Protein target profile

KP13_05499

3-oxoacyl-[acyl-carrier-protein] synthase 2

Genome: KpKP13 Gene: AHE44505.1 fabF 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GTQ4
Length 424
Pocket druggability 0.799
Direct ligand evidence 0 63 total records
Functional annotation 1 EC 5 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 (%)
48.077 Lower values reduce human off-target concern.
Human E-value
1.78e-10
Gut microbiome similarity
1.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
50.939 Higher values support similarity to known essential genes.
DEG E-value
4.19e-148 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.96 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 0.799
Structure A0A0H3GTQ4
Pocket Pocket 1
P2Rank 0.854
Structure A0A0H3GTQ4
Pocket Pocket 1
ColabFold model
FPocket 0.794 · Pocket 1
P2Rank 0.876 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 64 / 4744 genomes with a hit
Prevalence 1.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MGVSVKRIVVTGMGIVSPLGCGVQHVWQSLLAGKSGITRLSEQLVADIPCKVAGQVPSIESDPLHGFDPLATIPAKERKKMDRFIEFALVAAREALTQAGWSPASAAEQERTATVIATGIGGFSEIANAVHTTDERGPRRLSPFTIPSFLANLAAGHVSIAHGFRGPIGAPVTACAAGAQAIGDAARMIRSGEADIALCGGAEAAIHRVSLAGFAAARALSSASNDQPEAASRPFDRDRDGFVMGEGAGLIVIESLEHALARGATPLAELVGYGTSADAYHLTAGPEDGNGARRAMETAIRQAGVTVDEIDHINAHATSTQVGDKGELAAIKTLFGAHPVAITSTKSATGHLLGAAGGIEAIFTIQALRDQVVPPTLNLHHPDEEAAGLNLVALQARPQKMRYALSNGFGFGGVNASLLLKRWE

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:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
  • GO:0004315 Catalysis of the reaction: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein].
  • GO:0006633 The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
  • GO:0016747 Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
3 424 PIRSF PIRSF000447 KAS_II
3 424 InterPro IPR017568 3-oxoacyl-[acyl-carrier-protein] synthase 2
6 421 PANTHER PTHR11712 POLYKETIDE SYNTHASE-RELATED
6 421 InterPro IPR000794 Beta-ketoacyl synthase
166 182 ProSitePatterns PS00606 Ketosynthase family 3 (KS3) active site signature.
166 182 InterPro IPR018201 Beta-ketoacyl synthase, active site
6 264 SUPERFAMILY SSF53901 Thiolase-like
6 264 InterPro IPR016039 Thiolase-like
3 423 FunFam G3DSA:3.40.47.10:FF:000009 3-oxoacyl-[acyl-carrier-protein] synthase 2
2 424 Gene3D G3DSA:3.40.47.10 -
2 424 InterPro IPR016039 Thiolase-like
8 423 SMART SM00825 Beta-ketoacyl synthase
8 423 InterPro IPR020841 Polyketide synthase, beta-ketoacyl synthase domain
6 259 Pfam PF00109 Beta-ketoacyl synthase, N-terminal domain
6 259 InterPro IPR014030 Beta-ketoacyl synthase, N-terminal
5 422 ProSiteProfiles PS52004 Ketosynthase family 3 (KS3) domain profile.
5 422 InterPro IPR020841 Polyketide synthase, beta-ketoacyl synthase domain
6 420 CDD cd00834 KAS_I_II
6 420 InterPro IPR000794 Beta-ketoacyl synthase
267 379 Pfam PF02801 Beta-ketoacyl synthase, C-terminal domain
267 379 InterPro IPR014031 Beta-ketoacyl synthase, C-terminal
227 423 SUPERFAMILY SSF53901 Thiolase-like
227 423 InterPro IPR016039 Thiolase-like
6 421 NCBIfam TIGR03150 beta-ketoacyl-ACP synthase II
6 421 InterPro IPR017568 3-oxoacyl-[acyl-carrier-protein] synthase 2

