Protein target profile

KP13_01032

3-oxoacyl-[acyl-carrier-protein] synthase 1

Genome: KpKP13 Gene: fabB AHE43440.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GR90
Length 406
Pocket druggability 0.588
Direct ligand evidence 0 67 total records
Functional annotation 1 EC 4 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 (%)
33.81 Lower values reduce human off-target concern.
Human E-value
4.69e-62
Gut microbiome similarity
4.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
97.27 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.66 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 0.588
Structure A0A0H3GR90
Pocket Pocket 11
P2Rank 0.742
Structure A0A0H3GR90
Pocket Pocket 1
ColabFold model
FPocket 0.777 · Pocket 1
P2Rank 0.832 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 199 / 4744 genomes with a hit
Prevalence 4.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKRAVITGLGIVSSIGNNQQEVLASLREGRSGITFSQELKDSGMRSHVWGNVKLDTTGLIDRKVVRFMSDASIYAYLSMEQAVADAGLAPEAYQNNPRVGLIAGSGGGSPKFQVFGADAMRSPRGLKAVGPYVVTKAMASGVSACLATPFKIHGVNYSISSACATSAHCIGNAVEQIQLGKQDIVFAGGGEELCWEMACEFDAMGALSTKYNDTPEKASRTYDANRDGFVIAGGGGMVVVEELEHALARGAHIYAEIVGYGATSDGADMVAPSGEGAVRCMQMAMHGVDTPIDYLNSHGTSTPVGDVKELGAIREVFGDNSPAISATKAMTGHSLGAAGVQEAIYSLLMLEHGFIAPSINVEELDEQAAGLNIVTKPTDAKLTTVMSNSFGFGGTNATLVMRKYNA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • 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: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.

29 records
Show feature table
Start End DB Term Name
254 361 Pfam PF02801 Beta-ketoacyl synthase, C-terminal domain
254 361 InterPro IPR014031 Beta-ketoacyl synthase, C-terminal
1 253 SUPERFAMILY SSF53901 Thiolase-like
1 253 InterPro IPR016039 Thiolase-like
6 259 Gene3D G3DSA:3.40.47.10 -
6 259 InterPro IPR016039 Thiolase-like
25 406 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 403 ProSiteProfiles PS52004 Ketosynthase family 3 (KS3) domain profile.
1 403 InterPro IPR020841 Polyketide synthase, beta-ketoacyl synthase domain
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
215 404 SUPERFAMILY SSF53901 Thiolase-like
215 404 InterPro IPR016039 Thiolase-like
154 170 ProSitePatterns PS00606 Ketosynthase family 3 (KS3) active site signature.
154 170 InterPro IPR018201 Beta-ketoacyl synthase, active site
16 24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
260 405 FunFam G3DSA:3.40.47.10:FF:000005 3-oxoacyl-[acyl-carrier-protein] synthase I
4 406 SMART SM00825 Beta-ketoacyl synthase
4 406 InterPro IPR020841 Polyketide synthase, beta-ketoacyl synthase domain
6 259 FunFam G3DSA:3.40.47.10:FF:000006 3-oxoacyl-[acyl-carrier-protein] synthase I
1 24 Phobius SIGNAL_PEPTIDE Signal peptide region
2 404 PANTHER PTHR11712 POLYKETIDE SYNTHASE-RELATED
2 404 InterPro IPR000794 Beta-ketoacyl synthase
3 246 Pfam PF00109 Beta-ketoacyl synthase, N-terminal domain
3 246 InterPro IPR014030 Beta-ketoacyl synthase, N-terminal
4 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
260 406 Gene3D G3DSA:3.40.47.10 -
260 406 InterPro IPR016039 Thiolase-like
2 401 CDD cd00834 KAS_I_II
2 401 InterPro IPR000794 Beta-ketoacyl synthase

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 #11
0.588
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Surrounding area
Site 2 FPocket #1
0.466
Likely same site as P2Rank 1 0.8 Å 17 shared residues 100% of smaller site
Unusual size
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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
0.742
Likely same site as FPocket 1 0.8 Å 17 shared residues 100% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.523
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Surrounding area
Site 3 P2Rank #3
0.031
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Surrounding area
Site 4 P2Rank #4
0.004
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.003
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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_A0A0H3GR90
AlphaFold DB full sequence Viewing
ColabFold KP13_01032
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.

67 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 17 records from similar proteins
Structural ligands 17 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
07K PDB via homolog 158.2 Da · LogP 2.13 · TPSA 38.9 Open detail RCSB PDB
07L PDB via homolog Detail RCSB PDB
1LR PDB via homolog Detail RCSB PDB
1X9 PDB via homolog Detail RCSB PDB
1XG 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
07K RCSB PDB Q2YQQ9 158.2 Da LogP 2.13 TPSA 38.9 ✓ Ro5 ✓ Clean Cc1cccc2c1nccc2N
07L RCSB PDB Q2YQQ9 162.1 Da LogP 1.50 TPSA 50.4 ✓ Ro5 ✓ Clean c1cc2c(cc1O)OC(=O)C=C2
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
3MQ RCSB PDB Q2YQQ9 181.2 Da LogP 1.90 TPSA 46.3 ✓ Ro5 ✓ Clean c1cc(sc1)c2cc(no2)CO
6W5 RCSB PDB P0A953 395.3 Da LogP -1.59 TPSA 174.3 1 viol. ✓ Clean CC(C)(COP(=O)(O)O)[C@@H](C(=O)NCCC(=O)NCCNC(=O)…
CER RCSB PDB P0A953 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 P0A953 200.3 Da LogP 3.99 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCC(=O)O
DKA RCSB PDB P0A953 172.3 Da LogP 3.21 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCC(=O)O
MRJ RCSB PDB P0A953 523.6 Da LogP 2.14 TPSA 174.3 2 viol. ✓ Clean CCCCCCCCCCCC(=O)NCCNC(=O)CCNC(=O)[C@@H](C(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…
NH4 RCSB PDB P0A953 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
OCA RCSB PDB P0A953 144.2 Da LogP 2.43 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCC(=O)O
TL5 RCSB PDB P0A953 224.3 Da LogP 3.37 TPSA 37.3 ✓ Ro5 ✓ Clean C\C=C\C(=C\[C@@]1(C(=C(C(=O)S1)C)O)C)\C
TL6 RCSB PDB P0A953 196.3 Da LogP 2.59 TPSA 37.3 ✓ Ro5 ✓ Clean CC1=C([C@@](SC1=O)(C)\C=C\C=C)O
TLM RCSB PDB P0A953 210.3 Da LogP 2.98 TPSA 37.3 ✓ Ro5 ✓ Clean CC1=C([C@@](SC1=O)(C)\C=C(/C)\C=C)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.