85 594 PANTHER PTHR33121 CYCLIC DI-GMP PHOSPHODIESTERASE PDEF

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.798
Likely same site as FPocket 1 4.2 Å 18 shared residues 95% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.04
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.539 Unusual size
Likely same site as P2Rank 1 4.2 Å 18 shared residues 95% 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_A0A0H3GSE6
AlphaFold DB full sequence Viewing
ColabFold VK055_5065
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.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
C2E PDB via homolog 690.4 Da · LogP -3.05 · TPSA 349.6 Open detail RCSB PDB
ZINC12501894 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC33494013 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC4095501 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC88465990 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
C2E RCSB PDB Q3SJE6 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…

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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.