Protein target profile

VK055_2437

membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family protein

Genome: KpATCC43816 Gene: AIK81034.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GMQ0
Length 784
Pocket druggability 1
Direct ligand evidence 0 52 total records
Functional annotation 0 EC 6 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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
1.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
90.434 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
94.9 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 1
Structure A0A0H3GMQ0
Pocket Pocket 1
P2Rank 0.977
Structure A0A0H3GMQ0
Pocket Pocket 1
ColabFold model
FPocket 1 · Pocket 1
P2Rank 0.985 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 89 / 4744 genomes with a hit
Prevalence 1.9%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MTLTALFAAFCGLYLLIGGAWLVVLGGSWYYPIAGLVMLGVTVMLFRGKRAALWLYAALLLATMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLPVPSAGAVGALVVALLISGGMLTWAGFNDPQEVNGTLSADATPAAPISTVADGDWPAYGRNQEGQRFSPLKQINADNVKNLKEAWVFRTGDLKQPNDPGEITNEVTPIKVGDTLFLCTAHQRLFALDAATGKEKWHFDPQLNADPSFQHVTCRGVSYHEAKADNAPADVVADCPRRIILPVNDGRLFAVNADNGKLCETFANKGILNLQTNMPVTTPGMYEPTSPPIITDKTIVIAGAVTDNFSTREPSGVIRGFDVNTGKLLWAFDPGAKDPNAIPSDEHHFTLNSPNSWAPAAYDAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSIVALNATTGKLAWSYQTVHHDLWDMDMPSQPTLADIEVNGKTVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYVTKTQPFSDLSFRPKKDLTGADMWGATMFDQLVCRVIFHQLRYEGIFTPPSEQGTLVFPGNLGMFEWGGISVDPNRQVAIANPMALPFVSKLIPRGPGNPMEPPKDAKGSGTESGVQPQYGVPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSLPFPMPVKLPFTMGMPMLGGPISTAGNVLFIGATADNYLRAYNMSNGEKLWEARLPAGGQATPMTYEVNGKQYVVISAGGHGSFGTKMGDYIVAYALPNDAK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0016614 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • GO:0048038 Binding to a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
  • 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:0008876 Catalysis of the reaction: D-glucose + ubiquinone = D-glucono-1,5-lactone + ubiquinol.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

56 records
Show feature table
Start End DB Term Name
129 784 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
53 69 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
75 94 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
149 777 PANTHER PTHR32303 QUINOPROTEIN ALCOHOL DEHYDROGENASE (CYTOCHROME C)
3 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
3 780 NCBIfam TIGR03074 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family
3 780 InterPro IPR017511 PQQ-dependent membrane bound dehydrogenase
95 105 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
47 52 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
29 46 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
106 128 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
608 627 MobiDBLite mobidb-lite consensus disorder prediction
270 302 SMART SM00564 ire1_9
270 302 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
389 446 SMART SM00564 ire1_9
389 446 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
208 239 SMART SM00564 ire1_9
208 239 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
467 500 SMART SM00564 ire1_9
467 500 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
327 368 SMART SM00564 ire1_9
327 368 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
703 736 SMART SM00564 ire1_9
703 736 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
28 45 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
84 101 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
52 69 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
156 779 CDD cd10280 PQQ_mGDH
156 779 InterPro IPR017511 PQQ-dependent membrane bound dehydrogenase
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
392 413 ProSitePatterns PS00364 Bacterial quinoprotein dehydrogenases signature 2.
392 413 InterPro IPR001479 Quinoprotein dehydrogenase, conserved site
149 781 SUPERFAMILY SSF50998 Quinoprotein alcohol dehydrogenase-like
149 781 InterPro IPR011047 Quinoprotein alcohol dehydrogenase-like superfamily
143 784 Gene3D G3DSA:2.140.10.10 -
155 183 ProSitePatterns PS00363 Bacterial quinoprotein dehydrogenases signature 1.
155 183 InterPro IPR001479 Quinoprotein dehydrogenase, conserved site
1 19 Phobius SIGNAL_PEPTIDE Signal peptide region
16 19 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
5 24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
106 128 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
70 74 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
277 308 Pfam PF01011 PQQ enzyme repeat
277 308 InterPro IPR002372 Pyrrolo-quinoline quinone repeat
652 684 Pfam PF01011 PQQ enzyme repeat
652 684 InterPro IPR002372 Pyrrolo-quinoline quinone repeat
344 376 Pfam PF01011 PQQ enzyme repeat
344 376 InterPro IPR002372 Pyrrolo-quinoline quinone repeat
213 248 Pfam PF01011 PQQ enzyme repeat
213 248 InterPro IPR002372 Pyrrolo-quinoline quinone repeat
709 745 Pfam PF01011 PQQ enzyme repeat
709 745 InterPro IPR002372 Pyrrolo-quinoline quinone repeat
430 456 Pfam PF01011 PQQ enzyme repeat
430 456 InterPro IPR002372 Pyrrolo-quinoline quinone repeat
141 782 FunFam G3DSA:2.140.10.10:FF:000001 Quinoprotein glucose dehydrogenase
20 28 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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 #1
1.0
Likely same site as P2Rank 1 2.1 Å 45 shared residues 92% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #11
0.871
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Surrounding area
Site 3 FPocket #19
0.5
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Surrounding area
Site 4 FPocket #5
0.436
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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
0.977
Likely same site as FPocket 1 2.1 Å 45 shared residues 92% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.569
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Surrounding area
Site 3 P2Rank #3
0.179
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Surrounding area
Site 4 P2Rank #4
0.162
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Surrounding area
Site 5 P2Rank #5
0.068
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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_A0A0H3GMQ0
AlphaFold DB full sequence Viewing
ColabFold VK055_2437
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
15P PDB via homolog 1529.8 Da · LogP 0.17 · TPSA 334.1 Open detail RCSB PDB
TFB PDB via homolog Detail RCSB PDB
ZINC1580161 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC16052118 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC16052257 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
15P RCSB PDB I0JWN7 1529.8 Da LogP 0.17 TPSA 334.1 2 viol. ✓ Clean COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO…
TFB RCSB PDB Q46444 116.1 Da LogP 0.25 TPSA 46.5 ✓ Ro5 ✓ Clean C1C[C@H](OC1)C(=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.