KpATCC43816 Protein target profile

diguanylate cyclase domain protein

Accession: VK055_0808

Gene: AIK79431.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GTD8
Length 551
Pocket druggability (P2Rank · AlphaFold DB model) 0.788
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 54 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
0.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
91.68 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) 0.788
Structure A0A0H3GTD8
Pocket Pocket 1
Druggability (FPocket) 0.683
Structure A0A0H3GTD8
Pocket Pocket 13
ColabFold model
P2Rank 0.793 · Pocket 1
FPocket 0.669 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 4 / 4744 genomes with a hit
Prevalence 0.1%

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.

MSNDHLTDIAYRHFIESVKDYAIYMLSADGTVISWNEGARRAKGYLSDEIIGRYFGLFYSEAEQLSGVPAKNLEIALRSGQFEGEGWRYCKDGSRFWAHVMIDTIRDEQNTLLGFAKITRDISEQKAINDRIAWMARYDALTGLPNRVEFFERVEKLITGNDARRFAIFTIDLDKFKEINDLQGHLIGDQLLQRVAGAVLKTLQKEEMVARFGGDEFVAVKPFSDEGEVDAFAARLWHCFSGKQTFAATEVVLSASIGISVYPEDGTDINTILSNSDLAMYRAKSSLDHKICWYEREMDDKTRQRNMMAADIRRGIHAGEFSLHYQAIRNIKDRSITGYEALLRWQHPQLGTIPPDVFIPIAEESGAIVPLGYWVLEQVCNESLENGLNRKVSVNISPVQLRHRSFIEKVREILMRTAYPVSLLEFEVTETAFVINKQLAFSVLHHLQKMGISIALDDFGTGYSSLSMLRDFHFDVIKLDRSFMTDVESNPQVRSFVRAIISLGNSINTPLIAEGVETAGQLQILEEEGCDEMQGFLFGEPVDIKHLPDRR

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.

42 records
Show feature table
Start End DB Term Name
304 546 SMART SM00052 duf2_2
304 546 InterPro IPR001633 EAL domain
310 544 CDD cd01948 EAL
310 544 InterPro IPR001633 EAL domain
305 551 ProSiteProfiles PS50883 EAL domain profile.
305 551 InterPro IPR001633 EAL domain
11 129 NCBIfam TIGR00229 PAS domain S-box protein
11 129 InterPro IPR000014 PAS domain
310 541 Pfam PF00563 EAL domain
310 541 InterPro IPR001633 EAL domain
306 550 Gene3D G3DSA:3.20.20.450 EAL domain
306 550 InterPro IPR035919 EAL domain superfamily
141 295 SUPERFAMILY SSF55073 Nucleotide cyclase
141 295 InterPro IPR029787 Nucleotide cyclase
125 294 SMART SM00267 duf1_3
125 294 InterPro IPR000160 GGDEF domain
7 80 ProSiteProfiles PS50112 PAS repeat profile.
7 80 InterPro IPR000014 PAS domain
164 296 ProSiteProfiles PS50887 GGDEF domain profile.
164 296 InterPro IPR000160 GGDEF domain
311 547 SUPERFAMILY SSF141868 EAL domain-like
311 547 InterPro IPR035919 EAL domain superfamily
20 124 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain)
20 124 InterPro IPR035965 PAS domain superfamily
71 134 ProSiteProfiles PS50113 PAC domain profile.
71 134 InterPro IPR000700 PAS-associated, C-terminal
20 122 CDD cd00130 PAS
20 122 InterPro IPR000014 PAS domain
120 305 Gene3D G3DSA:3.30.70.270 -
120 305 InterPro IPR043128 Reverse transcriptase/Diguanylate cyclase domain
137 286 CDD cd01949 GGDEF
137 286 InterPro IPR000160 GGDEF domain
8 119 Gene3D G3DSA:3.30.450.20 PAS domain
83 125 SMART SM00086 pac_2
83 125 InterPro IPR001610 PAC motif
136 286 Pfam PF00990 Diguanylate cyclase, GGDEF domain
136 286 InterPro IPR000160 GGDEF domain
22 124 Pfam PF13426 PAS domain
22 124 InterPro IPR000014 PAS domain
22 543 PANTHER PTHR44757 DIGUANYLATE CYCLASE DGCP
133 287 NCBIfam TIGR00254 diguanylate cyclase (GGDEF) domain
133 287 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 · P2Rank

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

Pocket 1 P2Rank #1
0.788
Likely same site as FPocket 2 4.2 Å 15 shared residues 68% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.079
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Surrounding area
Pocket 3 P2Rank #3
0.029
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Surrounding area
Pocket 4 P2Rank #4
0.016
Likely same site as FPocket 13 5.2 Å 6 shared residues 86% of smaller site
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Surrounding area
Pocket 5 P2Rank #5
0.013
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #13
0.683 Unusual size
Likely same site as P2Rank 4 5.2 Å 6 shared residues 86% of smaller site
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Surrounding area
Pocket 2 FPocket #2
0.567 Unusual size
Likely same site as P2Rank 1 4.2 Å 15 shared residues 68% of smaller site
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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_A0A0H3GTD8
AlphaFold DB full sequence Viewing
ColabFold VK055_0808
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
C2E PDB via homolog 690.4 Da · LogP -3.05 · TPSA 349.6 Open detail RCSB PDB
DAO PDB via homolog Detail RCSB PDB
GEY PDB via homolog Detail RCSB PDB
OXY PDB via homolog Detail RCSB PDB
ZINC100022626 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…
DAO RCSB PDB C9XTL5 200.3 Da LogP 3.99 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCC(=O)O
GEY RCSB PDB C9XTL5 198.3 Da LogP 3.77 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCC/C=C\C(=O)O
OXY RCSB PDB P76129 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean 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.

Cross-references

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