Genome KpKP13

Protein target profile

Medium-chain-fatty-acid--CoA ligase

Accession: KP13_04878

Gene: alkK AHE45238.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A485XZH5
Length 538
Pocket druggability (P2Rank · AlphaFold DB model) 0.975
Direct ligand evidence 0 59 total records
Functional annotation 1 EC 2 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.

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 (%)
28.571 Lower values reduce human off-target concern.
Human E-value
1.05e-14
Gut microbiome similarity
0.2% 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.

Structure confidence

ColabFold pLDDT
92.78 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.975
Structure A0A485XZH5
Pocket Pocket 1
Druggability (FPocket) 0.396
Structure A0A485XZH5
Pocket Pocket 32
ColabFold model
P2Rank 0.975 · Pocket 1
FPocket 0.968 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 11 / 4744 genomes with a hit
Prevalence 0.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MIYQDLTTAALLGHAAQYHSETEIVSVSTGGEKERSCWGEVASRAQRLASALASLGLPPGARCATLAWNNRRHLEIYFAVASGGWVTHTVNPRLSVDHLRYILNDAADEVLFFDQTFLPLVAQLLPQLPTVKHVVLMESRSEAALSQLPSLLFYDDLLQQGMADYRWPQLNELTPASLCYTSGTTGRPKGVLNTHRSLVLHALSGNQPDAAGISAKDSLLPVVPMFHVNAWGTPFIAAMVGARLVLPGPHLDGDSLLQLLAAEKVTVGFGVPVIWAGLLAAMRRTEVRLPEFKRALVGGSALPPSMAEAFQRDYGIALTHAWGMTETSPIGTINTPLSKHDALPAQEQQKQCAGQGRPIFGIELQVVDVDGEPLPRDGQSQGYLQVRGHWVVEQYYGQDASALTAAGWFDTGDIGTLDANGYLVISDRAKDIIKSGGEWISTVELENIAIAHPGVRSAAAIAARHPRWDERPVLLCVRAEGGEVEETDLLSWFEKRVPKWQIPDRVIFVDALPVSATGKVLKNQLRQAYGEILMSEGK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

2
  • GO:0018858 Catalysis of the reaction: ATP + benzoate + CoA = AMP + benzoyl-CoA + diphosphate.
  • GO:0006631 The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
11 527 CDD cd12119 ttLC_FACS_AlkK_like
444 519 Pfam PF13193 AMP-binding enzyme C-terminal domain
444 519 InterPro IPR025110 AMP-binding enzyme, C-terminal domain
3 531 SUPERFAMILY SSF56801 Acetyl-CoA synthetase-like
430 533 Gene3D G3DSA:3.30.300.30 -
430 533 InterPro IPR045851 AMP-binding enzyme, C-terminal domain superfamily
178 189 ProSitePatterns PS00455 Putative AMP-binding domain signature.
178 189 InterPro IPR020845 AMP-binding, conserved site
1 429 Gene3D G3DSA:3.40.50.12780 -
1 429 InterPro IPR042099 ANL, N-terminal domain
5 529 PANTHER PTHR43859 ACYL-ACTIVATING ENZYME
15 435 Pfam PF00501 AMP-binding enzyme
15 435 InterPro IPR000873 AMP-dependent synthetase/ligase domain

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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Drag to rotate — click the view, then scroll to zoom.

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

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.975
Likely same site as FPocket 35 2.8 Å 45 shared residues 83% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.164
Likely same site as FPocket 32 3.1 Å 10 shared residues 83% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.081
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.068
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Surrounding area
Pocket 5 P2Rank #5
0.044
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #32
0.396
Likely same site as P2Rank 2 3.1 Å 10 shared residues 83% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #35
0.304 Unusual size
Likely same site as P2Rank 1 2.8 Å 45 shared residues 83% of smaller site
Show in viewer
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_A0A485XZH5
AlphaFold DB full sequence Viewing
ColabFold KP13_04878
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.

59 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 9 records from similar proteins
Structural ligands 9 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3UK PDB via homolog 466.3 Da · LogP -0.42 · TPSA 218.2 Open detail RCSB PDB
4UU PDB via homolog Detail RCSB PDB
4UV PDB via homolog Detail RCSB PDB
4UW PDB via homolog Detail RCSB PDB
ANP 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
3UK RCSB PDB F3Y661 466.3 Da LogP -0.42 TPSA 218.2 1 viol. ✓ Clean c1ccc(c(c1)C(=O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([…
4UU RCSB PDB O24146 493.4 Da LogP -0.30 TPSA 209.2 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
4UV RCSB PDB O24146 507.4 Da LogP -1.12 TPSA 226.3 2 viol. Alert c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
4UW RCSB PDB O24146 523.4 Da LogP -0.33 TPSA 218.4 2 viol. ✓ Clean COC1=CC(=CCC1=O)/C=C/C(=O)OP(=O)(O)OC[C@@H]2[C@…
ANP RCSB PDB Q5SKN9 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
JSA RCSB PDB P9WQ37 530.6 Da LogP 1.12 TPSA 194.9 2 viol. ✓ Clean CCCCCCCCCCC[C@H](NS(=O)(=O)OC[C@@H]1[C@H]([C@H]…
MLI RCSB PDB P9WQ37 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
OSB RCSB PDB P23971 222.2 Da LogP 1.43 TPSA 91.7 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)CCC(=O)O)C(=O)O
S0N RCSB PDB P23971 954.7 Da LogP -1.12 TPSA 430.0 3 viol. ✓ Clean CC(C)(CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H](…

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.