KpKP13 Protein target profile

S-ribosylhomocysteine lyase

Accession: KP13_16560

Gene: luxS ANJ86588.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A6A8ECI3
Length 171
Pocket druggability (P2Rank · AlphaFold DB model) 0.166
Direct ligand evidence 0 57 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
No hit
Gut microbiome similarity
4.3% 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
96.44 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) 0.166
Structure A0A6A8ECI3
Pocket Pocket 1
Druggability (FPocket) 0.563
Structure A0A6A8ECI3
Pocket Pocket 1
ColabFold model
P2Rank 0.35 · Pocket 1
FPocket 0.359 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 205 / 4744 genomes with a hit
Prevalence 4.3%

Sequence

Primary amino-acid sequence viewer.

MPLLDSFTVDHTRMEAPAVRVAKKMNTPHGDEITVFDLRFCVPNQEVMPERGIHTLEHLFAGFMRDHLNGNGVEIIDISPMGCRTGFYMSLIGTPDEQRVADAWKAAMSDVLKVKDQNQIPELNVYQCGTYTMHSLEEAQDIARHIIERDVRINSNDELALPKEKLQELHI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0043768 Catalysis of the reaction: S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine.
  • GO:0005506 Binding to an iron (Fe) ion.
  • GO:0046872 Binding to a metal ion.
  • GO:0009372 The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
1 159 PANTHER PTHR35799 S-RIBOSYLHOMOCYSTEINE LYASE
1 159 InterPro IPR003815 S-ribosylhomocysteinase (LuxS)
49 67 PRINTS PR01487 Bacterial autoinducer-2 (AI-2) production protein LuxS signature
49 67 InterPro IPR003815 S-ribosylhomocysteinase (LuxS)
28 46 PRINTS PR01487 Bacterial autoinducer-2 (AI-2) production protein LuxS signature
28 46 InterPro IPR003815 S-ribosylhomocysteinase (LuxS)
121 140 PRINTS PR01487 Bacterial autoinducer-2 (AI-2) production protein LuxS signature
121 140 InterPro IPR003815 S-ribosylhomocysteinase (LuxS)
5 23 PRINTS PR01487 Bacterial autoinducer-2 (AI-2) production protein LuxS signature
5 23 InterPro IPR003815 S-ribosylhomocysteinase (LuxS)
77 95 PRINTS PR01487 Bacterial autoinducer-2 (AI-2) production protein LuxS signature
77 95 InterPro IPR003815 S-ribosylhomocysteinase (LuxS)
1 171 Gene3D G3DSA:3.30.1360.80 -
1 171 InterPro IPR037005 S-ribosylhomocysteinase (LuxS) superfamily
1 162 PIRSF PIRSF006160 AI2
1 162 InterPro IPR003815 S-ribosylhomocysteinase (LuxS)
4 152 Pfam PF02664 S-Ribosylhomocysteinase (LuxS)
4 152 InterPro IPR003815 S-ribosylhomocysteinase (LuxS)
1 159 Hamap MF_00091 S-ribosylhomocysteine lyase [luxS].
1 171 FunFam G3DSA:3.30.1360.80:FF:000001 S-ribosylhomocysteine lyase
4 162 SUPERFAMILY SSF63411 LuxS/MPP-like metallohydrolase
4 162 InterPro IPR011249 Metalloenzyme, LuxS/M16 peptidase-like

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.

Download VMD script Full viewer

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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

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

Pocket 1 P2Rank #1
0.166
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.069
Likely same site as FPocket 1 1.3 Å 9 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.065
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.563
Likely same site as P2Rank 2 1.3 Å 9 shared residues 100% 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_A0A6A8ECI3
AlphaFold DB full sequence Viewing
ColabFold KP13_16560
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.

57 records
Chemistry signal

Bioactivity evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 0 0 loaded crystals
Measured bioactivity 7 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CHEMBL208091 ChEMBL via homolog pchembl 6.43 (~371.5 nM) 268.3 Da · LogP -2.25 · TPSA 153.1 Open detail ChEMBL
CHEMBL593446 ChEMBL via homolog · pchembl 6.37 (~426.6 nM) Detail ChEMBL
CHEMBL595659 ChEMBL via homolog · pchembl 6.16 (~691.8 nM) Detail ChEMBL
CHEMBL207406 ChEMBL via homolog · pchembl 6.14 (~724.4 nM) Detail ChEMBL
CHEMBL1078480 ChEMBL via homolog Detail ChEMBL

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

Show only:
Ligand UniProt (homolog) pchembl MW · LogP · TPSA Lipinski PAINS SMILES
CHEMBL208091 ChEMBL O34667 6.43 ~371.5 nM 268.3 Da LogP -2.25 TPSA 153.1 1 viol. ✓ Clean N[C@@H](CCSC[C@H](O)[C@@H](O)C(=O)NO)C(=O)O
CHEMBL593446 ChEMBL O34667 6.37 ~426.6 nM 267.3 Da LogP -2.04 TPSA 133.2 ✓ Ro5 ✓ Clean N[C@@H](CCSC[C@H]1OC(O)[C@H](O)[C@@H]1O)C(=O)O
CHEMBL595659 ChEMBL O34667 6.16 ~691.8 nM 269.3 Da LogP -1.06 TPSA 113.0 ✓ Ro5 ✓ Clean N[C@@H](CCSC[C@H]1OC(O)[C@H](O)[C@@H]1F)C(=O)O
CHEMBL207406 ChEMBL O34667 6.14 ~724.4 nM 268.3 Da LogP -2.25 TPSA 153.1 1 viol. ✓ Clean N[C@@H](CCSC[C@@H](O)[C@@H](O)C(=O)NO)C(=O)O
CHEMBL1078480 ChEMBL P45578 310.0 Da LogP 3.62 TPSA 26.3 ✓ Ro5 ✓ Clean CCCCC1=CC(=C(Br)Br)OC1=O
CHEMBL1078481 ChEMBL P45578 253.9 Da LogP 2.06 TPSA 26.3 ✓ Ro5 ✓ Clean O=C1C=CC(=C(Br)Br)O1
CHEMBL448241 ChEMBL P45578 310.0 Da LogP 3.62 TPSA 26.3 ✓ Ro5 ✓ Clean CCCCC1=C(Br)/C(=C/Br)OC1=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.

Cross-references

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