Protein target profile

KP13_31484

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

Genome: KpKP13 Gene: AHE45277.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GLG4
Length 413
Pocket druggability 0.967
Direct ligand evidence 0 78 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 (%)
44.928 Lower values reduce human off-target concern.
Human E-value
2.64e-118
Gut microbiome similarity
17.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
98.08 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 0.967
Structure A0A0H3GLG4
Pocket Pocket 2
P2Rank 0.871
Structure A0A0H3GLG4
Pocket Pocket 1
ColabFold model
FPocket 0.729 · Pocket 1
P2Rank 0.893 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 813 / 4744 genomes with a hit
Prevalence 17.1%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSKRRVVVTGLGMLSPVGNTVESTWKALLAGQSGISLIDHFDTSAYATKFAGLVKDFNCDDIISRKEQRKMDAFIQYGIVAGVQAMQDSGLEVTEENATRIGAAIGSGIGGLGLIEENHSSLVNGGPRKISPFFVPSTIVNMVAGHLTIMFGLRGPSISIATACTSGVHNIGQAARIIAYGDADAMVAGGAEKASTPLGVGGFGAARALSTRNDNPQAASRPWDKDRDGFVLGDGAGMVVLEEYEHAKKRGAKIYAEIVGFGMSSDAYHMTSPPEDGAGAALAMVNAIRDAGIEPGQIGYVNAHGTSTPAGDKAEAQAVKSVFGDAASRVLVSSTKSMTGHLLGAAGAVESIYSILALRDQAVPPTINLDNPDEGCDLDFVPHEARQVSGMEYTLCNSFGFGGTNGSLIFKKV

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.

30 records
Show feature table
Start End DB Term Name
4 411 NCBIfam TIGR03150 beta-ketoacyl-ACP synthase II
4 411 InterPro IPR017568 3-oxoacyl-[acyl-carrier-protein] synthase 2
4 410 CDD cd00834 KAS_I_II
4 410 InterPro IPR000794 Beta-ketoacyl synthase
1 413 PIRSF PIRSF000447 KAS_II
1 413 InterPro IPR017568 3-oxoacyl-[acyl-carrier-protein] synthase 2
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
1 5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
6 413 SMART SM00825 Beta-ketoacyl synthase
6 413 InterPro IPR020841 Polyketide synthase, beta-ketoacyl synthase domain
3 252 SUPERFAMILY SSF53901 Thiolase-like
3 252 InterPro IPR016039 Thiolase-like
3 412 PANTHER PTHR11712 POLYKETIDE SYNTHASE-RELATED
3 412 InterPro IPR000794 Beta-ketoacyl synthase
215 412 SUPERFAMILY SSF53901 Thiolase-like
215 412 InterPro IPR016039 Thiolase-like
3 412 ProSiteProfiles PS52004 Ketosynthase family 3 (KS3) domain profile.
3 412 InterPro IPR020841 Polyketide synthase, beta-ketoacyl synthase domain
255 369 Pfam PF02801 Beta-ketoacyl synthase, C-terminal domain
255 369 InterPro IPR014031 Beta-ketoacyl synthase, C-terminal
15 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 413 FunFam G3DSA:3.40.47.10:FF:000009 3-oxoacyl-[acyl-carrier-protein] synthase 2
4 247 Pfam PF00109 Beta-ketoacyl synthase, N-terminal domain
4 247 InterPro IPR014030 Beta-ketoacyl synthase, N-terminal
1 413 Gene3D G3DSA:3.40.47.10 -
1 413 InterPro IPR016039 Thiolase-like
155 171 ProSitePatterns PS00606 Ketosynthase family 3 (KS3) active site signature.
155 171 InterPro IPR018201 Beta-ketoacyl synthase, active site
6 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
21 413 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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 #2
0.967
Likely same site as P2Rank 2 4.2 Å 19 shared residues 95% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #3
0.472
Likely same site as P2Rank 1 0.8 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
0.871
Likely same site as FPocket 3 0.8 Å 22 shared residues 96% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.473
Likely same site as FPocket 2 4.2 Å 19 shared residues 95% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.375
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.205
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.012
Likely same site as FPocket 3 7.2 Å 8 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:152-152 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_A0A0H3GLG4
AlphaFold DB full sequence Viewing
ColabFold KP13_31484
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.

78 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 28 records from similar proteins
Structural ligands 13 0 loaded crystals
Measured bioactivity 15 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 P0AAI5 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.