Protein profile

VK055_0550

cytochrome d ubiquinol oxidase, subunit II

Genome: KpATCC43816

Gene: cydB2 AIK79173.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GYP3

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Amino acids 336

Annotations 6

Features 31

PDB binders 5

Druggability 0.999

Overview

Basic information about this protein and its source genome.

Accession: VK055_0550
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: cydB2 AIK79173.1
Status: annotated
Amino acids: 336
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: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: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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 29.223
Localization: CytoplasmicMembrane
ColabFold pLDDT: 92.52

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 0.999

Structure A0A0H3GYP3

Pocket Pocket 32

P2Rank 0.997

Structure A0A0H3GYP3

Pocket Pocket 1

ColabFold model

FPocket 0.999 · Pocket 24

P2Rank 0.995 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 137 / 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.

6 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: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: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 Features

Domain/signature hits from InterPro and related databases.

31 records

Show feature table

Start	End	DB	Term	Name
5	23	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
326	336	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
201	224	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
261	283	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	332	PANTHER	PTHR43141	CYTOCHROME BD2 SUBUNIT II
1	332	InterPro	IPR003317	Cytochrome ubiquinol oxidase subunit 2
284	302	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
5	213	NCBIfam	TIGR00203	cytochrome d ubiquinol oxidase subunit II
5	213	InterPro	IPR003317	Cytochrome ubiquinol oxidase subunit 2
77	99	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
158	180	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
303	325	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
230	249	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
119	141	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
139	157	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
156	178	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
24	73	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
261	283	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
250	260	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
181	200	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
97	116	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
74	96	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
7	23	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
303	325	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
117	138	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
225	229	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
5	325	Pfam	PF02322	Cytochrome bd terminal oxidase subunit II
5	325	InterPro	IPR003317	Cytochrome ubiquinol oxidase subunit 2
230	249	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	6	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
198	220	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; 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_A0A0H3GYP3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0550	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
32				0.999

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	84.68	0.994
2	5.99	0.295
3	2.3	0.059
4	2.16	0.051
5	1.95	0.041

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
24				0.999

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	45.15	0.973
2	35.6	0.954
3	5.53	0.264
4	2.83	0.089
5	2.64	0.077

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	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	6RKO	P0ABK2	32.0 Da LogP 0.07 TPSA 34.1	✓ Ro5	✓ Clean	`O=O`
PEE	6RX4	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	6RKO	P0ABK2	760.1 Da LogP 11.17 TPSA 111.2	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](CO[P@](=O)([O-])OC…`
UQ8	6RKO	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…`

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)…`
ZINC8214428	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.