Protein profile

PA2250

branched-chain alpha-keto acid dehydrogenase complex dihydrolipoyl dehydrogenase

Genome: NC_002516.2

Gene: lpdV PA2250 Structure source: AlphaFold UniProt Q9I1L9

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Amino acids 464

Annotations 7

Features 36

PDB binders 5

Druggability 0.73

Overview

Basic information about this protein and its source genome.

Accession: PA2250
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: lpdV PA2250
Status: annotated
Amino acids: 464
Structure source: AlphaFold

1.8.1.4

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0004148 Catalysis of the reaction: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD+ = N(6)-[(R)-lipoyl]-L-lysyl-[protein] + NADH + H+. GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. GO:0006103 The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0016668 Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 54.167
Human E-value: 3.37e-16
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 0.73

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MSQILKTSLLIVGGGPGGYVAAIRAGQLGIPTVLVEGAALGGTCLNVGCIPSKALIHAAEEYLKARHYASRSALGIQVQAPSIDIARTVEWKDAIVDRLTSGVAALLKKHGVDVVQGWARILDGKSVAVELAGGGSQRIECEHLLLAAGSQSVELPILPLGGKVISSTEALAPGSLPKRLVVVGGGYIGLELGTAYRKLGVEVAVVEAQPRILPGYDEELTKPVAQALRRLGVELYLGHSLLGPSENGVRVRDGAGEEREIAADQVLVAVGRKPRSEGWNLESLGLDMNGRAVKVDDQCRTSMRNVWAIGDLAGEPMLAHRAMAQGEMVAELIAGKRRQFAPVAIPAVCFTDPEVVVAGLSPEQAKDAGLDCLVASFPFAANGRAMTLEANEGFVRVVARRDNHLVVGWQAVGKAVSELSTAFAQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHI

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1.8.1.4

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0004148 Catalysis of the reaction: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD+ = N(6)-[(R)-lipoyl]-L-lysyl-[protein] + NADH + H+.
GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
GO:0006103 The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GO:0016668 Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records

Show feature table

Start	End	DB	Term	Name
8	326	Pfam	PF07992	Pyridine nucleotide-disulphide oxidoreductase
8	326	InterPro	IPR023753	FAD/NAD(P)-binding domain
40	55	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
144	153	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
428	448	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
8	30	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
341	362	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
264	278	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
179	204	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
406	421	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
306	313	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
6	336	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
6	336	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
344	464	FunFam	G3DSA:3.30.390.30:FF:000001	Dihydrolipoyl dehydrogenase
8	464	NCBIfam	TIGR01350	dihydrolipoyl dehydrogenase
8	464	InterPro	IPR006258	Dihydrolipoamide dehydrogenase
344	463	SUPERFAMILY	SSF55424	FAD/NAD-linked reductases, dimerisation (C-terminal) domain
344	463	InterPro	IPR016156	FAD/NAD-linked reductase, dimerisation domain superfamily
153	270	Gene3D	G3DSA:3.50.50.60	-
153	270	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
344	464	Gene3D	G3DSA:3.30.390.30	-
344	464	InterPro	IPR016156	FAD/NAD-linked reductase, dimerisation domain superfamily
9	331	Gene3D	G3DSA:3.50.50.60	-
9	331	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
7	457	PANTHER	PTHR22912	DISULFIDE OXIDOREDUCTASE
41	51	ProSitePatterns	PS00076	Pyridine nucleotide-disulphide oxidoreductases class-I active site.
41	51	InterPro	IPR012999	Pyridine nucleotide-disulphide oxidoreductase, class I, active site
141	159	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
291	313	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
263	279	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
179	197	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
9	28	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
2	457	PIRSF	PIRSF000350	Hg-II_reductase_MerA
2	457	InterPro	IPR001100	Pyridine nucleotide-disulphide oxidoreductase, class I
345	454	Pfam	PF02852	Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
345	454	InterPro	IPR004099	Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain

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 PA2250	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
1				0.73

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.

