Overview
Basic information about this protein and its source genome.
- Accession
- PA5016
- Gene
- aceF PA5016 aceB
- Status
- annotated
- Amino acids
- 547
- Structure source
- AlphaFold
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.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene 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.
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.
Loading 3D structure...
Structural evidence
0 + 1Experimental 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.
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 |
|---|---|---|---|---|---|---|
| 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
|
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).
No ChEMBL hits found through similar proteins.
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 |
|---|---|---|---|---|---|
| ZINC100006925 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@@H]1C[C@H]2O[C@@H]2/C=C\C=C/C(=O)Cc2c(Cl)c(…
|
| ZINC100013319 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@@H]1C[C@H]2O[C@H]2/C=C/C=C\C(=O)Cc2c(Cl)c(O…
|
| ZINC100013323 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@H]1C[C@H]2O[C@H]2/C=C/C=C\C(=O)Cc2c(Cl)c(O)…
|
| ZINC100152234 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@@H]1C[C@H]2O[C@@H]2/C=C/C=C/C(=O)Cc2c(Cl)c(…
|
| ZINC13521629 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@@H]1C[C@H]2O[C@@H]2/C=C\C=C\C(=O)Cc2c(Cl)c(…
|
| ZINC2061000778 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@H]1C[C@@H]2O[C@H]2C=CC=CC(=O)Cc2c(Cl)c(O)cc…
|
| ZINC253952046 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@@H]1C[C@@H]2O[C@H]2C=CC=CC(=O)Cc2c(Cl)c(O)c…
|
| ZINC253987424 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@@H]1C[C@H]2O[C@@H]2C=CC=CC(=O)Cc2c(Cl)c(O)c…
|
| ZINC253987427 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@@H]1C[C@H]2O[C@H]2C=CC=CC(=O)Cc2c(Cl)c(O)cc…
|
| ZINC253987428 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@@H]1C[C@@H]2O[C@@H]2C=CC=CC(=O)Cc2c(Cl)c(O)…
|
| ZINC33838895 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@@H]1C[C@H]2O[C@H]2/C=C\C=C/C(=O)Cc2c(Cl)c(O…
|
| ZINC45789132 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@@H]1C[C@H]2O[C@@H]2/C=C/C=C\C(=O)Cc2c(Cl)c(…
|
| ZINC45789135 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@H]1C[C@H]2O[C@@H]2/C=C/C=C\C(=O)Cc2c(Cl)c(O…
|
| ZINC5492965 | 1.000 | 364.8 Da LogP 2.69 TPSA 96.4 | ✓ Ro5 | ✓ Clean |
C[C@@H]1C[C@@H]2O[C@H]2/C=C\C=C\C(=O)Cc2c(Cl)c(…
|
| ZINC1529363 | 0.704 | 208.3 Da LogP 2.25 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCC[C@H](S)CCS
|
| ZINC3869601 | 0.704 | 208.3 Da LogP 2.25 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCC[C@@H](S)CCS
|
| ZINC34603442 | 0.703 | 215.3 Da LogP 0.28 TPSA 67.1 | ✓ Ro5 | ✓ Clean |
NCCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
|
| ZINC34182012 | 0.667 | 230.3 Da LogP 0.70 TPSA 61.4 | ✓ Ro5 | ✓ Clean |
O=C1N[C@@H]2[C@H](CCCCCO)SC[C@@H]2N1
|
| ZINC1532548 | 0.634 | 244.3 Da LogP 0.80 TPSA 78.4 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCC[C@H]1SC[C@@H]2NC(=O)N[C@@H]21
|
| ZINC2169825 | 0.634 | 244.3 Da LogP 0.80 TPSA 78.4 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCC[C@H]1SC[C@H]2NC(=O)N[C@H]21
|
| ZINC2169827 | 0.634 | 244.3 Da LogP 0.80 TPSA 78.4 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCC[C@H]1SC[C@@H]2NC(=O)N[C@H]21
|
| ZINC3869709 | 0.634 | 243.3 Da LogP 0.20 TPSA 84.2 | ✓ Ro5 | ✓ Clean |
NC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21
|
| ZINC3869710 | 0.634 | 243.3 Da LogP 0.20 TPSA 84.2 | ✓ Ro5 | ✓ Clean |
NC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
|
