Protein profile

VK055_2163

cytochrome o ubiquinol oxidase subunit IV

Genome: KpATCC43816

Gene: cyoD AIK80768.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GSQ5

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Amino acids 109

Annotations 7

Features 15

PDB binders 4

Druggability 0.922

Overview

Basic information about this protein and its source genome.

Accession: VK055_2163
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: cyoD AIK80768.1
Status: annotated
Amino acids: 109
Structure source: AlphaFold + ColabFold

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0009486 Catalysis of the reaction: 2 ubiquinol + O2 + 4 H+ = 2 ubiquinone + 2 H2O + 4 H+ [periplasmic space]. GO:0015990 The transport of protons against an electrochemical gradient, using energy from electron transport. GO:0009319 A protein complex that possesses cytochrome o ubiquinol oxidase activity; consists of four polypeptide subunits and associated prosthetic groups. 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:0015078 Enables the transfer of a proton from one side of a membrane to the other.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 86.239
DEG E-value: 4.13e-64
Localization: CytoplasmicMembrane
ColabFold pLDDT: 85.08

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.922

Structure A0A0H3GSQ5

Pocket Pocket 1

P2Rank 0.005

Structure A0A0H3GSQ5

Pocket Pocket 1

ColabFold model

FPocket 0.524 · Pocket 4

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 139 / 4744 genomes with a hit

Normalized 0.029

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0009486 Catalysis of the reaction: 2 ubiquinol + O2 + 4 H+ = 2 ubiquinone + 2 H2O + 4 H+ [periplasmic space].
GO:0015990 The transport of protons against an electrochemical gradient, using energy from electron transport.
GO:0009319 A protein complex that possesses cytochrome o ubiquinol oxidase activity; consists of four polypeptide subunits and associated prosthetic groups.
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:0015078 Enables the transfer of a proton from one side of a membrane to the other.
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 Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
101	109	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
18	37	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
44	66	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
76	98	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	109	PANTHER	PTHR36835	CYTOCHROME BO(3) UBIQUINOL OXIDASE SUBUNIT 4
78	100	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
12	107	NCBIfam	TIGR02847	cytochrome o ubiquinol oxidase subunit IV
12	107	InterPro	IPR014210	Cytochrome o ubiquinol oxidase subunit IV
38	43	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
44	66	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
15	37	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
20	92	Pfam	PF03626	Prokaryotic Cytochrome C oxidase subunit IV
20	92	InterPro	IPR005171	Cytochrome C oxidase subunit IV, prokaryotes
67	77	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	17	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; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GSQ5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_2163	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.922

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
4				0.524
1				0.316

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.

