Protein profile

VK055_1790

cytochrome d ubiquinol oxidase subunit 1

Genome: KpATCC43816

Gene: AIK80403.1 cydA Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ20

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Amino acids 522

Annotations 7

Features 36

PDB binders 5

Druggability 0.995

Overview

Basic information about this protein and its source genome.

Accession: VK055_1790
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK80403.1 cydA
Status: annotated
Amino acids: 522
Structure source: AlphaFold + ColabFold

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. 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:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring. GO:0046872 Binding to a metal ion.

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 (%): 93.87
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 95.44

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 0.995

Structure A0A0H3GQ20

Pocket Pocket 40

P2Rank 0.993

Structure A0A0H3GQ20

Pocket Pocket 1

ColabFold model

FPocket 0.999 · Pocket 9

P2Rank 0.995 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 240 / 4744 genomes with a hit

Normalized 0.051

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

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.
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:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records

Show feature table

Start	End	DB	Term	Name
96	118	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
209	219	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
184	206	TMHMM	TMhelix	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.
472	494	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
445	470	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
130	152	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
495	522	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
239	387	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
128	151	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
117	127	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
388	409	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
72	90	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
421	443	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
471	494	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	19	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
20	42	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
410	420	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
54	71	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
219	238	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
353	521	PIRSF	PIRSF006446	Cyt_quinol_oxidase_1
353	521	InterPro	IPR002585	Cytochrome ubiquinol oxidase subunit 1
1	328	PIRSF	PIRSF006446	Cyt_quinol_oxidase_1
1	328	InterPro	IPR002585	Cytochrome ubiquinol oxidase subunit 1
387	409	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
421	444	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
43	53	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
2	505	PANTHER	PTHR30365	CYTOCHROME D UBIQUINOL OXIDASE
2	505	InterPro	IPR002585	Cytochrome ubiquinol oxidase subunit 1
54	76	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
91	116	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
7	501	Pfam	PF01654	Cytochrome bd terminal oxidase subunit I
7	501	InterPro	IPR002585	Cytochrome ubiquinol oxidase subunit 1
152	183	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
20	42	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
220	238	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; 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_A0A0H3GQ20	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_1790	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
40				0.995
37				0.771
38				0.749

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	68.89	0.991
2	40.84	0.964
3	20.84	0.863
4	4.77	0.211
5	3.01	0.099

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
9				0.999
32				0.972
30				0.441

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	75.16	0.992
2	38.62	0.96
3	23.95	0.894
4	6.01	0.296
5	3.02	0.099

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

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
HDD	6RKO	P0ABJ9	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	6RKO	P0ABJ9	32.0 Da LogP 0.07 TPSA 34.1	✓ Ro5	✓ Clean	`O=O`
PEE	6RX4	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	6RKO	P0ABJ9	760.1 Da LogP 11.17 TPSA 111.2	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](CO[P@](=O)([O-])OC…`
UQ8	6RKO	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…`

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
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`
ZINC102190506	0.872	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	0.872	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)C…`
ZINC27416437	0.851	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	0.851	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)CCC…`
ZINC1501016364	0.769	465.6 Da LogP 4.63 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O…`
ZINC1559692	0.730	250.3 Da LogP 2.32 TPSA 52.6	✓ Ro5	Alert	`COC1=C(OC)C(=O)C(CC=C(C)C)=C(C)C1=O`
ZINC13544781	0.696	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	0.696	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)…`
ZINC13543439	0.679	454.5 Da LogP 3.44 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@](=O)(O)OCC[N+](C)(C)C)…`
ZINC13543441	0.679	454.5 Da LogP 3.44 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)O…`
ZINC102190945	0.654	411.5 Da LogP 3.29 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCCN`
ZINC32840692	0.654	425.5 Da LogP 3.68 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCCN`
ZINC32840693	0.654	425.5 Da LogP 3.68 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCCN`
ZINC32840704	0.654	453.6 Da LogP 4.46 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCCN`
ZINC32840705	0.654	453.6 Da LogP 4.46 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCCN`
ZINC95635984	0.654	397.4 Da LogP 2.90 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCCN`
ZINC102191119	0.648	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@@H](O)CO…`
ZINC58649551	0.648	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](O)CO)…`
ZINC36178999	0.640	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC36179002	0.640	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC33822387	0.632	426.5 Da LogP 2.66 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC[N+](C)(C)C)O…`
ZINC33822389	0.632	426.5 Da LogP 2.66 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCC[N+](C)(C)C)…`
ZINC13543394	0.630	455.4 Da LogP 2.15 TPSA 171.7	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](N)C(=O)…`
ZINC5820131	0.620	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC5820134	0.620	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC12834352	0.569	398.4 Da LogP 1.88 TPSA 108.4	✓ Ro5	✓ Clean	`CCCC(=O)OC[C@@H](CO[P@](=O)(O)OCC[N+](C)(C)C)OC…`
ZINC12834353	0.569	398.4 Da LogP 1.88 TPSA 108.4	✓ Ro5	✓ Clean	`CCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)OC(…`
ZINC144389541	0.564	422.5 Da LogP 4.65 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC144246453	0.561	422.5 Da LogP 4.02 TPSA 128.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC/C=C/[C@@H](O)[C@@H](N)CO[P@@](=O)…`
ZINC4521879	0.553	386.5 Da LogP 4.73 TPSA 78.9	✓ Ro5	✓ Clean	`CCCCCC(=O)OCC(COC(=O)CCCCC)OC(=O)CCCCC`
ZINC13507461	0.534	434.5 Da LogP 4.81 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C/CCCCCCCC(=O)OC[C@@H](O)COP(=O)(…`
ZINC5510441	0.534	434.5 Da LogP 4.81 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C/CCCCCCCC(=O)OC[C@H](O)COP(=O)(O…`
ZINC32840817	0.529	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCCC(=O)OC(CO)CO`
ZINC32840818	0.529	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCCCCCC(=O)OC(CO)CO`
ZINC102189757	0.525	454.6 Da LogP 4.04 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OCC[N+…`
ZINC13544128	0.525	370.4 Da LogP 1.70 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+](C)(C…`
ZINC14880038	0.525	440.5 Da LogP 3.65 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+]…`
ZINC14880039	0.525	440.5 Da LogP 3.65 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OCC[N+]…`
ZINC15297567	0.525	468.6 Da LogP 4.43 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[…`
ZINC32789157	0.525	412.5 Da LogP 2.87 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+](C…`
ZINC32789161	0.525	412.5 Da LogP 2.87 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCC[N+](C)…`
ZINC32822149	0.525	468.6 Da LogP 4.43 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCC[N+…`
ZINC32822162	0.525	482.6 Da LogP 4.82 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC…`
ZINC32822163	0.525	482.6 Da LogP 4.82 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCC[N…`
ZINC44305349	0.525	454.6 Da LogP 4.04 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N…`
ZINC44405718	0.525	398.5 Da LogP 2.48 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N+](C…`
ZINC44405722	0.525	426.5 Da LogP 3.26 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N+]…`
ZINC85576534	0.525	384.4 Da LogP 2.09 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N+](C)…`
ZINC36079847	0.510	344.5 Da LogP 4.15 TPSA 72.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO)OC(=O)CCCCCCC`

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.