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 #1
0.799
Likely same site as P2Rank 1 1.8 Å 25 shared residues 96% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #13
0.252
Likely same site as P2Rank 3 7.5 Å 3 shared residues 43% of smaller site
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.854
Likely same site as FPocket 1 1.8 Å 25 shared residues 96% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.09
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.076
Likely same site as FPocket 13 7.5 Å 3 shared residues 43% of smaller site
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.02
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.009
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:175-175 For beta-ketoacyl synthase activity
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_A0A0H3GTQ4
AlphaFold DB full sequence Viewing
ColabFold KP13_05499
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.

63 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 13 records from similar proteins
Structural ligands 13 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1LR PDB via homolog 257.2 Da · LogP 2.34 · TPSA 86.6 Open detail RCSB PDB
1X9 PDB via homolog Detail RCSB PDB
1XG PDB via homolog Detail RCSB PDB
840 PDB via homolog Detail RCSB PDB
CER 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
1LR RCSB PDB G3XDA2 257.2 Da LogP 2.34 TPSA 86.6 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)Nc2cccc(c2O)C(=O)O
1X9 RCSB PDB O34340 223.3 Da LogP 1.11 TPSA 72.7 ✓ Ro5 ✓ Clean C/C=C/C/C=C/CCC(=O)[C@@H]1[C@@H](O1)C(=O)N
1XG RCSB PDB O34340 225.3 Da LogP 1.09 TPSA 80.4 ✓ Ro5 ✓ Clean C/C=C/C/C=C/CCC(=O)[C@@H](CC(=O)N)O
840 RCSB PDB P0AAI5 455.5 Da LogP 1.96 TPSA 153.4 ✓ Ro5 ✓ Clean C[C@@]1([C@H]2[C@@]34C[C@]35CC2(C=CC1=O)[C@H]([…
CER RCSB PDB P0AAI5 225.3 Da LogP 1.09 TPSA 80.4 ✓ Ro5 ✓ Clean C\C=C\C\C=C\CCC(=O)[C@H](CC(=O)N)O
DAO RCSB PDB P0AAI5 200.3 Da LogP 3.99 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCC(=O)O
MRJ RCSB PDB P0AAI5 523.6 Da LogP 2.14 TPSA 174.3 2 viol. ✓ Clean CCCCCCCCCCCC(=O)NCCNC(=O)CCNC(=O)[C@@H](C(C)(C)…
MU4 RCSB PDB P0AAI5 579.7 Da LogP 3.70 TPSA 174.3 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)NCCNC(=O)CCNC(=O)[C@@H](C(C…
N32 RCSB PDB A4JL30 425.5 Da LogP 4.02 TPSA 123.9 ✓ Ro5 ✓ Clean C[C@@]1([C@@H]2C[C@@H]3CC[C@]2(CC3=C)C=CC1=O)CC…
N3A RCSB PDB P0AAI5 441.5 Da LogP 2.99 TPSA 144.2 ✓ Ro5 ✓ Clean C[C@@]1([C@@H]2C[C@@H]3C[C@H]([C@]2(CC3=C)C=CC1…
P9A RCSB PDB P0AAI5 443.5 Da LogP 3.46 TPSA 133.2 ✓ Ro5 ✓ Clean C[C@@]12C[C@@]34CCC(=O)[C@@]([C@@H]3[C@@H](O1)C…
P9C RCSB PDB P0AAI5 519.6 Da LogP 4.85 TPSA 133.2 1 viol. ✓ Clean C[C@]12C[C@]34C[C@H]1C[C@@H]([C@H]3[C@](C(=O)C[…
PMN RCSB PDB P0AAI5 441.5 Da LogP 3.23 TPSA 133.2 ✓ Ro5 ✓ Clean C[C@]12C[C@]34C[C@H]1C[C@@H]([C@H]3[C@](C(=O)C=…

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.