54 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
3PE	6WTI	P0ABJ6	748.1 Da LogP 12.06 TPSA 134.4	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…`
HEO	6WTI	P0ABJ6	838.9 Da LogP 8.07 TPSA 110.7	2 viol.	✓ Clean	`Cc1c2cc3[n+]4c(cc5c(c(c6n5[Fe]47n2c(c1CCC(=O)O)…`
U9V	6WTI	P0ABJ6	524.9 Da LogP 10.65 TPSA 52.6	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OCCOC(=O)CCCCCCCCCCCCCC`
UQ8	6WTI	P0ABJ6	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…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC102190506	1.000	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCCN)OC(=O)CC…`
ZINC102190512	1.000	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)C…`
ZINC17654239	1.000	314.5 Da LogP 4.79 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OCCOC(=O)CCCCCCC`
ZINC27416437	0.976	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCCN)OC(=O)CCCCC`
ZINC33902364	0.976	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)CCC…`
ZINC1532641	0.972	318.4 Da LogP 4.04 TPSA 52.6	✓ Ro5	Alert	`COC1=C(OC)C(=O)C(C/C=C(\C)CCC=C(C)C)=C(C)C1=O`
ZINC4691823	0.952	258.4 Da LogP 3.23 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCCC(=O)OCCOC(=O)CCCCC`
ZINC100302690	0.875	258.4 Da LogP 4.10 TPSA 35.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OCCOC`
ZINC101034896	0.875	402.6 Da LogP 4.83 TPSA 71.1	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OCCOCCOCCOC(=O)CCCCCCC`
ZINC206748657	0.875	374.5 Da LogP 4.05 TPSA 71.1	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OCCOCCOCCOC(=O)CCCCC`
ZINC218215426	0.875	402.6 Da LogP 4.83 TPSA 71.1	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OCCOCCOCCOC(=O)CCCCC`
ZINC1608549	0.870	200.3 Da LogP 3.69 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OCCCC`
ZINC1608718	0.870	214.3 Da LogP 4.08 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OCCCCC`
ZINC1615264	0.870	214.3 Da LogP 4.08 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCOC(=O)CCCCC`
ZINC1677794	0.870	200.3 Da LogP 3.69 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCC(=O)OCCCCC`
ZINC1684740	0.870	200.3 Da LogP 3.69 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCOC(=O)CCCCC`
ZINC1684760	0.870	228.4 Da LogP 4.47 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCOC(=O)CCCCC`
ZINC1845930	0.870	228.4 Da LogP 4.47 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCOC(=O)CCCCCC`
ZINC2034460	0.870	228.4 Da LogP 4.47 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OCCCC`
ZINC2039906	0.870	228.4 Da LogP 4.47 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OCCCCCC`
ZINC2516185	0.870	214.3 Da LogP 4.08 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OCCC`
ZINC32147174	0.870	214.3 Da LogP 4.08 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCOC(=O)CCCCCC`
ZINC3875771	0.870	314.5 Da LogP 4.79 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCCCOC(=O)CCCCC(=O)OCCCCCC`
ZINC85590383	0.870	242.4 Da LogP 4.86 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OCCC`
ZINC85936592	0.870	242.4 Da LogP 4.86 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OCCCCC`
ZINC86022556	0.870	242.4 Da LogP 4.86 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCOC(=O)CCCCCCC`
ZINC5820125	0.833	346.5 Da LogP 3.27 TPSA 71.1	✓ Ro5	✓ Clean	`CCCCCC(=O)OCCOCCOCCOC(=O)CCCCC`
ZINC3875764	0.826	314.5 Da LogP 4.79 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCOC(=O)CCCCCCCCC(=O)OCCCC`
ZINC4100226	0.826	300.4 Da LogP 4.40 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCOC(=O)CCCCCCCC(=O)OCCCC`
ZINC4410479	0.826	286.4 Da LogP 4.01 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCCC(=O)OCCCCOC(=O)CCCCC`
ZINC4721921	0.826	272.4 Da LogP 3.62 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCOC(=O)CCCCCC(=O)OCCCC`
ZINC1848564	0.808	230.3 Da LogP 3.32 TPSA 35.5	✓ Ro5	✓ Clean	`CCCCCCC(=O)OCCOCCCC`
ZINC4429686	0.808	274.4 Da LogP 3.33 TPSA 44.8	✓ Ro5	✓ Clean	`CCCCCCC(=O)OCCOCCOCCCC`
ZINC100036663	0.800	272.4 Da LogP 4.22 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OCCO`
ZINC138343271	0.800	230.3 Da LogP 3.05 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)OCCO`
ZINC77871962	0.800	244.4 Da LogP 3.44 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OCCO`
ZINC78062261	0.800	243.4 Da LogP 3.41 TPSA 52.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OCCN`
ZINC104333637	0.792	242.4 Da LogP 4.86 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCCOC(=O)CCCC`
ZINC1584002	0.792	200.3 Da LogP 3.69 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCOC(=O)CCCC`
ZINC1584009	0.792	214.3 Da LogP 4.08 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCOC(=O)CCCC`
ZINC1682726	0.783	244.3 Da LogP 2.84 TPSA 52.6	✓ Ro5	✓ Clean	`CCCOC(=O)CCCCCC(=O)OCCC`
ZINC3875751	0.783	258.4 Da LogP 3.23 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCOC(=O)CCCCC(=O)OCCCC`
ZINC4722486	0.783	272.4 Da LogP 3.62 TPSA 52.6	✓ Ro5	✓ Clean	`CCCOC(=O)CCCCCCCC(=O)OCCC`
ZINC13544781	0.771	482.6 Da LogP 4.22 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@@H](CO[P@](=O)(O)OCC[N+](C)(C)C…`
ZINC13544783	0.771	482.6 Da LogP 4.22 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)…`
ZINC100300463	0.769	232.4 Da LogP 3.60 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OCCS`
ZINC1566534	0.769	216.3 Da LogP 2.93 TPSA 35.5	✓ Ro5	✓ Clean	`CCCCCC(=O)OCCOCCCC`
ZINC4430035	0.769	260.4 Da LogP 2.94 TPSA 44.8	✓ Ro5	✓ Clean	`CCCCCC(=O)OCCOCCOCCCC`
ZINC4977298	0.769	402.6 Da LogP 4.83 TPSA 71.1	✓ Ro5	✓ Clean	`CCCCOCCOC(=O)CCCCCCCCC(=O)OCCOCCCC`
ZINC1648324	0.750	200.3 Da LogP 3.69 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OCC`

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.