Protein profile

PA5016

dihydrolipoamide acetyltransferase

Genome: NC_002516.2

Gene: aceF PA5016 aceB Structure source: AlphaFold UniProt Q59638
Amino acids 547
Annotations 6
Features 42
PDB binders 7
Druggability 0.843

Overview

Basic information about this protein and its source genome.

Accession
PA5016
Gene
aceF PA5016 aceB
Status
annotated
Amino acids
547
Structure source
AlphaFold
GO
GO:0045254 A multi-enzyme complex that catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: pyruvate dehydrogenase (E1, which may be a homodimer or a heterotetramer of two alpha and two beta subunits, depending on species), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present. GO:0004742 Catalysis of the reaction: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + acetyl-CoA = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CoA. GO:0006086 The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate. In most organisms, this pathway links glycolysis to the TCA cycle, by a series of three reactions carried out by a multisubunit complex called the 'pyruvate dehydrogenase complex', even though pyruvate dehydrogenase activity describes only one of those reactions. The combination of the three reactions can be summarized as: pyruvate + coenzyme A + NAD+ -> acetyl-CoA + CO2 + NADH. 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: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 (%)
34.222
Human E-value
1.85e-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 0.843
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0045254 A multi-enzyme complex that catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: pyruvate dehydrogenase (E1, which may be a homodimer or a heterotetramer of two alpha and two beta subunits, depending on species), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present.
  • GO:0004742 Catalysis of the reaction: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + acetyl-CoA = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CoA.
  • GO:0006086 The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate. In most organisms, this pathway links glycolysis to the TCA cycle, by a series of three reactions carried out by a multisubunit complex called the 'pyruvate dehydrogenase complex', even though pyruvate dehydrogenase activity describes only one of those reactions. The combination of the three reactions can be summarized as: pyruvate + coenzyme A + NAD+ -> acetyl-CoA + CO2 + NADH.
  • 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: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.

42 records
Show feature table
Start End DB Term Name
4 547 NCBIfam TIGR01348 dihydrolipoyllysine-residue acetyltransferase
4 547 InterPro IPR006256 Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex
247 292 FunFam G3DSA:4.10.320.10:FF:000003 Acetyltransferase component of pyruvate dehydrogenase complex
247 292 Gene3D G3DSA:4.10.320.10 -
247 292 InterPro IPR036625 E3-binding domain superfamily
202 250 MobiDBLite mobidb-lite consensus disorder prediction
247 282 Pfam PF02817 e3 binding domain
247 282 InterPro IPR004167 Peripheral subunit-binding domain
119 193 ProSiteProfiles PS50968 Biotinyl/lipoyl domain profile.
119 193 InterPro IPR000089 Biotin/lipoyl attachment
5 108 PANTHER PTHR43178 DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX
1 80 FunFam G3DSA:2.40.50.100:FF:000009 Acetyltransferase component of pyruvate dehydrogenase complex
120 192 CDD cd06849 lipoyl_domain
118 212 SUPERFAMILY SSF51230 Single hybrid motif
118 212 InterPro IPR011053 Single hybrid motif
306 547 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
318 546 Pfam PF00198 2-oxoacid dehydrogenases acyltransferase (catalytic domain)
318 546 InterPro IPR001078 2-oxoacid dehydrogenase acyltransferase, catalytic domain
305 547 Gene3D G3DSA:3.30.559.10 -
305 547 InterPro IPR023213 Chloramphenicol acetyltransferase-like domain superfamily
120 198 Gene3D G3DSA:2.40.50.100 -
2 79 Gene3D G3DSA:2.40.50.100 -
25 54 ProSitePatterns PS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.
25 54 InterPro IPR003016 2-oxo acid dehydrogenase, lipoyl-binding site
118 198 FunFam G3DSA:2.40.50.100:FF:000009 Acetyltransferase component of pyruvate dehydrogenase complex
4 93 SUPERFAMILY SSF51230 Single hybrid motif
4 93 InterPro IPR011053 Single hybrid motif
248 285 ProSiteProfiles PS51826 Peripheral subunit-binding (PSBD) domain profile.
248 285 InterPro IPR004167 Peripheral subunit-binding domain
72 117 MobiDBLite mobidb-lite consensus disorder prediction
2 75 ProSiteProfiles PS50968 Biotinyl/lipoyl domain profile.
2 75 InterPro IPR000089 Biotin/lipoyl attachment
143 172 ProSitePatterns PS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.
143 172 InterPro IPR003016 2-oxo acid dehydrogenase, lipoyl-binding site
242 286 SUPERFAMILY SSF47005 Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
242 286 InterPro IPR036625 E3-binding domain superfamily
302 547 FunFam G3DSA:3.30.559.10:FF:000004 Acetyltransferase component of pyruvate dehydrogenase complex
5 74 CDD cd06849 lipoyl_domain
5 74 Pfam PF00364 Biotin-requiring enzyme
5 74 InterPro IPR000089 Biotin/lipoyl attachment
121 192 Pfam PF00364 Biotin-requiring enzyme
121 192 InterPro IPR000089 Biotin/lipoyl attachment

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 PA5016
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 0.843
4 0.418
3 0.254

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.

57 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
BTI A0A0H3JRU9 228.3 Da LogP 0.91 TPSA 58.2 ✓ Ro5 ✓ Clean C1[C@H]2[C@@H]([C@@H](S1)CCCCC=O)NC(=O)N2
CAO 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 P10802 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
LPM P10802 207.4 Da LogP 1.65 TPSA 43.1 ✓ Ro5 ✓ Clean C(CCC(=O)N)C[C@H](CCS)S
PYR A0A0H3JRU9 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
RDC 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 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.