Protein target profile

KP13_02900

Dihydrolipoamide acetyltransferase

Genome: KpKP13 Gene: AHE46176.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSC6
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Length 511
Pocket druggability 0.894
Direct ligand evidence 0 47 total records
Functional annotation 1 EC 3 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Strong predicted binding pocket FPocket selected-pocket score 0.89. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 5 structural and 0 bioactivity records.

Risks to review

Human similarity Top human hit identity: 43.478%. This target also has a predicted binding pocket (FPocket 0.89) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 10 of 4744 screened genomes (0.2%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.89) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.37.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
43.478 Lower values reduce human off-target concern.
Human E-value
9.17e-74
Gut microbiome similarity
0.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
44.737 Higher values support similarity to known essential genes.
DEG E-value
4.72e-77 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
83.38 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.894
Structure A0A0H3GSC6
Pocket Pocket 22
P2Rank 0.37
Structure A0A0H3GSC6
Pocket Pocket 1
ColabFold model
FPocket 0.773 · Pocket 26
P2Rank 0.232 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 10 / 4744 genomes with a hit
Prevalence 0.2%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GSC6

Sequence

Primary amino-acid sequence viewer.

MSEIKTLEMPKWGLSMEEGLLARWAIQEGDDFTRGQEICEIETSKIVNVLEAPFAGTLRRILAREGETLQVGAVLALAADASVSDAELDEFVARLATAKPAAPGPEAAAPDVAAQAGAKPASVVSPPSNSPEPPVGQTVIPVSLQGVTDVTQVNATPHALRLSARWGVDLKKVRGSGRGDRISVSDLESAIVAAGGRLASPTPPVRRSKAPRSHADDSQVSATPLARRLAGKLGINLHDCRSSGSRGRVSRDDVLAAALLLDEHPQTSPVQESAPAPFESIPMSGMRRAIASRLQTSKQQSPHFRLSVDLDLERLLALRQDINREVPGVKISVNDLLVKACALALVAVPDVNIQFDEAAQSIRRFTDADISVAVALPAGLITPIVRSANRKSISDISNEIHSLVTRAKAGTLKPEEFQGGTFSLSNLGMLGVRQFDAIINPPQSAILAIGAGEVRAVVRDGQIVARQQMTVSLSCDHRVIDGAAGAAFLRELKRLIETPTLMFIQETSYAR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • 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:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

36 records
Show feature table
Start End DB Term Name
151 191 Gene3D G3DSA:4.10.320.10 -
151 191 InterPro IPR036625 E3-binding domain superfamily
218 258 Gene3D G3DSA:4.10.320.10 -
218 258 InterPro IPR036625 E3-binding domain superfamily
221 258 ProSiteProfiles PS51826 Peripheral subunit-binding (PSBD) domain profile.
221 258 InterPro IPR004167 Peripheral subunit-binding domain
214 257 SUPERFAMILY SSF47005 Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
214 257 InterPro IPR036625 E3-binding domain superfamily
5 77 CDD cd06849 lipoyl_domain
267 503 SUPERFAMILY SSF52777 CoA-dependent acyltransferases
198 220 MobiDBLite mobidb-lite consensus disorder prediction
152 190 SUPERFAMILY SSF47005 Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
152 190 InterPro IPR036625 E3-binding domain superfamily
29 58 ProSitePatterns PS00189 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.
29 58 InterPro IPR003016 2-oxo acid dehydrogenase, lipoyl-binding site
104 136 MobiDBLite mobidb-lite consensus disorder prediction
154 188 Pfam PF02817 e3 binding domain
154 188 InterPro IPR004167 Peripheral subunit-binding domain
221 255 Pfam PF02817 e3 binding domain
221 255 InterPro IPR004167 Peripheral subunit-binding domain
4 79 ProSiteProfiles PS50968 Biotinyl/lipoyl domain profile.
4 79 InterPro IPR000089 Biotin/lipoyl attachment
4 92 SUPERFAMILY SSF51230 Single hybrid motif
4 92 InterPro IPR011053 Single hybrid motif
266 504 FunFam G3DSA:3.30.559.10:FF:000007 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex
3 213 PANTHER PTHR23151 DIHYDROLIPOAMIDE ACETYL/SUCCINYL-TRANSFERASE-RELATED
3 213 InterPro IPR045257 Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component
278 503 Pfam PF00198 2-oxoacid dehydrogenases acyltransferase (catalytic domain)
278 503 InterPro IPR001078 2-oxoacid dehydrogenase acyltransferase, catalytic domain
6 76 Pfam PF00364 Biotin-requiring enzyme
6 76 InterPro IPR000089 Biotin/lipoyl attachment
261 507 Gene3D G3DSA:3.30.559.10 -
261 507 InterPro IPR023213 Chloramphenicol acetyltransferase-like domain superfamily
1 101 Gene3D G3DSA:2.40.50.100 -
154 191 ProSiteProfiles PS51826 Peripheral subunit-binding (PSBD) domain profile.
154 191 InterPro IPR004167 Peripheral subunit-binding domain

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #22
0.894
Likely same site as P2Rank 1 2.3 Å 13 shared residues 81% of smaller site
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Surrounding area
Site 2 FPocket #31
0.356
Likely same site as P2Rank 5 3.8 Å 9 shared residues 100% of smaller site
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Surrounding area
Site 3 FPocket #12
0.348
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.37
Likely same site as FPocket 22 2.3 Å 13 shared residues 81% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.134
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Surrounding area
Site 3 P2Rank #3
0.019
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Surrounding area
Site 4 P2Rank #4
0.018
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Surrounding area
Site 5 P2Rank #5
0.016
Likely same site as FPocket 31 3.8 Å 9 shared residues 100% of smaller site
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Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GSC6
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_02900
ColabFold — — full sequence — Loaded

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
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 42 similarity-based ZINC candidates
Best available ligand signal
CAO PDB via homolog 783.5 Da · LogP -1.39 · TPSA 366.8 Open detail RCSB PDB
DTT PDB via homolog Detail RCSB PDB
LPM PDB via homolog Detail RCSB PDB
RDC PDB via homolog Detail RCSB PDB
RED PDB via homolog Detail RCSB PDB

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 RCSB PDB
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 RCSB PDB
1EAC
P10802 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
LPM RCSB PDB
1EAB
P10802 207.4 Da LogP 1.65 TPSA 43.1 ✓ Ro5 ✓ Clean C(CCC(=O)N)C[C@H](CCS)S
RDC RCSB PDB
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 RCSB PDB
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.