Protein profile

PA1585

2-oxoglutarate dehydrogenase subunit E1

Genome: NC_002516.2

Gene: sucA PA1585 Structure source: AlphaFold UniProt Q9I3D3

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Amino acids 943

Annotations 8

Features 29

PDB binders 11

Druggability 0.453

Overview

Basic information about this protein and its source genome.

Accession: PA1585
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: sucA PA1585
Status: annotated
Amino acids: 943
Structure source: AlphaFold

1.2.4.2

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0045252 A multi-enzyme complex that catalyzes the oxidative decarboxylation of alpha-ketoglutarate (also known as 2-oxoglutarate) to form succinyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present. GO:0004591 Catalysis of the reaction: N(6)-[(R)-lipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] + 2-oxoglutarate + H+ = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] + CO2. GO:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases. GO:0006096 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules. GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 46.358
Human E-value: 8.700000000000001e-43
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 0.453

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1.2.4.2

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0045252 A multi-enzyme complex that catalyzes the oxidative decarboxylation of alpha-ketoglutarate (also known as 2-oxoglutarate) to form succinyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present.
GO:0004591 Catalysis of the reaction: N(6)-[(R)-lipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] + 2-oxoglutarate + H+ = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] + CO2.
GO:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
GO:0006096 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
GO:0016624 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide.

Sequence Features

Domain/signature hits from InterPro and related databases.

29 records

Show feature table

Start	End	DB	Term	Name
12	50	Pfam	PF16078	2-oxoglutarate dehydrogenase N-terminus
12	50	InterPro	IPR032106	2-oxoglutarate dehydrogenase E1 component, N-terminal domain
88	170	FunFam	G3DSA:1.10.287.1150:FF:000004	2-oxoglutarate dehydrogenase E1 component
582	799	SUPERFAMILY	SSF52518	Thiamin diphosphate-binding fold (THDP-binding)
582	799	InterPro	IPR029061	Thiamin diphosphate-binding fold
15	941	NCBIfam	TIGR00239	2-oxoglutarate dehydrogenase E1 component
15	941	InterPro	IPR011603	2-oxoglutarate dehydrogenase E1 component
561	808	FunFam	G3DSA:3.40.50.12470:FF:000009	2-oxoglutarate dehydrogenase E1 component
219	480	CDD	cd02016	TPP_E1_OGDC_like
1	943	PIRSF	PIRSF000157	Oxoglu_dh_E1
1	943	InterPro	IPR011603	2-oxoglutarate dehydrogenase E1 component
729	940	Gene3D	G3DSA:3.40.50.11610	-
729	940	InterPro	IPR042179	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily
599	793	Pfam	PF02779	Transketolase, pyrimidine binding domain
599	793	InterPro	IPR005475	Transketolase-like, pyrimidine-binding domain
88	170	Gene3D	G3DSA:1.10.287.1150	TPP helical domain
561	808	Gene3D	G3DSA:3.40.50.12470	-
797	941	Pfam	PF16870	2-oxoglutarate dehydrogenase C-terminal
797	941	InterPro	IPR031717	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal
599	792	SMART	SM00861	Transket_pyr_3
599	792	InterPro	IPR005475	Transketolase-like, pyrimidine-binding domain
171	537	FunFam	G3DSA:3.40.50.970:FF:000014	2-oxoglutarate dehydrogenase E1 component
172	536	Gene3D	G3DSA:3.40.50.970	-
12	941	PANTHER	PTHR23152	2-OXOGLUTARATE DEHYDROGENASE
12	941	InterPro	IPR011603	2-oxoglutarate dehydrogenase E1 component
220	526	Pfam	PF00676	Dehydrogenase E1 component
220	526	InterPro	IPR001017	Dehydrogenase, E1 component
126	550	SUPERFAMILY	SSF52518	Thiamin diphosphate-binding fold (THDP-binding)
126	550	InterPro	IPR029061	Thiamin diphosphate-binding fold

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

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA1585	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
30				0.425
15				0.278
6				0.228

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.

