Protein profile

PA1586

2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase

Genome: NC_002516.2

Gene: sucB PA1586 Structure source: AlphaFold UniProt Q9I3D2
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Amino acids 409
Annotations 7
Features 27
PDB binders 5
Druggability 0.748

Overview

Basic information about this protein and its source genome.

Accession
PA1586
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
sucB PA1586
Status
annotated
Amino acids
409
Structure source
AlphaFold
EC
2.3.1.61
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:0004149 Catalysis of the reaction: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[2-oxoglutarate dehydrogenase complex component E2] + succinyl-CoA = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[2-oxoglutarate dehydrogenase complex component E2] + CoA. GO:0033512 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA, via the intermediate L-saccharopine. 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:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
57.54
Human E-value
9.16e-92
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 0.748
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MAIEIKAPTFPESVADGTVATWHKKPGEAVKRDELIVDIETDKVVIEVLAEADGVLAEIIKNEGDTVLSNELLGKLNEGGAAAPAAPAAAAPAAAPAAQAAAPAAAGGDDAILSPAARKLAEEAGIDPNSIAGTGKGGRVTKEDVVAAVEAKKNAPAAPAKPAAPAAEAPIFAAGDRVEKRVPMTRLRAKVAERLVEAQSAMAMLTTFNEVNMKPIMDLRSKYKDLFEKKHNGVRLGFMSFFVKAATEALKRFPGVNASIDGNDIVYHGYQDIGVAVSSDRGLVVPVLRNAEFMSLAEIEGGIANFGKKAKEGKLTIEDMTGGTFTISNGGVFGSLLSTPIVNPPQTAILGMHKIQERPMAVNGQVVILPMMYLALSYDHRLIDGKEAVSFLVAIKDLLEDPARLLLDV

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • 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:0004149 Catalysis of the reaction: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[2-oxoglutarate dehydrogenase complex component E2] + succinyl-CoA = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[2-oxoglutarate dehydrogenase complex component E2] + CoA.
  • GO:0033512 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including acetyl-CoA, via the intermediate L-saccharopine.
  • 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:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
160 405 Gene3D G3DSA:3.30.559.10 -
160 405 InterPro IPR023213 Chloramphenicol acetyltransferase-like domain superfamily
113 154 Gene3D G3DSA:4.10.320.10 -
113 154 InterPro IPR036625 E3-binding domain superfamily
3 76 CDD cd06849 lipoyl_domain
179 407 Pfam PF00198 2-oxoacid dehydrogenases acyltransferase (catalytic domain)
179 407 InterPro IPR001078 2-oxoacid dehydrogenase acyltransferase, catalytic domain
27 56 ProSitePatterns PS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.
27 56 InterPro IPR003016 2-oxo acid dehydrogenase, lipoyl-binding site
179 408 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
2 80 Gene3D G3DSA:2.40.50.100 -
167 407 FunFam G3DSA:3.30.559.10:FF:000007 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex
3 409 NCBIfam TIGR01347 dihydrolipoyllysine-residue succinyltransferase
3 409 InterPro IPR006255 Dihydrolipoamide succinyltransferase
4 76 Pfam PF00364 Biotin-requiring enzyme
4 76 InterPro IPR000089 Biotin/lipoyl attachment
105 150 SUPERFAMILY SSF47005 Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
105 150 InterPro IPR036625 E3-binding domain superfamily
112 149 ProSiteProfiles PS51826 Peripheral subunit-binding (PSBD) domain profile.
112 149 InterPro IPR004167 Peripheral subunit-binding domain
1 96 SUPERFAMILY SSF51230 Single hybrid motif
1 96 InterPro IPR011053 Single hybrid motif
2 408 PANTHER PTHR43416 DIHYDROLIPOYLLYSINE-RESIDUE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL-RELATED
2 77 ProSiteProfiles PS50968 Biotinyl/lipoyl domain profile.
2 77 InterPro IPR000089 Biotin/lipoyl attachment
112 145 Pfam PF02817 e3 binding domain
112 145 InterPro IPR004167 Peripheral subunit-binding domain

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 PA1586
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 0.748
2 0.235

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.

47 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
CAO
1EAC
P10802 783.5 Da LogP -1.39 TPSA 366.8 3 viol. ✓ Clean CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([…
DTT
1EAC
P10802 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
LPM
1EAB
P10802 207.4 Da LogP 1.65 TPSA 43.1 ✓ Ro5 ✓ Clean C(CCC(=O)N)C[C@H](CCS)S
RDC
2Q8I
P10515 364.8 Da LogP 2.69 TPSA 96.4 ✓ Ro5 ✓ Clean C[C@@H]1C[C@@H]2[C@H](O2)\C=C/C=C/C(=O)Cc3c(c(c…
RED
1Y8N
P10515 208.3 Da LogP 2.25 TPSA 37.3 ✓ Ro5 ✓ Clean C(CCC(=O)O)C[C@H](CCS)S

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.