Protein profile

PA2639

NADH:-quinone oxidoreductase subunit C/D

Genome: NC_002516.2

Gene: nuoCD PA2639 nuoC nuoD Structure source: AlphaFold UniProt Q9I0J9

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Amino acids 593

Annotations 9

Features 28

PDB binders 16

Druggability 0.457

Overview

Basic information about this protein and its source genome.

Accession: PA2639
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: nuoCD PA2639 nuoC nuoD
Status: annotated
Amino acids: 593
Structure source: AlphaFold

7.1.1.-

GO:0030964 An integral membrane complex that possesses NADH oxidoreductase activity. The complex is one of the components of the electron transport chain. It catalyzes the transfer of a pair of electrons from NADH to a quinone. 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:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 43.75
Human E-value: 2.8000000000000002e-33
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

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 0.457

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

7.1.1.-

Gene Ontology (GO)

GO:0030964 An integral membrane complex that possesses NADH oxidoreductase activity. The complex is one of the components of the electron transport chain. It catalyzes the transfer of a pair of electrons from NADH to a quinone.
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:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
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: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:0016651 Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.

Sequence Features

Domain/signature hits from InterPro and related databases.

28 records

Show feature table

Start	End	DB	Term	Name
209	593	Gene3D	G3DSA:1.10.645.10	-
209	593	InterPro	IPR029014	[NiFe]-hydrogenase, large subunit
209	593	FunFam	G3DSA:1.10.645.10:FF:000001	NADH-quinone oxidoreductase subunit C/D
209	593	NCBIfam	TIGR01962	NADH dehydrogenase (quinone) subunit D
209	593	InterPro	IPR022885	NAD(P)H-quinone oxidoreductase subunit D/H
18	223	SUPERFAMILY	SSF143243	Nqo5-like
18	223	InterPro	IPR037232	NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily
323	593	Pfam	PF00346	Respiratory-chain NADH dehydrogenase, 49 Kd subunit
323	593	InterPro	IPR001135	NADH-quinone oxidoreductase, subunit D
205	593	Hamap	MF_01358	NAD(P)H-quinone oxidoreductase subunit H, chloroplastic [ndhH].
205	593	InterPro	IPR022885	NAD(P)H-quinone oxidoreductase subunit D/H
44	171	Pfam	PF00329	Respiratory-chain NADH dehydrogenase, 30 Kd subunit
44	171	InterPro	IPR001268	NADH:ubiquinone oxidoreductase, 30kDa subunit
246	257	ProSitePatterns	PS00535	Respiratory chain NADH dehydrogenase 49 Kd subunit signature.
246	257	InterPro	IPR014029	NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site
19	179	Hamap	MF_01357	NAD(P)H-quinone oxidoreductase subunit J, chloroplastic [ndhJ].
19	179	InterPro	IPR010218	NADH dehydrogenase, subunit C
219	593	SUPERFAMILY	SSF56762	HydB/Nqo4-like
219	593	InterPro	IPR029014	[NiFe]-hydrogenase, large subunit
202	593	PANTHER	PTHR11993	NADH-UBIQUINONE OXIDOREDUCTASE 49 KDA SUBUNIT
202	593	InterPro	IPR022885	NAD(P)H-quinone oxidoreductase subunit D/H
1	151	FunFam	G3DSA:3.30.460.80:FF:000001	NADH-quinone oxidoreductase subunit C/D
6	151	Gene3D	G3DSA:3.30.460.80	NADH:ubiquinone oxidoreductase, 30kDa subunit
6	151	InterPro	IPR037232	NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily
43	170	NCBIfam	TIGR01961	NADH (or F420H2) dehydrogenase, subunit C
43	170	InterPro	IPR010218	NADH dehydrogenase, subunit C
10	593	Hamap	MF_01359	NADH-quinone oxidoreductase subunit C/D [nuoC].
10	593	InterPro	IPR023062	NADH dehydrogenase, subunit CD

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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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 PA2639	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				0.389
5				0.316
1				0.302

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.

