Protein profile

PA2638

NADH-quinone oxidoreductase subunit B

Genome: NC_002516.2

Gene: nuoB PA2638 Structure source: AlphaFold UniProt Q9I0K0

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Amino acids 225

Annotations 11

Features 12

PDB binders 17

Druggability 0.687

Overview

Basic information about this protein and its source genome.

Accession: PA2638
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: nuoB PA2638
Status: annotated
Amino acids: 225
Structure source: AlphaFold

7.1.1.-

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:0045271 Respiratory chain complex I is an enzyme of the respiratory chain. It consists of several polypeptide chains and is L-shaped, with a horizontal arm lying in the membrane and a vertical arm that projects into the matrix. The electrons of NADH enter the chain at this complex. GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0005506 Binding to an iron (Fe) ion. GO:0050136 Catalysis of the reaction: NADH + H+ + a quinone = NAD+ + a quinol. GO:0008137 Catalysis of the reaction: NADH + ubiquinone + 5 H+(in) = NAD+ + ubiquinol + 4 H+(out).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 56.41
Human E-value: 6.76e-42
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: CytoplasmicMembrane

Selected Druggability evidence

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 0.687

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MQYKLTRIDPDAANDQYPIGERETVADPLVEGQVHKNIFMGKLEDVLNSTVNWGRKNSLWPYNFGLSCCYVEMTTAFTAPHDIARFGAEVIRASPRQADFMVIAGTCFIKMAPVIQRLYEQMLEPKWVISMGSCANSGGMYDIYSVVQGVDKFLPVDVYIPGCPPRPEAFLQGLMLLQESIGQERRPLSWVVGDQGVYRAEMPAQKDLKREQRIQVTNLRSPDEV

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

7.1.1.-

Gene Ontology (GO)

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:0045271 Respiratory chain complex I is an enzyme of the respiratory chain. It consists of several polypeptide chains and is L-shaped, with a horizontal arm lying in the membrane and a vertical arm that projects into the matrix. The electrons of NADH enter the chain at this complex.
GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0005506 Binding to an iron (Fe) ion.
GO:0050136 Catalysis of the reaction: NADH + H+ + a quinone = NAD+ + a quinol.
GO:0008137 Catalysis of the reaction: NADH + ubiquinone + 5 H+(in) = NAD+ + ubiquinol + 4 H+(out).
GO:0048038 Binding to a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
GO:0009060 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
GO:0015990 The transport of protons against an electrochemical gradient, using energy from electron transport.
GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
47	183	NCBIfam	TIGR01957	NADH-quinone oxidoreductase subunit B
47	183	InterPro	IPR006138	NADH-ubiquinone oxidoreductase, 20 Kd subunit
28	182	Hamap	MF_01356	NAD(P)H-quinone oxidoreductase subunit K, chloroplastic [ndhK].
28	182	InterPro	IPR006138	NADH-ubiquinone oxidoreductase, 20 Kd subunit
26	192	Gene3D	G3DSA:3.40.50.12280	-
37	191	PANTHER	PTHR11995	NADH DEHYDROGENASE
44	190	SUPERFAMILY	SSF56770	HydA/Nqo6-like
149	165	ProSitePatterns	PS01150	Respiratory-chain NADH dehydrogenase 20 Kd subunit signature.
149	165	InterPro	IPR006138	NADH-ubiquinone oxidoreductase, 20 Kd subunit
87	175	Pfam	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit
87	175	InterPro	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit
25	193	FunFam	G3DSA:3.40.50.12280:FF:000002	NADH-quinone oxidoreductase subunit B

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 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA2638	AlphaFold	—	—	full sequence	—	Viewing

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
3				0.687
1				0.481
2				0.456

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.

68 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	6ZKF	A0A6P7E5N1	748.1 Da LogP 12.06 TPSA 134.4	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…`
8Q1	5XTB	O75251	540.7 Da LogP 3.29 TPSA 162.3	1 viol.	✓ Clean	`CCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)…`
CDL	2YBB	Q56218	1464.1 Da LogP 23.31 TPSA 242.6	3 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…`
DCQ	6I0D	Q56218	322.4 Da LogP 4.49 TPSA 52.6	✓ Ro5	Alert	`CCCCCCCCCCC1=C(C(=O)C(=C(C1=O)OC)OC)C`
FES	2FUG	Q56218	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
HQH	6Q8O	Q56218	415.6 Da LogP 5.05 TPSA 71.6	1 viol.	✓ Clean	`C/C=C(\C)/[C@@H]([C@H](C)/C=C(\C)/C=C/C/C(=C/CC…`
HQK	6Q8X	Q56218	364.9 Da LogP 5.24 TPSA 34.9	1 viol.	✓ Clean	`CC(C)(C)c1ccc(cc1)CSC2=C(C(=O)N(N=C2)C(C)(C)C)Cl`
HQW	6Q8W	Q56218	397.4 Da LogP 4.66 TPSA 91.8	✓ Ro5	✓ Clean	`CC1=C(OC(=C(C1=O)C)OC)[C@H]2C/C(=C/C(=C/c3ccc(c…`
MYR	6ZKF	A0A6P7E5N1	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
PC1	7DGQ	P42026	790.2 Da LogP 12.17 TPSA 111.2	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])…`
PEE	5XTH	O75251	744.0 Da LogP 11.61 TPSA 134.4	2 viol.	✓ Clean	`CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN…`
PLX	5XTD	O75251	767.1 Da LogP 11.61 TPSA 114.7	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCCC[C@@H](O)O[C@H](CO[C@@H](CCCCC…`
PNS	5LNK	P42026	358.4 Da LogP -0.96 TPSA 145.2	1 viol.	✓ Clean	`CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O`
SMA	2YBB	Q56218	514.7 Da LogP 6.14 TPSA 87.4	2 viol.	✓ Clean	`C/C=C(\C)/C=C/C=C[C@@H]([C@@H](C)[C@H]([C@@H](C…`
UQ1	2YBB	Q56218	250.3 Da LogP 2.32 TPSA 52.6	✓ Ro5	Alert	`CC1=C(C(=O)C(=C(C1=O)OC)OC)CC=C(C)C`
UQ2	7DGQ	P42026	318.4 Da LogP 4.04 TPSA 52.6	✓ Ro5	Alert	`CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CCC=C(C)C`
ZMP	5LNK	P42026	568.7 Da LogP 4.07 TPSA 162.3	1 viol.	✓ Clean	`CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(C…`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DXH	O75251	8.51	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cnn(c3nc(n2)c4cccnc4)C)C(=O)Nc5c…`

