Protein target profile

VK055_1308

bacterial Cytochrome Ubiquinol Oxidase family protein

Genome: KpATCC43816 Gene: AIK79931.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRN7
Length 468
Pocket druggability 1
Direct ligand evidence 0 55 total records
Functional annotation 0 EC 3 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
2.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
91.09 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 1
Structure A0A0H3GRN7
Pocket Pocket 23
P2Rank 0.993
Structure A0A0H3GRN7
Pocket Pocket 1
ColabFold model
FPocket 0.999 · Pocket 31
P2Rank 0.991 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 136 / 4744 genomes with a hit
Prevalence 2.9%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MFEFDAFHLARLQFAFTVSFHILFPAITIGLASYLVVLEGMWLRTRDNVWRSLYNFWLKIFAVNFGMGVVSGLVMSYQFGTNWSGFSQFAGSITGPLLLYEVLTAFFLEAGFLGVMLFGWNKVPPALHFFTTCMVALGTLVSTFWILASNSWMQTPQGFIIENGHLIPQDWLAIIFNPSFPYRLFHMAIAAFLSSAMFVGASAAWHLLRGNDSPAIRKMLSMAMWMALLVAPIQAVVGDMHGLNTLEHQPAKIAAIEGHWENRPGEATPLLLFGLPDMEQERTRYGLEIPALGSLILTHSLHKQVPALKDFPKEDRPYSPAVFWSFRIMVGMGVLMIALGICSAWLRYRRRLYHSRPFQWFALCMGPAGLIALVAGWVTTEMGRQPWVIYGLLRTRDAVSLHSTLQMAISLLVFIVVYCAVFGVGYYYIFRLIKKGPQPVTELTSQTAGTPARPLSAAEPVRDEENAS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • 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.
  • 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: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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
220 237 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
97 120 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
221 238 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
37 55 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
209 219 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
127 148 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
56 77 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
184 208 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
9 437 Pfam PF01654 Cytochrome bd terminal oxidase subunit I
9 437 InterPro IPR002585 Cytochrome ubiquinol oxidase subunit 1
408 430 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
12 36 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
149 183 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 439 PANTHER PTHR30365 CYTOCHROME D UBIQUINOL OXIDASE
1 439 InterPro IPR002585 Cytochrome ubiquinol oxidase subunit 1
186 208 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
347 357 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
55 77 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
2 460 PIRSF PIRSF006446 Cyt_quinol_oxidase_1
2 460 InterPro IPR002585 Cytochrome ubiquinol oxidase subunit 1
358 378 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
20 42 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
238 320 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
443 468 MobiDBLite mobidb-lite consensus disorder prediction
379 406 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
97 119 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
430 468 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
321 346 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
78 96 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
126 148 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
407 429 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
323 345 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
121 126 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
358 380 TMHMM TMhelix 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 #23
1.0
Likely same site as P2Rank 1 2.1 Å 42 shared residues 98% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #20
0.953
Likely same site as P2Rank 2 0.1 Å 35 shared residues 97% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 3 FPocket #16
0.756
Likely same site as P2Rank 4 1.6 Å 12 shared residues 100% of smaller site
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Surrounding area
Site 4 FPocket #14
0.273
Likely same site as P2Rank 3 0.8 Å 13 shared residues 93% of smaller site
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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
0.993
Likely same site as FPocket 23 2.1 Å 42 shared residues 98% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.983
Likely same site as FPocket 20 0.1 Å 35 shared residues 97% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.608
Likely same site as FPocket 14 0.8 Å 13 shared residues 93% of smaller site
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.347
Likely same site as FPocket 16 1.6 Å 12 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.302
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_A0A0H3GRN7
AlphaFold DB full sequence Viewing
ColabFold VK055_1308
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 A4IKP6 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 P0ABJ9 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean O=O
PEE RCSB PDB P0ABJ9 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 P0ABJ9 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 P0ABJ9 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.