Protein profile

KP13_03276

Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex

Genome: KpKP13

Gene: AHE45655.1 sucB Structure source: AlphaFold + ColabFold UniProt A0A0H3GLJ0
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Amino acids 408
Annotations 7
Features 32
PDB binders 5
Druggability 0.683

Overview

Basic information about this protein and its source genome.

Accession
KP13_03276
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45655.1 sucB
Status
annotated
Amino acids
408
Structure source
AlphaFold + ColabFold
EC
2.3.1.61
GO
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: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). 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
58.167
Human E-value
7.31e-98
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
92.647
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
83.91

Selected Druggability evidence

AlphaFold / UniProt model

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 0.683
Structure A0A0H3GLJ0
Pocket Pocket 17
P2Rank 0.208
Structure A0A0H3GLJ0
Pocket Pocket 1
ColabFold model
FPocket 0.621 · Pocket 5
P2Rank 0.131 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 197 / 4744 genomes with a hit
Normalized 0.042

Sequence

Primary amino-acid sequence viewer.

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: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: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).
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
160 405 FunFam G3DSA:3.30.559.10:FF:000005 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
154 181 MobiDBLite mobidb-lite consensus disorder prediction
5 75 Pfam PF00364 Biotin-requiring enzyme
5 75 InterPro IPR000089 Biotin/lipoyl attachment
79 111 MobiDBLite mobidb-lite consensus disorder prediction
1 407 PANTHER PTHR43416 DIHYDROLIPOYLLYSINE-RESIDUE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL-RELATED
3 78 ProSiteProfiles PS50968 Biotinyl/lipoyl domain profile.
3 78 InterPro IPR000089 Biotin/lipoyl attachment
2 81 FunFam G3DSA:2.40.50.100:FF:000015 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
103 153 FunFam G3DSA:4.10.320.10:FF:000001 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
93 111 MobiDBLite mobidb-lite consensus disorder prediction
28 57 ProSitePatterns PS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.
28 57 InterPro IPR003016 2-oxo acid dehydrogenase, lipoyl-binding site
160 405 Gene3D G3DSA:3.30.559.10 -
160 405 InterPro IPR023213 Chloramphenicol acetyltransferase-like domain superfamily
106 151 SUPERFAMILY SSF47005 Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
106 151 InterPro IPR036625 E3-binding domain superfamily
114 147 Pfam PF02817 e3 binding domain
114 147 InterPro IPR004167 Peripheral subunit-binding domain
103 153 Gene3D G3DSA:4.10.320.10 -
103 153 InterPro IPR036625 E3-binding domain superfamily
178 407 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
4 77 CDD cd06849 lipoyl_domain
113 150 ProSiteProfiles PS51826 Peripheral subunit-binding (PSBD) domain profile.
113 150 InterPro IPR004167 Peripheral subunit-binding domain
178 406 Pfam PF00198 2-oxoacid dehydrogenases acyltransferase (catalytic domain)
178 406 InterPro IPR001078 2-oxoacid dehydrogenase acyltransferase, catalytic domain
2 95 SUPERFAMILY SSF51230 Single hybrid motif
2 95 InterPro IPR011053 Single hybrid motif
2 81 Gene3D G3DSA:2.40.50.100 -
4 408 NCBIfam TIGR01347 dihydrolipoyllysine-residue succinyltransferase
4 408 InterPro IPR006255 Dihydrolipoamide succinyltransferase

3D Structure

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

3D visualization script Full viewer

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Structural evidence

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GLJ0
AlphaFold — — full sequence — Viewing
ColabFold KP13_03276
ColabFold — — full sequence — Loaded
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
17 0.683

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 5.13 0.236
2 2.82 0.087
3 1.24 0.012

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.