Protein target profile

KP13_20485

Cytochrome o ubiquinol oxidase subunit 3

Genome: KpKP13 Gene: ANJ86623.1 cyoC 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A2X3IVB9
Length 203
Pocket druggability 0.043
Direct ligand evidence 0 80 total records
Functional annotation 0 EC 7 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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
Hit
Human identity (%)
27.891 Lower values reduce human off-target concern.
Human E-value
1.56e-09
Gut microbiome similarity
3.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
60.345 Higher values support similarity to known essential genes.
DEG E-value
8.240000000000001e-71 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
67.82 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 0.043
Structure A0A2X3IVB9
Pocket Pocket 3
P2Rank 0.155
Structure A0A2X3IVB9
Pocket Pocket 1
ColabFold model
FPocket 0.604 · Pocket 8
P2Rank 0.187 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 169 / 4744 genomes with a hit
Prevalence 3.6%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MATDTLAHTAHAHEHGHHDTGPMKVFGFWIYLMSDCIIFATLFATYAVLVNGTAGGPTGKDIFELPFVLVETALLLFSSITYGMAAIAMYKNNKSQVVSWLALTWLFGAGFIGMEIYEFHHLIMEGFGPDRSGFLSAFFALVGTHGLHVTSGLIWMAVLMFQVSRRGLTSTNRTRILCLSLFWHFLDVVWICVFSVVYLMGAM

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: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:0022904 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
  • GO:0009486 Catalysis of the reaction: 2 ubiquinol + O2 + 4 H+ = 2 ubiquinone + 2 H2O + 4 H+ [periplasmic space].
  • GO:0004129 Catalysis of the reaction: 4 Fe(II)-[cytochrome c] + O2 + 8 H+(in) = 4 Fe(III)-[cytochrome c] + 2 H2O + 4 H+(out).
  • 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
16 201 CDD cd02863 Ubiquinol_oxidase_III
16 201 InterPro IPR033946 Ubiquinol oxidase subunit III domain
97 117 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
26 202 ProSiteProfiles PS50253 Heme-copper oxidase subunit III family profile.
26 202 InterPro IPR000298 Cytochrome c oxidase subunit III-like
8 201 PANTHER PTHR11403 CYTOCHROME C OXIDASE SUBUNIT III
8 201 InterPro IPR024791 Cytochrome c oxidase subunit III
162 180 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
10 201 SUPERFAMILY SSF81452 Cytochrome c oxidase subunit III-like
10 201 InterPro IPR035973 Cytochrome c oxidase subunit III-like superfamily
15 201 Pfam PF00510 Cytochrome c oxidase subunit III
15 201 InterPro IPR000298 Cytochrome c oxidase subunit III-like
18 203 FunFam G3DSA:1.20.120.80:FF:000001 Cytochrome (Ubi)quinol oxidase subunit III
18 203 Gene3D G3DSA:1.20.120.80 -
18 203 InterPro IPR013833 Cytochrome c oxidase, subunit III, 4-helical bundle
137 159 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
26 48 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
91 96 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
180 202 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
24 203 NCBIfam TIGR02842 cytochrome o ubiquinol oxidase subunit III
24 203 InterPro IPR014206 Cytochrome o ubiquinol oxidase, subunit III
69 90 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
137 161 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
118 136 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
202 203 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
181 201 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 27 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
97 117 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
68 90 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
28 49 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
50 68 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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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

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

Site 1 P2Rank #1
0.155
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.044
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.04
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.029
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.029
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_A0A2X3IVB9
AlphaFold DB full sequence Viewing
ColabFold KP13_20485
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.