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
ZINC1529498	1.000	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417	1.000	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1559692	1.000	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`
ZINC1628119	1.000	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC2105913	1.000	397.4 Da LogP 4.66 TPSA 91.8	✓ Ro5	✓ Clean	`COc1oc([C@@H]2C/C(=C/C(C)=C/c3ccc([N+](=O)[O-])…`
ZINC2575028	1.000	322.4 Da LogP 4.49 TPSA 52.6	✓ Ro5	Alert	`CCCCCCCCCCC1=C(C)C(=O)C(OC)=C(OC)C1=O`
ZINC4025640	1.000	397.4 Da LogP 4.66 TPSA 91.8	✓ Ro5	✓ Clean	`COc1oc([C@H]2C/C(=C/C(C)=C/c3ccc([N+](=O)[O-])c…`
ZINC138457918	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCC(=O)O`
ZINC138458029	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCC(=O)O`
ZINC144395054	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCC(=O)O`
ZINC14619628	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCCCC(=O)O`
ZINC196749828	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCC(=O)O`
ZINC2113934076	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCC(=O)O`
ZINC2113934082	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCC(=O)O`
ZINC2113934083	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCC(=O)O`
ZINC2243670	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCC(=O)O`
ZINC2569203	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCC(=O)O`
ZINC4798470	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC5973005	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCC(=O)O`
ZINC71418182	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)CCCCC(=O)O`
ZINC79244776	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCCC(=O)O`
ZINC86037082	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC86037089	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCCCC(=O)O`
ZINC86039283	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCC(=O)O`
ZINC3160730	0.810	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCC(=O)O`
ZINC4582907	0.810	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCC(=O)O`
ZINC4727003	0.810	312.4 Da LogP 4.69 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCC(=O)CCCCCCCC(=O)O`
ZINC86037074	0.810	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CCCC(=O)O`
ZINC2378801	0.800	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCC(=O)O`
ZINC101154410	0.787	383.4 Da LogP 4.36 TPSA 102.8	✓ Ro5	✓ Clean	`CC(/C=C1\CO[C@@H](c2oc(O)c(C)c(=O)c2C)C1)=C\c1c…`
ZINC2113934081	0.762	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2243668	0.762	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCC(=O)O`
ZINC2378799	0.762	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCC(=O)O`
ZINC33820423	0.762	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCC(=O)O`
ZINC1532641	0.750	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`
ZINC2387442	0.739	246.4 Da LogP 4.34 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCSCCCCC(=O)O`
ZINC31778284	0.739	310.4 Da LogP 4.47 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)/C=C\C(=O)CCCCCCCC(=O)O`
ZINC5540108	0.739	310.4 Da LogP 4.47 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)/C=C/C(=O)CCCCCCCC(=O)O`
ZINC64633397	0.739	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCC(=O)O`
ZINC1542890	0.727	338.4 Da LogP 3.46 TPSA 72.8	✓ Ro5	Alert	`COC1=C(OC)C(=O)C(CCCCCCCCCCO)=C(C)C1=O`
ZINC59545317	0.727	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCC(=O)O`
ZINC59545320	0.727	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)CCC(=O)O`
ZINC59545336	0.727	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCC(=O)O`
ZINC100243309	0.708	278.4 Da LogP 3.02 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCCCC(=O)O`
ZINC100243318	0.708	306.5 Da LogP 3.80 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCCCCCC(=O)O`
ZINC100246022	0.708	262.4 Da LogP 3.35 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC[S@@](=O)CCCCC(=O)O`
ZINC100246029	0.708	262.4 Da LogP 3.35 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC[S@](=O)CCCCC(=O)O`
ZINC1600678	0.708	264.4 Da LogP 2.63 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCCS(=O)(=O)CCCCC(=O)O`
ZINC1600679	0.708	264.4 Da LogP 2.63 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCS(=O)(=O)CCCCCC(=O)O`
ZINC58649551	0.708	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)…`

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.