Protein target profile

KP13_01043

3-ketoacyl-CoA thiolase

Genome: KpKP13 Gene: fadI AHE43429.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWF1
Length 436
Pocket druggability 0.76
Direct ligand evidence 0 60 total records
Functional annotation 1 EC 8 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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 (%)
47.761 Lower values reduce human off-target concern.
Human E-value
7.17e-59
Gut microbiome similarity
2.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.72 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 0.76
Structure A0A0H3GWF1
Pocket Pocket 28
P2Rank 0.853
Structure A0A0H3GWF1
Pocket Pocket 1
ColabFold model
FPocket 0.792 · Pocket 26
P2Rank 0.85 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 123 / 4744 genomes with a hit
Prevalence 2.6%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSQALPLITRQGDRIAIVTGLRTPFARQATAFHGVPAIDLGKMVVGEMLARSDIPAEVIEQLVFGQVVQMPEAPNIAREIVLGTGMSVHTDAYSVSRACATSFQAVANVAESLMAGTIRAGIAGGADSSSVLPIGVSKTLARTLVDANKARTLSQKLKLFSRLRPRDLLPVPPAVAEYSTGLRMGDTAEQMAKSWGISREQQDALAHRSHQLAAKAWEEGKLSAEVMTAYAPPFREPLEQDNNIRKNSTLADYQKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLRPLGYLRSYAFTAIDVWQDMLLGPAWSTPLALERAGLTLADLTLIDMHEAFAAQTLANLQCLASDRFAREVLGRSQATGEVDESKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVTACAAGGLGAAMIVEAE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
  • GO:0016042 The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0006631 The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
  • GO:0016747 Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
  • GO:0003988 Catalysis of the reaction: acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-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:0006635 A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
15 295 SUPERFAMILY SSF53901 Thiolase-like
15 295 InterPro IPR016039 Thiolase-like
297 434 SUPERFAMILY SSF53901 Thiolase-like
297 434 InterPro IPR016039 Thiolase-like
8 435 Gene3D G3DSA:3.40.47.10 -
8 435 InterPro IPR016039 Thiolase-like
9 436 PIRSF PIRSF000429 Ac-CoA_Ac_transf
9 436 InterPro IPR002155 Thiolase
296 434 Pfam PF02803 Thiolase, C-terminal domain
296 434 InterPro IPR020617 Thiolase, C-terminal
417 430 ProSitePatterns PS00099 Thiolases active site.
417 430 InterPro IPR020610 Thiolase, active site
15 288 Pfam PF00108 Thiolase, N-terminal domain
15 288 InterPro IPR020616 Thiolase, N-terminal
17 434 NCBIfam TIGR01930 acetyl-CoA C-acyltransferase
17 434 InterPro IPR002155 Thiolase
382 398 ProSitePatterns PS00737 Thiolases signature 2.
382 398 InterPro IPR020613 Thiolase, conserved site
16 420 CDD cd00751 thiolase
16 420 InterPro IPR002155 Thiolase
7 435 FunFam G3DSA:3.40.47.10:FF:000011 3-ketoacyl-CoA thiolase
8 436 NCBIfam TIGR02446 acetyl-CoA C-acyltransferase FadI
8 436 InterPro IPR012806 Acetyl-CoA C-acyltransferase FadI
95 113 ProSitePatterns PS00098 Thiolases acyl-enzyme intermediate signature.
95 113 InterPro IPR020615 Thiolase, acyl-enzyme intermediate active site
12 435 PANTHER PTHR42689 ACETYL-COA ACYLTRANSFERASE FADA2 (3-KETOACYL-COA THIOLASE) (BETA-KETOTHIOLASE)-RELATED
2 436 Hamap MF_01618 3-ketoacyl-CoA thiolase [fadI].
2 436 InterPro IPR012806 Acetyl-CoA C-acyltransferase FadI

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 #28
0.76
Likely same site as P2Rank 1 0.9 Å 22 shared residues 96% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.853
Likely same site as FPocket 28 0.9 Å 22 shared residues 96% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.038
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.03
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.011
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Surrounding area
Site 5 P2Rank #5
0.01
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Surrounding area
Residue sets
UniProt: Active site:392-392 Proton acceptor
UniProt: Active site:422-422 Proton acceptor
UniProt: Active site:99-99 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_A0A0H3GWF1
AlphaFold DB full sequence Viewing
ColabFold KP13_01043
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.

60 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 10 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
1VU PDB via homolog Detail RCSB PDB
5UG PDB via homolog Detail RCSB PDB
CAA PDB via homolog Detail RCSB PDB
COZ 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…
1VU RCSB PDB F1KYX0 823.6 Da LogP -0.93 TPSA 363.6 3 viol. ✓ Clean CCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O…
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+]
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
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.