80 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 30 records from similar proteins
Structural ligands 30 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3PE PDB via homolog 748.1 Da · LogP 12.06 · TPSA 134.4 Open detail RCSB PDB
4AG PDB via homolog Detail RCSB PDB
5PL PDB via homolog Detail RCSB PDB
7E8 PDB via homolog Detail RCSB PDB
7E9 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
3PE RCSB PDB P0ABJ3 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
4AG RCSB PDB P98005 568.9 Da LogP 10.40 TPSA 72.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@@H](CO)OC(=O)CCCCCCCCC…
5PL RCSB PDB P98005 1233.7 Da LogP 15.13 TPSA 245.7 4 viol. ✓ Clean CCCCCCCCCCCCCCCCCCCNC(=O)[C@@H](CO[C@@H]1[C@@H]…
7E8 RCSB PDB P98005 300.4 Da LogP 3.36 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCC/C=C\CCCCCC(=O)OC[C@@H](CO)O
7E9 RCSB PDB P98005 300.4 Da LogP 3.36 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCC/C=C\CCCCCC(=O)OC(CO)CO
9Y0 RCSB PDB A0R049 718.0 Da LogP 11.05 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCC/C=C\C…
9YF RCSB PDB A0R049 853.1 Da LogP 8.75 TPSA 209.5 4 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCC[C@@H]…
AZI RCSB PDB P00415 42.0 Da LogP 0.87 TPSA 58.7 ✓ Ro5 Alert [N-]=[N+]=[N-]
CDL RCSB PDB A0R049 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
CHD RCSB PDB P00415 408.6 Da LogP 3.45 TPSA 98.0 ✓ Ro5 ✓ Clean C[C@H](CCC(=O)O)[C@H]1CC[C@@H]2[C@@]1([C@H](C[C…
CMO RCSB PDB P00415 28.0 Da LogP -0.04 TPSA 19.9 ✓ Ro5 ✓ Clean [C-]#[O+]
CQX RCSB PDB P00415 364.5 Da LogP 0.96 TPSA 108.6 ✓ Ro5 ✓ Clean CCCCCCCCCCOCCO[C@@H]1[C@H]([C@H]([C@@H]([C@H](O…
CUA RCSB PDB P00415 127.1 Da LogP -0.01 TPSA 0.0 ✓ Ro5 ✓ Clean [Cu][Cu]
DCW RCSB PDB P00415 224.3 Da LogP 2.95 TPSA 41.1 ✓ Ro5 ✓ Clean C1CCC(CC1)NC(=O)NC2CCCCC2
DMU RCSB PDB P00415 482.6 Da LogP -1.23 TPSA 178.5 2 viol. ✓ Clean CCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)C…
FES RCSB PDB A0R049 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FME RCSB PDB P00415 177.2 Da LogP -0.06 TPSA 66.4 ✓ Ro5 ✓ Clean CSCC[C@@H](C(=O)O)NC=O
HEO RCSB PDB P0ABJ3 838.9 Da LogP 8.07 TPSA 110.7 2 viol. ✓ Clean Cc1c2cc3[n+]4c(cc5c(c(c6n5[Fe]47n2c(c1CCC(=O)O)…
LMU RCSB PDB P84153 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O…
MQ9 RCSB PDB A0R049 785.3 Da LogP 17.55 TPSA 34.1 2 viol. Alert CC1=C(C(=O)c2ccccc2C1=O)C\C=C(/C)\CC\C=C(/C)\CC…
O RCSB PDB P00415 18.0 Da LogP -0.82 TPSA 31.5 ✓ Ro5 ✓ Clean O
OXY RCSB PDB P00415 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean O=O
PEE RCSB PDB P00414 744.0 Da LogP 11.61 TPSA 134.4 2 viol. ✓ Clean CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN…
PEK RCSB PDB P00415 768.1 Da LogP 11.94 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCCN…
PER RCSB PDB P00415 32.0 Da LogP -2.38 TPSA 46.1 ✓ Ro5 ✓ Clean [O-][O-]
PGV RCSB PDB P00415 749.0 Da LogP 10.45 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OC[C@H…
PSC RCSB PDB P00415 759.1 Da LogP 11.58 TPSA 108.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC[N…
TGL RCSB PDB P00415 891.5 Da LogP 18.77 TPSA 78.9 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OCC(COC(=O)CCCCCCCCCCCCCC…
U9V RCSB PDB P0ABJ3 524.9 Da LogP 10.65 TPSA 52.6 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OCCOC(=O)CCCCCCCCCCCCCC
UQ8 RCSB PDB P0ABJ3 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.