KpATCC43816 Protein target profile

putative cyclic-di-GMP phosphodiesterase AdrB

Accession: VK055_0119

Gene: AIK78747.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GRU7
Length 525
Pocket druggability (P2Rank · AlphaFold DB model) 0.753
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 52 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
1.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
89.09 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) 0.753
Structure A0A0H3GRU7
Pocket Pocket 1
Druggability (FPocket) 0.697
Structure A0A0H3GRU7
Pocket Pocket 6
ColabFold model
P2Rank 0.852 · Pocket 1
FPocket 0.567 · Pocket 12
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 61 / 4744 genomes with a hit
Prevalence 1.3%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a consuming chokepoint reaction, no human homolog detected.

Relative network centrality 0.0% more central than 0.0% 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.

MQTAQKVITAYRHKRIIVCLLVALATLGATLAIRFISQRSVNEDYIRTAASQRVAALNDILRPLSAQRATLLPLVGKPCPDIHLTLRKMAASLQTIRSVALVTSGIVYCSSIFGPRQADLHRLQPALPAPRPLLLFSNDSSLLKGSPVLIQWYPAAENGLDGVMLVVNIELLGTLILNEKSALISDVSLQVGDRYFSSRHGLLEKTHVPQGTVIYRQRSTEFPFTVNINGPGASAIALEELPGELPLALIFSLLMTGIAWLATAGRMSFSREISLGISAREFALWCQPLQDARSGRCCGVEILLRWNNPRRGTISPEVFIPIAEGNNLIIPLTRYVIAETARRLDAFPRDRHFHIAINVAARHFANGLLLRDLHNYWFSVDPVQQLVVELTERDVLQDGDQHMAEHLHFKGVQLAIDDFGTGNTSLSWLEKLRPDVLKIDRSFTSSVGIDSVNATVTDIIIALANRLHIVTVAEGVETLEQENYLRSHGVDVLQGFYYARPMPVEAFPAWLASREESEDESETTE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

2
  • 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:0071111 Catalysis of the reaction: cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'->5')guanosine + 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
271 506 CDD cd01948 EAL
271 506 InterPro IPR001633 EAL domain
1 15 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
28 32 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
16 38 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
265 506 SMART SM00052 duf2_2
265 506 InterPro IPR001633 EAL domain
16 27 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 32 Phobius SIGNAL_PEPTIDE Signal peptide region
46 237 Pfam PF12792 CSS motif domain associated with EAL
46 237 InterPro IPR024744 Putative cyclic diguanylate phosphodiesterase, CSS motif-containing domain
33 244 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
270 514 PANTHER PTHR33121 CYCLIC DI-GMP PHOSPHODIESTERASE PDEF
272 514 SUPERFAMILY SSF141868 EAL domain-like
272 514 InterPro IPR035919 EAL domain superfamily
265 525 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
266 524 Gene3D G3DSA:3.20.20.450 EAL domain
266 524 InterPro IPR035919 EAL domain superfamily
245 264 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
271 501 Pfam PF00563 EAL domain
271 501 InterPro IPR001633 EAL domain
266 515 ProSiteProfiles PS50883 EAL domain profile.
266 515 InterPro IPR001633 EAL 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
0.753
Likely same site as FPocket 1 4.5 Å 16 shared residues 80% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.514
Likely same site as FPocket 6 1.3 Å 14 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.485
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Surrounding area
Pocket 4 P2Rank #4
0.09
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Surrounding area
Pocket 5 P2Rank #5
0.018
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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 #6
0.697
Likely same site as P2Rank 2 1.3 Å 14 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #1
0.567
Likely same site as P2Rank 1 4.5 Å 16 shared residues 80% 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_A0A0H3GRU7
AlphaFold DB full sequence Viewing
ColabFold VK055_0119
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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 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
HB0 PDB via homolog 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

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 P21514 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…
HB0 RCSB PDB P21514 130.2 Da LogP 0.53 TPSA 40.5 ✓ Ro5 ✓ Clean C1CC(CCC1CO)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.