Protein target profile

VK055_1789

cytochrome d ubiquinol oxidase, subunit II

Genome: KpATCC43816 Gene: cydB AIK80402.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GLJ5
Length 379
Pocket druggability 0.999
Direct ligand evidence 0 55 total records
Functional annotation 0 EC 7 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
4.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
89.446 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
96.09 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 0.999
Structure A0A0H3GLJ5
Pocket Pocket 1
P2Rank 0.997
Structure A0A0H3GLJ5
Pocket Pocket 1
ColabFold model
FPocket 1 · Pocket 4
P2Rank 0.998 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 228 / 4744 genomes with a hit
Prevalence 4.8%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MIDYEVLRFIWWLLIGILLIGFAVADGFDMGVGMLTRFLGRNDTERRIMINAIAPHWDGNQVWLITAGGALFAAWPMVYAAAFSGFYVAMILVLASLFFRPVGFDYRSKIEDTRWRNMWDWGIFIGSFVPPLVIGVAFGNLLQGVPFHVDEYLRLFYTGNFFQLLNPFGLLAGIVSVAMILTQGATYLQMRTVGELHLRTRTVSMVAALVTLVCFALAGVWVYYGIDGYVVKSVIDHTGPSNPLTKEVVREAGAWMVNFNNMPALWAVPALGVVLPLLTVVSTKADKGAWAFLFSSLTLACIILTAGIAMFPFIMPSSTMLNASLTMWDATSSQRTLNLMTYVAIVFVPIILAYTSWCYWKMFGRITREDIEKNTHSLY

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0070069 A protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.
  • 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:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
  • GO:0046872 Binding to a metal ion.
  • GO:0016682 Catalysis of an oxidation-reduction (redox) reaction in which a diphenol, or related compound, acts as a hydrogen or electron donor and reduces oxygen.
  • GO:0019646 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to oxygen to generate a transmembrane electrochemical gradient.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
293 315 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
160 182 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
290 315 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
264 283 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
29 47 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
77 99 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
7 362 Pfam PF02322 Cytochrome bd terminal oxidase subunit II
7 362 InterPro IPR003317 Cytochrome ubiquinol oxidase subunit 2
262 281 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
7 25 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
316 338 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
361 379 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
182 201 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 375 PANTHER PTHR43141 CYTOCHROME BD2 SUBUNIT II
1 375 InterPro IPR003317 Cytochrome ubiquinol oxidase subunit 2
338 360 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 379 NCBIfam TIGR00203 cytochrome d ubiquinol oxidase subunit II
1 379 InterPro IPR003317 Cytochrome ubiquinol oxidase subunit 2
2 378 PIRSF PIRSF000267 Cyt_oxidse_sub2
2 378 InterPro IPR003317 Cytochrome ubiquinol oxidase subunit 2
78 99 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
161 181 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
142 160 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
339 360 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
6 28 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
100 118 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
73 77 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
225 263 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
202 224 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
48 72 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
203 225 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
123 145 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
284 289 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
119 141 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.

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
0.999
Likely same site as P2Rank 1 5.5 Å 30 shared residues 86% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #14
0.997
Likely same site as P2Rank 1 5.3 Å 29 shared residues 85% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.997
Likely same site as FPocket 14 5.3 Å 29 shared residues 85% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.692
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.653
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.331
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.131
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_A0A0H3GLJ5
AlphaFold DB full sequence Viewing
ColabFold VK055_1789
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
HDD PDB via homolog 632.5 Da · LogP 3.21 · TPSA 101.9 Open detail RCSB PDB
OXY PDB via homolog Detail RCSB PDB
PEE PDB via homolog Detail RCSB PDB
POV PDB via homolog Detail RCSB PDB
UQ8 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
HDD RCSB PDB P0ABK2 632.5 Da LogP 3.21 TPSA 101.9 1 viol. ✓ Clean Cc1c2n3c(c1CCC(=O)O)C=C4[C@]5(CCC(=O)O5)[C@@](C…
OXY RCSB PDB P0ABK2 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean O=O
PEE RCSB PDB P0ABK2 744.0 Da LogP 11.61 TPSA 134.4 2 viol. ✓ Clean CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN…
POV RCSB PDB P0ABK2 760.1 Da LogP 11.17 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@@H](CO[P@](=O)([O-])OC…
UQ8 RCSB PDB P0ABK2 727.1 Da LogP 14.40 TPSA 52.6 2 viol. Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)CC=C(C)CC\C=C(/C)\CC…

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.