Protein target profile

KP13_00817

Holo-[acyl-carrier-protein] synthase

Genome: KpKP13 Gene: acpS AHE43181.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GW85
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Length 126
Pocket druggability 0.047
Direct ligand evidence 0 58 total records
Functional annotation 1 EC 4 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 4 structural and 4 bioactivity records.

Risks to review

Microbiome similarity 115 of 4744 screened genomes (2.4%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.05. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.14.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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
No hit
Gut microbiome similarity
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
87.302 Higher values support similarity to known essential genes.
DEG E-value
1.77e-79 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.69 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 0.047
Structure A0A0H3GW85
Pocket Pocket 2
P2Rank 0.139
Structure A0A0H3GW85
Pocket Pocket 1
ColabFold model
FPocket 0.49 · Pocket 1
P2Rank 0.135 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 115 / 4744 genomes with a hit
Prevalence 2.4%

Cross-references

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

Sequence

UniProt A0A0H3GW85

Chemistry

ChEMBL CHEMBL130657 ChEMBL CHEMBL335756 ChEMBL CHEMBL371442 ChEMBL CHEMBL130683

Sequence

Primary amino-acid sequence viewer.

MAILGLGTDIVEIARIEAVIARSGDRLARRVLSDHEWSIWEQHQQPVRFLAKRFAVKEAAAKALGTGIRNGLAFNQFEVYNDELGKPKLRLWGEANLLAERMGVSAIHVTLADERHYACATVIVES

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:0008897 Catalysis of the reaction: CoA + substrate-serine = adenosine 3',5'-bisphosphate + substrate-serine-4'-phosphopantetheine. The transfer of the 4'-phosphopantetheine (Ppant) co-factor from coenzyme A to the hydroxyl side chain of the serine residue of acyl- or peptidyl-carrier protein (ACP or PCP) to convert them from the apo to the holo form.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
4 126 Hamap MF_00101 Holo-[acyl-carrier-protein] synthase [acpS].
4 126 InterPro IPR002582 Holo-[acyl carrier protein] synthase
2 126 NCBIfam TIGR00516 holo-[acyl-carrier-protein] synthase
2 126 InterPro IPR002582 Holo-[acyl carrier protein] synthase
3 126 NCBIfam TIGR00556 phosphopantetheine--protein transferase domain
3 126 InterPro IPR004568 Phosphopantetheine-protein transferase domain
1 126 Gene3D G3DSA:3.90.470.20 -
1 126 InterPro IPR037143 4'-phosphopantetheinyl transferase domain superfamily
1 126 FunFam G3DSA:3.90.470.20:FF:000001 Holo-[acyl-carrier-protein] synthase
5 122 Pfam PF01648 4'-phosphopantetheinyl transferase superfamily
5 122 InterPro IPR008278 4'-phosphopantetheinyl transferase domain
3 125 SUPERFAMILY SSF56214 4'-phosphopantetheinyl transferase
3 125 InterPro IPR037143 4'-phosphopantetheinyl transferase domain superfamily

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

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

Site 1 P2Rank #1
0.139
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:58-58
UniProt: Binding site:9-9
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_A0A0H3GW85
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_00817
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.

58 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 4 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
A3P PDB via homolog 427.2 Da · LogP -1.75 · TPSA 232.6 Open detail RCSB PDB
DTT PDB via homolog Detail RCSB PDB
MLI PDB via homolog Detail RCSB PDB
PNS PDB via homolog Detail RCSB PDB
CHEMBL130657 ChEMBL via homolog · pchembl 6.89 (~128.8 nM) Detail ChEMBL

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
A3P RCSB PDB
3HYK
Q81JG3 427.2 Da LogP -1.75 TPSA 232.6 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DTT RCSB PDB
1F7T
P96618 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
MLI RCSB PDB
4DXE
Q5HED0 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PNS RCSB PDB
5VCB
P24224 358.4 Da LogP -0.96 TPSA 145.2 1 viol. ✓ Clean CC(C)(COP(=O)(O)O)[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.