64 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
A5X	6CFO	P08559	533.4 Da LogP 0.47 TPSA 226.5	2 viol.	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)P(=O)O)CC…`
DW3	6KMA	A0A3Q0L1E1	60.1 Da LogP -0.82 TPSA 37.3	✓ Ro5	✓ Clean	`C(C=O)O`
JQ5	6R2C	A0R2B1	210.1 Da LogP 0.60 TPSA 100.9	✓ Ro5	✓ Clean	`CCOP(=O)(C(=O)CCC(=O)O)O`
OAA	6VEF	P0AFG3	131.1 Da LogP -2.22 TPSA 94.5	✓ Ro5	✓ Clean	`C(C(=O)C(=O)O)C(=O)[O-]`
QSP	6R29	A0R2B1	608.4 Da LogP 0.82 TPSA 283.4	3 viol.	✓ Clean	`Cc1ncc(c(n1)N)CN2[C@H](SC(=C2C)CCOP(=O)(O)OP(=O…`
TD6	3ZHS	A0R2B1	527.4 Da LogP 0.74 TPSA 226.5	2 viol.	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](CCC(=O)O)O)CCO…`
TD7	2Y0P	A0R2B1	526.4 Da LogP 2.36 TPSA 225.9	3 viol.	✓ Clean	`Cc1ncc(c(n1)N)CN2C(=C(SC2=C(CCC(=O)O)O)CCO[P@](…`
TD8	3ZHU	A0R2B1	541.4 Da LogP 1.13 TPSA 226.5	2 viol.	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@H](CCCC(=O)O)O)C…`
TD9	3ZHT	A0R2B1	541.4 Da LogP 1.13 TPSA 226.5	2 viol.	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](CCCC(=O)O)O)CC…`
TDW	3ZHV	A0R2B1	469.4 Da LogP 0.90 TPSA 189.2	✓ Ro5	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](C)O)CCOP(=O)(O…`
ZP1	6R2A	A0R2B1	636.5 Da LogP 1.87 TPSA 272.4	3 viol.	✓ Clean	`CCOP(=O)([C@@](CCC(=O)O)([C@@H]1N(C(=C(S1)CCOP(…`

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	P08559	7.04	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cnn(c3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
DWT	P08559	6.35	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
CHEMBL1061	P26284	—	223.3 Da LogP 1.29 TPSA 66.4	✓ Ro5	✓ Clean	`O=C1NC(=O)C(Cc2ccc(O)cc2)S1`

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
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC26575565	1.000	223.3 Da LogP 1.29 TPSA 66.4	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](Cc2ccc(O)cc2)S1`
ZINC26575566	1.000	223.3 Da LogP 1.29 TPSA 66.4	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](Cc2ccc(O)cc2)S1`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1453005	0.750	241.7 Da LogP 2.23 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](Cc2ccc(Cl)cc2)S1`
ZINC1453006	0.750	241.7 Da LogP 2.23 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](Cc2ccc(Cl)cc2)S1`
ZINC22059407	0.750	225.2 Da LogP 1.72 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](Cc2ccc(F)cc2)S1`
ZINC22059410	0.750	225.2 Da LogP 1.72 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](Cc2ccc(F)cc2)S1`
ZINC136823231	0.727	286.1 Da LogP 2.34 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](Cc2ccc(Br)cc2)S1`
ZINC136823276	0.727	286.1 Da LogP 2.34 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](Cc2ccc(Br)cc2)S1`
ZINC1395202	0.727	222.3 Da LogP 1.16 TPSA 72.2	✓ Ro5	Alert	`Nc1ccc(C[C@@H]2SC(=O)NC2=O)cc1`
ZINC1395203	0.727	222.3 Da LogP 1.16 TPSA 72.2	✓ Ro5	Alert	`Nc1ccc(C[C@H]2SC(=O)NC2=O)cc1`
ZINC1453011	0.727	221.3 Da LogP 1.89 TPSA 46.2	✓ Ro5	✓ Clean	`Cc1ccc(C[C@@H]2SC(=O)NC2=O)cc1`
ZINC1453012	0.727	221.3 Da LogP 1.89 TPSA 46.2	✓ Ro5	✓ Clean	`Cc1ccc(C[C@H]2SC(=O)NC2=O)cc1`
ZINC1453007	0.719	207.3 Da LogP 1.58 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](Cc2ccccc2)S1`
ZINC1453008	0.719	207.3 Da LogP 1.58 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](Cc2ccccc2)S1`
ZINC115086873	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC33876997	0.686	239.3 Da LogP 0.99 TPSA 86.6	✓ Ro5	Alert	`O=C1NC(=O)[C@@H](Cc2ccc(O)c(O)c2)S1`
ZINC33876999	0.686	239.3 Da LogP 0.99 TPSA 86.6	✓ Ro5	Alert	`O=C1NC(=O)[C@H](Cc2ccc(O)c(O)c2)S1`
ZINC1386519	0.676	208.2 Da LogP 0.98 TPSA 59.1	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](Cc2ccncc2)S1`
ZINC4052182	0.676	208.2 Da LogP 0.98 TPSA 59.1	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](Cc2ccncc2)S1`
ZINC144529043	0.667	223.3 Da LogP 1.29 TPSA 66.4	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](Cc2cccc(O)c2)S1`
ZINC144529255	0.667	223.3 Da LogP 1.29 TPSA 66.4	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](Cc2cccc(O)c2)S1`
ZINC144169243	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`

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.