| ZINC3869711 | 0.634 | 243.3 Da LogP 0.20 TPSA 84.2 | ✓ Ro5 | ✓ Clean |
NC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@H]21
|
| ZINC3869712 | 0.634 | 243.3 Da LogP 0.20 TPSA 84.2 | ✓ Ro5 | ✓ Clean |
NC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]12
|
| ZINC22052067 | 0.609 | 301.4 Da LogP -0.09 TPSA 107.5 | ✓ Ro5 | ✓ Clean |
O=C(O)CNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
|
| ZINC59286406 | 0.609 | 300.4 Da LogP -0.69 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
NC(=O)CNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
|
| ZINC222024244 | 0.600 | 283.4 Da LogP 0.99 TPSA 70.2 | ✓ Ro5 | ✓ Clean |
O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]12)NC1CC1
|
| ZINC48391181 | 0.600 | 283.4 Da LogP 0.99 TPSA 70.2 | ✓ Ro5 | ✓ Clean |
O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NC1CC1
|
| ZINC53464107 | 0.600 | 283.4 Da LogP 0.99 TPSA 70.2 | ✓ Ro5 | ✓ Clean |
O=C(CCCC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21)NC1CC1
|
| ZINC53464111 | 0.600 | 283.4 Da LogP 0.99 TPSA 70.2 | ✓ Ro5 | ✓ Clean |
O=C(CCCC[C@@H]1SC[C@H]2NC(=O)N[C@H]21)NC1CC1
|
| ZINC2121285 | 0.578 | 258.3 Da LogP 0.89 TPSA 67.4 | ✓ Ro5 | ✓ Clean |
COC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@H]21
|
| ZINC4038545 | 0.578 | 258.3 Da LogP 0.89 TPSA 67.4 | ✓ Ro5 | ✓ Clean |
COC(=O)CCCC[C@H]1SC[C@H]2NC(=O)N[C@H]21
|
| ZINC5005298 | 0.578 | 258.3 Da LogP 0.89 TPSA 67.4 | ✓ Ro5 | ✓ Clean |
COC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21
|
| ZINC5224322 | 0.578 | 258.3 Da LogP 0.89 TPSA 67.4 | ✓ Ro5 | ✓ Clean |
COC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
|
| ZINC90514224 | 0.578 | 258.3 Da LogP 0.89 TPSA 67.4 | ✓ Ro5 | ✓ Clean |
COC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]12
|
| ZINC27065097 | 0.574 | 311.5 Da LogP 1.77 TPSA 70.2 | ✓ Ro5 | ✓ Clean |
O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NC1CCCC1
|
| ZINC5157321 | 0.574 | 287.4 Da LogP -0.18 TPSA 90.5 | ✓ Ro5 | ✓ Clean |
O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NCCO
|
| ZINC206908803 | 0.571 | 315.4 Da LogP 0.00 TPSA 96.5 | ✓ Ro5 | ✓ Clean |
COC(=O)CNC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21
|
| ZINC334161970 | 0.571 | 315.4 Da LogP 0.00 TPSA 96.5 | ✓ Ro5 | ✓ Clean |
COC(=O)CNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]…
|
| ZINC62001297 | 0.571 | 315.4 Da LogP 0.00 TPSA 96.5 | ✓ Ro5 | ✓ Clean |
COC(=O)CNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
|
| ZINC75611263 | 0.571 | 315.4 Da LogP 0.00 TPSA 96.5 | ✓ Ro5 | ✓ Clean |
COC(=O)CNC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@H]21
|
| ZINC104112886 | 0.568 | 242.3 Da LogP 0.57 TPSA 78.4 | ✓ Ro5 | ✓ Clean |
O=C(O)/C=C\CC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21
|
| ZINC13543600 | 0.568 | 242.3 Da LogP 0.57 TPSA 78.4 | ✓ Ro5 | ✓ Clean |
O=C(O)/C=C\CC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
|
| ZINC4216800 | 0.568 | 242.3 Da LogP 0.57 TPSA 78.4 | ✓ Ro5 | ✓ Clean |
O=C(O)/C=C/CC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
|
| ZINC5082085 | 0.568 | 242.3 Da LogP 0.57 TPSA 78.4 | ✓ Ro5 | ✓ Clean |
O=C(O)/C=C/CC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21
|
| ZINC5082088 | 0.568 | 242.3 Da LogP 0.57 TPSA 78.4 | ✓ Ro5 | ✓ Clean |
O=C(O)/C=C/CC[C@@H]1SC[C@H]2NC(=O)N[C@H]21
|
| ZINC5082090 | 0.568 | 242.3 Da LogP 0.57 TPSA 78.4 | ✓ Ro5 | ✓ Clean |
O=C(O)/C=C/CC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]12
|
| ZINC77273222 | 0.568 | 428.6 Da LogP 1.36 TPSA 119.6 | ✓ Ro5 | ✓ Clean |
O=C1N[C@@H]2[C@H](CCCC(CCC[C@@H]3SC[C@@H]4NC(=O…
|
| ZINC79671662 | 0.566 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…
|
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.