KpATCC43816 Protein target profile

3-oxoadipyl-CoA thiolase

Accession: VK055_0963

Gene: pcaF AIK79586.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GSY7
Length 400
Pocket druggability (P2Rank · AlphaFold DB model) 0.793
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 61 total records
Functional annotation 1 EC 4 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing 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 (%)
46.444 Lower values reduce human off-target concern.
Human E-value
8.63e-53
Gut microbiome similarity
2.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
60.0 Higher values support similarity to known essential genes.
DEG E-value
2.86e-21 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.99 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.793
Structure A0A0H3GSY7
Pocket Pocket 1
Druggability (FPocket) 0.704
Structure A0A0H3GSY7
Pocket Pocket 1
ColabFold model
P2Rank 0.847 · Pocket 1
FPocket 0.781 · Pocket 9
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 117 / 4744 genomes with a hit
Prevalence 2.5%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: more central than 96.3% of genes in this genome.

Relative network centrality 96.3% more central than 96.3% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reactions

2 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MNQAFICDAVRTPFGRFGGALATMRADDLAALPLKALLARNPGLDPSRIDDVIFGCANQAGEDNRNVARMALLLAGLPESVPGSTINRLCGSSLDAIGVAARAIKSGETQLMIAGGVESMSRAPFVMGKAESAFSRSMQMEDTTIGWRFINPQMKALYGVHSMPETAENVADEFAISRADQDAFALRSQLRTAAAQEAGRFADELIAVQVPQRKGEPLLFSRDEHPRSTSLEALAKLRGVVRADGSVTAGNASGVNDGACALLLASETALSANDLQPLARVVGVATAGVAPRIMGFGPAPAVRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDDAAHVNPNGGAIALGHPLGASGGRLAMTAAYQLKRTGGRYALCTMCIGVGQGIALIIERV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0016747 Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
  • GO:0019619 The chemical reactions and pathways resulting in the breakdown of 3,4-dihydroxybenzoate.
  • GO:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
  • GO:0033812 Catalysis of the reaction: succinyl-CoA + acetyl-CoA = CoA + 3-oxoadipyl-CoA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
5 399 CDD cd00751 thiolase
5 399 InterPro IPR002155 Thiolase
1 400 PIRSF PIRSF000429 Ac-CoA_Ac_transf
1 400 InterPro IPR002155 Thiolase
5 267 Pfam PF00108 Thiolase, N-terminal domain
5 267 InterPro IPR020616 Thiolase, N-terminal
4 272 SUPERFAMILY SSF53901 Thiolase-like
4 272 InterPro IPR016039 Thiolase-like
3 400 NCBIfam TIGR02430 3-oxoadipyl-CoA thiolase
3 400 InterPro IPR012793 Beta-ketoadipyl CoA thiolase
86 104 ProSitePatterns PS00098 Thiolases acyl-enzyme intermediate signature.
86 104 InterPro IPR020615 Thiolase, acyl-enzyme intermediate active site
2 400 PANTHER PTHR18919 ACETYL-COA C-ACYLTRANSFERASE
1 400 Gene3D G3DSA:3.40.47.10 -
1 400 InterPro IPR016039 Thiolase-like
6 398 NCBIfam TIGR01930 acetyl-CoA C-acyltransferase
6 398 InterPro IPR002155 Thiolase
346 362 ProSitePatterns PS00737 Thiolases signature 2.
346 362 InterPro IPR020613 Thiolase, conserved site
1 399 FunFam G3DSA:3.40.47.10:FF:000010 Acetyl-CoA acetyltransferase (Thiolase)
276 399 SUPERFAMILY SSF53901 Thiolase-like
276 399 InterPro IPR016039 Thiolase-like
381 394 ProSitePatterns PS00099 Thiolases active site.
381 394 InterPro IPR020610 Thiolase, active site
276 399 Pfam PF02803 Thiolase, C-terminal domain
276 399 InterPro IPR020617 Thiolase, C-terminal

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.793
Likely same site as FPocket 1 3.6 Å 12 shared residues 80% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.704
Likely same site as P2Rank 1 3.6 Å 12 shared residues 80% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #12
0.488
Likely same site as P2Rank 1 4.6 Å 14 shared residues 78% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:356-356 Proton acceptor
UniProt: Active site:386-386 Proton acceptor
UniProt: Active site:90-90 Acyl-thioester intermediate
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_A0A0H3GSY7
AlphaFold DB full sequence Viewing
ColabFold VK055_0963
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.

61 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 11 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
168 PDB via homolog 388.5 Da · LogP 0.15 · TPSA 131.0 Open detail RCSB PDB
5UG PDB via homolog Detail RCSB PDB
CAA PDB via homolog Detail RCSB PDB
COZ PDB via homolog Detail RCSB PDB
DNO 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
168 RCSB PDB P07097 388.5 Da LogP 0.15 TPSA 131.0 ✓ Ro5 ✓ Clean CC(=O)OCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COC(=O)C(C…
5UG RCSB PDB P76461 438.3 Da LogP -0.85 TPSA 191.7 1 viol. ✓ Clean CC(C)(COP(=O)(O)OP(=O)(O)O)[C@@H](C(=O)NCCC(=O)…
CAA RCSB PDB P07097 851.6 Da LogP -1.36 TPSA 380.7 3 viol. ✓ Clean CC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P…
COZ RCSB PDB P76461 767.5 Da LogP -1.67 TPSA 346.6 3 viol. ✓ Clean CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([…
DNO RCSB PDB P07097 180.2 Da LogP -3.38 TPSA 118.2 ✓ Ro5 ✓ Clean C([C@H]([C@H]([C@@H]([C@@H](C=O)O)O)O)O)O
DTT RCSB PDB P42765 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
NH4 RCSB PDB Q4WCL5 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
O8Y RCSB PDB Q88N39 100.2 Da LogP 1.77 TPSA 17.1 ✓ Ro5 ✓ Clean CCCCCC=O
OPI RCSB PDB P07097 346.4 Da LogP -0.42 TPSA 125.0 ✓ Ro5 ✓ Clean CC(C)(C)C(=O)OCC(C)(C)[C@H](C(=O)NCCC(=O)NCCO)O
OYA RCSB PDB Q88N39 128.2 Da LogP 2.55 TPSA 17.1 ✓ Ro5 ✓ Clean CCCCCCCC=O
PN5 RCSB PDB P07097 362.5 Da LogP 0.52 TPSA 104.7 ✓ Ro5 ✓ Clean CC(C)(C)C(=O)OCC(C)(C)[C@H](C(=O)NCCC(=O)NCCS)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.

Cross-references

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