KpATCC43816 Protein target profile

lysR substrate binding domain protein

Accession: VK055_5142

Gene: AIK83665.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A2W1MQC1
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Length 231
Pocket druggability (P2Rank · AlphaFold DB model) 0.914
Functional annotation 0 EC 3 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. Second pocket predictor agrees P2Rank predicted binding-site probability 0.91. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 26 of 4744 screened genomes (0.5%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.91) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant. Best pocket may be a modeling artifact FPocket selected-pocket score 0.91, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

Evidence gaps

No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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
0.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
28.448 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
89.75 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) 0.914
Structure A0A2W1MQC1
Pocket Pocket 1
Druggability (FPocket) 0.907
Structure A0A2W1MQC1
Pocket Pocket 12
ColabFold model
P2Rank 0.885 · Pocket 1
FPocket 0.232 · Pocket 10
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 26 / 4744 genomes with a hit
Prevalence 0.5%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MEDAENSLSSAAMTPRGRLRVDVPSPLARLILVPALPAFHARYPDIQIDMGVSDRVVDLIGDNVDCVLRGGQITDQSLIARHVGDLQIGVYVAPSYVERLGAPAHPRELQNTDHCIVGFLSSRTSKIDPLVLCSENERIEITGNYVLAVDDGNAYLEAGLVGLGVIALPNYMAAAHQAVGALIPLFTQWRISPMPLYLAFPPNRHVNAKLRVFIDWIVEVMLQHVPIANNQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

3
  • GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
  • GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
  • GO:0006351 The synthesis of an RNA transcript from a DNA template.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

7 records
Show feature table
Start End DB Term Name
15 220 Pfam PF03466 LysR substrate binding domain
15 220 InterPro IPR005119 LysR, substrate-binding
17 220 CDD cd08472 PBP2_CrgA_like_3
87 192 Gene3D G3DSA:3.40.190.10 -
1 221 PANTHER PTHR30537 HTH-TYPE TRANSCRIPTIONAL REGULATOR
15 223 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
16 217 Gene3D G3DSA:3.40.190.10 -

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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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
0.914
Likely same site as FPocket 12 4.1 Å 29 shared residues 97% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.02
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.006
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #12
0.907 Unusual size
Likely same site as P2Rank 1 4.1 Å 29 shared residues 97% 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_A0A2W1MQC1
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_5142
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A2W1MQC1