KpKP13 Protein target profile

putative diguanylate cyclase

Accession: KP13_04239

Gene: AHE45470.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GUU2
Length 379
Pocket druggability (P2Rank · AlphaFold DB model) 0.548
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 5 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 (%)
0.0 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) 0.548
Structure A0A0H3GUU2
Pocket Pocket 1
Druggability (FPocket) 0.831
Structure A0A0H3GUU2
Pocket Pocket 4
ColabFold model
P2Rank 0.606 · Pocket 1
FPocket 0.706 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 6 / 4744 genomes with a hit
Prevalence 0.1%

Sequence

Primary amino-acid sequence viewer.

MLTNKRERARQQRAALWATRDNVQRHALSMSMPWLAFVNIAFALMIFFRNLIFTYFDKRLLTHRAVIPYIEAALIAVIIISAILVIIALTPRLAQGRYTLNIITGLLLALSLCWSLSNYCFIFFWTLPFAWPLLVILMTTGLTALYHHWPGITAFMLPLWVTALLAGIQLHYHTEIRFLILWAIFTAILLYGRRILQRWYDEAWDTHQENMQLIQRLESIANQDALTGTANRRALNAYLAAIWQQKTPLALMMIDVDYFKRYNDRYGHQAGDECLSSVAQVLKMAVRAEGDLVARYGGEEFVVVLPGVSLAHATAIAERIQQKIREAGLPHAASAVASEVTVSIGIVASDGTVPIETLIARADSALYQAKNKGRNQWSY

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • 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:0052621 Catalysis of the reaction: 2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate + 2 H+.
  • GO:0005525 Binding to GTP, guanosine triphosphate.
  • GO:0043709 The attachment of a cell to a solid substrate, via cell adhesion molecules, during the formation of a biofilm composed of microorganisms of the same species.
  • GO:1902201 Any process that stops, prevents or reduces the frequency, rate or extent of bacterial-type flagellum-dependent cell motility.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

37 records
Show feature table
Start End DB Term Name
178 195 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
217 377 NCBIfam TIGR00254 diguanylate cyclase (GGDEF) domain
217 377 InterPro IPR000160 GGDEF domain
30 220 Pfam PF17178 Membrane-associated sensor
30 220 InterPro IPR033444 Membrane-associated sensor MASE5
149 171 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
98 117 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
66 88 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 33 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
123 145 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
34 56 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
210 379 SMART SM00267 duf1_3
210 379 InterPro IPR000160 GGDEF domain
206 379 Gene3D G3DSA:3.30.70.270 -
206 379 InterPro IPR043128 Reverse transcriptase/Diguanylate cyclase domain
31 53 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
221 376 Pfam PF00990 Diguanylate cyclase, GGDEF domain
221 376 InterPro IPR000160 GGDEF domain
226 378 SUPERFAMILY SSF55073 Nucleotide cyclase
226 378 InterPro IPR029787 Nucleotide cyclase
176 192 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
146 151 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
222 377 CDD cd01949 GGDEF
222 377 InterPro IPR000160 GGDEF domain
57 67 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
118 122 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
90 97 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
152 170 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
193 379 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
247 379 ProSiteProfiles PS50887 GGDEF domain profile.
247 379 InterPro IPR000160 GGDEF domain
216 379 FunFam G3DSA:3.30.70.270:FF:000001 Diguanylate cyclase domain protein
123 145 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
171 175 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
98 116 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
68 89 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
157 377 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 · P2Rank

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

Pocket 1 P2Rank #1
0.548
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.247
Likely same site as FPocket 4 1.2 Å 11 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.17
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.066
Likely same site as FPocket 5 2.6 Å 6 shared residues 100% of smaller site
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Surrounding area
Pocket 5 P2Rank #5
0.01
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #4
0.831
Likely same site as P2Rank 2 1.2 Å 11 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #5
0.358
Likely same site as P2Rank 4 2.6 Å 6 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_A0A0H3GUU2
AlphaFold DB full sequence Viewing
ColabFold KP13_04239
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
BEF PDB via homolog 66.0 Da · LogP 0.88 · TPSA 0.0 Open detail RCSB PDB
BEZ PDB via homolog Detail RCSB PDB
C2E PDB via homolog Detail RCSB PDB
GAV PDB via homolog Detail RCSB PDB
TLA 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
BEF RCSB PDB B8GZM2 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
BEZ RCSB PDB P0AA89 122.1 Da LogP 1.38 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)O
C2E RCSB PDB B8GZM2 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 B8GZM2 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…
TLA RCSB PDB Q9HXT9 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=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.

Cross-references

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