66 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	5LNK	W5PJ73	748.1 Da LogP 12.06 TPSA 134.4	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…`
CDL	5GUP	F1S1A8	1464.1 Da LogP 23.31 TPSA 242.6	3 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…`
DCQ	6I0D	Q56220	322.4 Da LogP 4.49 TPSA 52.6	✓ Ro5	Alert	`CCCCCCCCCCC1=C(C(=O)C(=C(C1=O)OC)OC)C`
EHZ	6G2J	Q91WD5	584.7 Da LogP 3.04 TPSA 182.5	2 viol.	✓ Clean	`CCCCCCCCCCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H]…`
FES	5LNK	W5PJ73	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
HQH	6Q8O	Q56220	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	Q56220	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	Q56220	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…`
PC1	5LNK	W5PJ73	790.2 Da LogP 12.17 TPSA 111.2	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])…`
PEE	5GUP	F1S1A8	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	5GUP	F1S1A8	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	W5PJ73	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	Q56220	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	Q56220	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	P17694	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	5GUP	F1S1A8	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).

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
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…`
ZINC1532641	1.000	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`
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-])…`
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…`
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…`
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…`
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…`
ZINC13544781	0.780	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	0.780	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	0.760	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	0.760	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…`
ZINC1559692	0.750	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`
ZINC102190945	0.739	411.5 Da LogP 3.29 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCCN`
ZINC32840692	0.739	425.5 Da LogP 3.68 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCCN`
ZINC32840693	0.739	425.5 Da LogP 3.68 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCCN`
ZINC32840704	0.739	453.6 Da LogP 4.46 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCCN`
ZINC32840705	0.739	453.6 Da LogP 4.46 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCCN`
ZINC95635984	0.739	397.4 Da LogP 2.90 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCCN`
ZINC102191119	0.729	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	0.729	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	0.727	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC36179002	0.727	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC13543394	0.708	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)…`
ZINC33822387	0.706	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	0.706	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)…`
ZINC5820131	0.705	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC5820134	0.705	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC1501016364	0.654	465.6 Da LogP 4.63 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O…`
ZINC4521879	0.650	386.5 Da LogP 4.73 TPSA 78.9	✓ Ro5	✓ Clean	`CCCCCC(=O)OCC(COC(=O)CCCCC)OC(=O)CCCCC`
ZINC116913009	0.645	276.4 Da LogP 4.93 TPSA 34.1	✓ Ro5	Alert	`CCCCCCCCCC1=C(C)C(=O)C(C)=C(C)C1=O`
ZINC12834352	0.635	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	0.635	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(…`
ZINC137999083	0.622	424.5 Da LogP 4.87 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCC(=O)OC[C@H](O)COP(=O)(O)O`
ZINC42851452	0.622	424.5 Da LogP 4.87 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC62624856	0.622	382.4 Da LogP 3.70 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)COP(=O)(O)O`
ZINC62624861	0.622	382.4 Da LogP 3.70 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC8218993	0.622	410.5 Da LogP 4.48 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)COP(=O)(O)O`
ZINC8219000	0.622	410.5 Da LogP 4.48 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC13552119	0.600	270.2 Da LogP 0.58 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC36079847	0.591	344.5 Da LogP 4.15 TPSA 72.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO)OC(=O)CCCCCCC`
ZINC8214428	0.591	344.5 Da LogP 4.15 TPSA 72.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO)OC(=O)CCCCCCC`
ZINC4521911	0.585	344.4 Da LogP 3.56 TPSA 78.9	✓ Ro5	✓ Clean	`CCCCC(=O)OCC(COC(=O)CCCC)OC(=O)CCCC`
ZINC85603366	0.585	344.5 Da LogP 4.15 TPSA 72.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OCC(O)COC(=O)CCCCCCC`
ZINC13544128	0.582	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…`
ZINC32822162	0.582	482.6 Da LogP 4.82 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC…`
ZINC32822163	0.582	482.6 Da LogP 4.82 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCC[N…`
ZINC44405718	0.582	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	0.582	426.5 Da LogP 3.26 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N+]…`
ZINC85576534	0.582	384.4 Da LogP 2.09 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N+](C)…`

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.