Protein target profile

VK055_1222

ydjC-like family protein

Genome: KpATCC43816 Gene: AIK79845.1 3D evidence: Experimental + ColabFold model UniProt A6T7U7
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Length 252
Pocket druggability 0.809
Functional annotation 0 EC 3 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.

Main supporting evidence

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.81, P2Rank 0.75). Use the 3D pocket comparison to verify whether they identify the same site. Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Strong predicted binding pocket FPocket selected-pocket score 0.81. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.75. Review the complete evidence below

Risks to review

Low human similarity A human hit was flagged, but identity is only 28.956% - a weak match, lower risk than a close homolog. This target also has a predicted binding pocket (FPocket 0.81) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 85 of 4744 screened genomes (1.8%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.81) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. 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
Hit
Human identity (%)
28.956 Lower values reduce human off-target concern.
Human E-value
5.36e-22
Gut microbiome similarity
1.8% 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.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.99 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.809
Structure 7VI8
Pocket Pocket 1
P2Rank 0.754
Structure 7VI8
Pocket Pocket 1
ColabFold model
FPocket 0.338 · Pocket 4
P2Rank 0.783 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 85 / 4744 genomes with a hit
Prevalence 1.8%

Cross-references

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

Sequence

UniProt A6T7U7

Structure

PDB 7VI8

Sequence

Primary amino-acid sequence viewer.

MERILIVNADDFGLSKGQNYGIIEACRNGVVTSTTALVNGAAIDHAAQLSRSTPELAVGMHFVLTLGEPLSAMPGLTRDGRLGKWIWQQAEEDSLPLEEIAHELACQYHRFVELFGHEPTHIDSHHHVHMFAQIYPIVAAFAREKGIALRIDRQVAAQSGLDQQAARSSAGFSSEFYGEAVSEELFLQTLDASIARGERSLEVMCHPAYVDRIIMGSAYCYPRLDELDVLTSASLKAAVADRGYRLGTYRDV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0016811 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0000272 The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
5 236 CDD cd10803 YdjC_EF3048_like
5 236 InterPro IPR022948 Chitooligosaccharide deacetylase ChbG-like, bacteria
5 240 Pfam PF04794 YdjC-like protein
5 240 InterPro IPR006879 Carbohydrate deacetylase YdjC-like
1 252 FunFam G3DSA:3.20.20.370:FF:000001 Chitooligosaccharide deacetylase
159 252 PANTHER PTHR31609 YDJC DEACETYLASE FAMILY MEMBER
159 252 InterPro IPR006879 Carbohydrate deacetylase YdjC-like
1 252 Gene3D G3DSA:3.20.20.370 Glycoside hydrolase/deacetylase
3 249 Hamap MF_01246 Chitooligosaccharide deacetylase [chbG].
3 249 InterPro IPR022948 Chitooligosaccharide deacetylase ChbG-like, bacteria
1 252 SUPERFAMILY SSF88713 Glycoside hydrolase/deacetylase
1 252 InterPro IPR011330 Glycoside hydrolase/deacetylase, beta/alpha-barrel

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 #1
0.809
Likely same site as P2Rank 1 1.3 Å 15 shared residues 100% 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
0.754
Likely same site as FPocket 1 1.3 Å 15 shared residues 100% of smaller site
Show in viewer
Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 7VI8
X-ray — A —
PDBe RCSB PDBj File
Viewing
ColabFold VK055_1222
ColabFold — — full sequence — Loaded