Protein target profile

VK055_4093

alanine racemase, N-terminal domain protein

Genome: KpATCC43816 Gene: AIK82639.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GVD8
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Length 233
Pocket druggability 0.873
Metabolic reactions 1
Chokepoint No
Functional annotation 0 EC 1 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

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Structure available AlphaFold DB model + ColabFold model

Risks to review

Human similarity Top human hit identity: 66.667%. This target also has a predicted binding pocket (FPocket 0.87) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 223 of 4744 screened genomes (4.7%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.87) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.87, 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. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.21.

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
Hit
Human identity (%)
66.667 Lower values reduce human off-target concern.
Human E-value
9.32e-06
Gut microbiome similarity
4.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
62.5 Higher values support similarity to known essential genes.
DEG E-value
2.48e-97 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.0 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 0.873
Structure A0A0H3GVD8
Pocket Pocket 1
P2Rank 0.208
Structure A0A0H3GVD8
Pocket Pocket 1
ColabFold model
FPocket 0.554 · Pocket 3
P2Rank 0.156 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 223 / 4744 genomes with a hit
Prevalence 4.7%

Cross-references

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

Sequence

UniProt A0A0H3GVD8

Pathways

KEGG R00401 BioCyc ALARACECAT-RXN

Metabolic context

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

Explore metabolic network
Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways
D-Amino acid metabolism
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MNDIAHNLAQVRDKISGAAARCGRAPEEVTLLAVSKTKPASAIEEAIAAGQRAFGENYVQEGVEKINHFQQAGVSGLQWHFIGPLQSNKSRLVAEHFDWCHTVDRLKIATRLNEQRPAHLPPLKVLIQINISDEQSKSGIPLEALDGLAAEIAELPHLELRGLMAIPAPESEYVRQFAVARQMAVAFARLKTRYPTVDTLSLGMSDDMEAAIAAGSTMVRIGTAIFGARDYSK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
6 228 Hamap MF_02087 Pyridoxal phosphate homeostasis protein.
6 228 InterPro IPR011078 Pyridoxal phosphate homeostasis protein
79 93 ProSitePatterns PS01211 Uncharacterized protein family UPF0001 signature.
79 93 InterPro IPR011078 Pyridoxal phosphate homeostasis protein
1 228 FunFam G3DSA:3.20.20.10:FF:000004 Pyridoxal phosphate homeostasis protein
5 229 Pfam PF01168 Alanine racemase, N-terminal domain
5 229 InterPro IPR001608 Alanine racemase, N-terminal
1 229 NCBIfam TIGR00044 YggS family pyridoxal phosphate-dependent enzyme
1 229 InterPro IPR011078 Pyridoxal phosphate homeostasis protein
1 227 SUPERFAMILY SSF51419 PLP-binding barrel
1 227 InterPro IPR029066 PLP-binding barrel
1 228 Gene3D G3DSA:3.20.20.10 Alanine racemase
1 228 InterPro IPR029066 PLP-binding barrel
1 233 PIRSF PIRSF004848 YBL036c_PLPDEIII
1 233 InterPro IPR011078 Pyridoxal phosphate homeostasis protein
3 233 PANTHER PTHR10146 PROLINE SYNTHETASE CO-TRANSCRIBED BACTERIAL HOMOLOG PROTEIN
3 233 InterPro IPR011078 Pyridoxal phosphate homeostasis protein
3 228 CDD cd06824 PLPDE_III_Yggs_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 · FPocket

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

Site 1 FPocket #1
0.873
Likely same site as P2Rank 1 7.6 Å 12 shared residues 100% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #10
0.556
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.208
Likely same site as FPocket 1 7.6 Å 12 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.037
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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_A0A0H3GVD8
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4093
ColabFold — — full sequence — Loaded