60 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 60 via homologs

Structural ligands 5 0 loaded crystals

Bioactive compounds 5 50 ZINC candidates

Drug-like & clean 31 4 PAINS alerts

Best available ligand signal

3II PDB via homolog 625.6 Da · LogP 4.65 · TPSA 91.4

3II PDB via homolog BTB PDB via homolog MLT PDB via homolog NHE PDB via homolog

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
3II	3II4	P9WHH9	625.6 Da LogP 4.65 TPSA 91.4	1 viol.	✓ Clean	`COc1ccc(c(c1)OC)C(=O)N2CCC3(CC2)C(=O)N(CN3c4ccc…`
BTB	5NHG	P09622-2	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
MLT	6CMZ	B4EEF2	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)C(=O)O`
NHE	3RNM	P09622-2	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCS(=O)(=O)O`
RBF	6N7F	Q9A0E2	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([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
CHEMBL1451931	P9WHH9	7.00	263.3 Da LogP 2.58 TPSA 46.2	✓ Ro5	Alert	`O=C1C=C(NCc2ccccc2)c2ccccc2C1=O`
CHEMBL3949128	P9WHH9	6.16	463.7 Da LogP 2.35 TPSA 114.6	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)CN(C)S(=O)(=O)c2cc(Br)cnc2N)cc1Cl`
CHEMBL3935059	P9WHH9	6.08	441.4 Da LogP 2.81 TPSA 105.4	✓ Ro5	✓ Clean	`CC(C)c1ccc(NC(=O)CN(C)S(=O)(=O)c2cc(Br)cnc2N)cc1`
CHEMBL3983097	P9WHH9	6.08	459.3 Da LogP 1.70 TPSA 123.9	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)CN(C)S(=O)(=O)c2cc(Br)cnc2N)cc1OC`
M52	P9WHH9	6.02	429.3 Da LogP 1.69 TPSA 114.6	✓ Ro5	✓ Clean	`C[N@@](CC(=O)Nc1ccc(cc1)OC)S(=O)(=O)c2cc(cnc2N)…`

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
ZINC11565587	1.000	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](O)…`
ZINC1532585	1.000	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC1615342	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC1710230	1.000	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC1769096	1.000	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC2036848	1.000	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC3650334	1.000	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC3831422	1.000	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](O)…`
ZINC3831423	1.000	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC3831424	1.000	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC4353342	0.957	406.4 Da LogP -2.36 TPSA 181.8	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC4353343	0.957	406.4 Da LogP -2.36 TPSA 181.8	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](O)…`
ZINC4353344	0.957	406.4 Da LogP -2.36 TPSA 181.8	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC4353345	0.957	406.4 Da LogP -2.36 TPSA 181.8	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC2004116	0.860	396.8 Da LogP -1.38 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2c(cc1Cl)nc1c(=O)[nH]c(=O)nc-1n2C[C@H](O)[…`
ZINC149168378	0.857	374.4 Da LogP -0.31 TPSA 141.3	✓ Ro5	✓ Clean	`CC[C@@H](O)[C@@H](O)[C@@H](O)Cn1c2nc(=O)[nH]c(=…`
ZINC3650235	0.843	377.4 Da LogP -2.45 TPSA 187.6	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC4430211	0.843	396.8 Da LogP -1.38 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC5545623	0.843	377.4 Da LogP -2.45 TPSA 187.6	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](O)…`
ZINC5545624	0.843	377.4 Da LogP -2.45 TPSA 187.6	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC5545628	0.843	377.4 Da LogP -2.45 TPSA 187.6	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC4430517	0.820	404.4 Da LogP -1.22 TPSA 161.6	✓ Ro5	✓ Clean	`CCc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)…`
ZINC35653106	0.811	405.4 Da LogP -1.97 TPSA 164.8	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC2004372	0.786	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.786	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC4262829	0.781	263.3 Da LogP 2.74 TPSA 46.2	✓ Ro5	Alert	`O=C1C=C(NCc2ccccc2)C(=O)c2ccccc21`
ZINC4430765	0.765	447.2 Da LogP -1.67 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO)c3…`
ZINC4430766	0.765	447.2 Da LogP -1.67 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO)c…`
ZINC4430767	0.765	447.2 Da LogP -1.67 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)c…`
ZINC4430768	0.765	447.2 Da LogP -1.67 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)…`
ZINC43763773	0.759	410.8 Da LogP -1.12 TPSA 161.6	✓ Ro5	✓ Clean	`CCc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)…`
ZINC43763774	0.759	410.8 Da LogP -1.12 TPSA 161.6	✓ Ro5	✓ Clean	`CCc1cc2c(cc1Cl)nc1c(=O)[nH]c(=O)nc-1n2C[C@H](O)…`
ZINC13513101	0.750	456.4 Da LogP -1.90 TPSA 204.9	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC3831425	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC3831426	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](O)…`
ZINC3831427	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC3831428	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC8551105	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC8551106	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC8551108	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC4430761	0.717	412.8 Da LogP -2.33 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO)c3…`
ZINC4430762	0.717	412.8 Da LogP -2.33 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO)c…`
ZINC4430763	0.717	412.8 Da LogP -2.33 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)c…`
ZINC4430764	0.717	412.8 Da LogP -2.33 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)…`
ZINC1574811	0.714	378.3 Da LogP -2.33 TPSA 170.8	✓ Ro5	✓ Clean	`COc1ccc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](…`
ZINC5386869	0.714	378.3 Da LogP -2.33 TPSA 170.8	✓ Ro5	✓ Clean	`COc1ccc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O…`
ZINC5386870	0.714	378.3 Da LogP -2.33 TPSA 170.8	✓ Ro5	✓ Clean	`COc1ccc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](…`
ZINC5386872	0.714	378.3 Da LogP -2.33 TPSA 170.8	✓ Ro5	✓ Clean	`COc1ccc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H]…`
ZINC102949042	0.706	277.3 Da LogP 2.63 TPSA 46.2	✓ Ro5	Alert	`O=C1C=C(NCCc2ccccc2)c2ccccc2C1=O`
ZINC101357336	0.700	318.4 Da LogP 2.49 TPSA 58.2	✓ Ro5	Alert	`O=C1C=C(NCc2ccccc2)C(=O)C=C1NCc1ccccc1`

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.