KpATCC43816 Protein target profile

UDP-L-Ara4O C-4' transaminase

Accession: VK055_3623

Gene: arnB AIK82178.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GUE5
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Length 379
Pocket druggability (P2Rank · AlphaFold DB model) 0.893
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 22 total records
Functional annotation 1 EC 8 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Metabolic chokepoint Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Central metabolic position More central than 89.5% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Review the complete evidence below

Risks to review

Microbiome similarity 116 of 4744 screened genomes (2.4%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.89) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.56, 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 coverage

Core evidence streams are available for this target.
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
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
96.11 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) 0.893
Structure A0A0H3GUE5
Pocket Pocket 1
Druggability (FPocket) 0.56
Structure A0A0H3GUE5
Pocket Pocket 3
ColabFold model
P2Rank 0.828 · Pocket 1
FPocket 0.809 · Pocket 4
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 116 / 4744 genomes with a hit
Prevalence 2.4%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing & consuming chokepoint reaction in Biosynthesis of various nucleotide sugars, no isoenzyme backup detected, more central than 89.5% of genes in this genome, no human homolog detected.

Relative network centrality 89.5% more central than 89.5% of genes in this genome
Chokepoint Chokepoint gene
Pathways
Biosynthesis of various nucleotide sugars
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.

MSDFLPFSRPSMGDAELAALREVLASGWITTGPKNQALEAAFCQLTGNRHAIAVSSATGGMHVTLMALGIGPGDEVITPSQTWVSTLNMICLLGATPVMIDVDNDNLMITPAAVEAAITSRTKAIIPVHYAGAPADIDAIRAVGERHGISVIEDAAHAAGTHYKGRHVGWQGTAIFSFHAIKNMTCAEGGLIVTDDDELASRIRSLKFHGLGVDAYDRQTHGRAPQAEVITPGFKYNLADINAALALVQLEKLSHANQRRTEIAQRYLRELADTPFKPLSVPTWDHQHAWHLFIIRVDEAACGISRDALMEKLKAMGIGTGLHFRAAHTQKYYRERFPEVSLPNTEWNSARICSLPLFPDMTDDDVTRVISALRQLSGR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0099620 Catalysis of the reaction: UDP-4-amino-4-deoxy-beta-L-arabinose + 2-oxoglutarate = UDP-beta-L-threo-pentopyranos-4-ulose + L-glutamate.
  • GO:0009245 The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
  • GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
  • GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
16 374 CDD cd00616 AHBA_syn
16 374 InterPro IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase
12 374 Pfam PF01041 DegT/DnrJ/EryC1/StrS aminotransferase family
12 374 InterPro IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase
4 376 SUPERFAMILY SSF53383 PLP-dependent transferases
4 376 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
5 375 PANTHER PTHR30244 TRANSAMINASE
5 375 InterPro IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase
1 252 Gene3D G3DSA:3.40.640.10 -
1 252 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
1 379 PIRSF PIRSF000390 PLP_StrS
1 379 InterPro IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase
253 377 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
253 377 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
1 252 FunFam G3DSA:3.40.640.10:FF:000040 UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
1 379 Hamap MF_01167 UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase [arnB].
1 379 InterPro IPR022850 UDP-4-amino-4-deoxy-L-arabinose-oxoglutarate aminotransferase, ArnB
253 379 FunFam G3DSA:3.90.1150.10:FF:000030 UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase

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 · P2Rank

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

Pocket 1 P2Rank #1
0.893
Likely same site as FPocket 3 0.5 Å 20 shared residues 95% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.16
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Surrounding area
Pocket 3 P2Rank #3
0.09
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Surrounding area
Pocket 4 P2Rank #4
0.078
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Surrounding area
Pocket 5 P2Rank #5
0.041
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #3
0.56 Unusual size
Likely same site as P2Rank 1 0.5 Å 20 shared residues 95% of smaller site
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Surrounding area
Residue sets
UniProt: Active site:182-182 Proton acceptor
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_A0A0H3GUE5
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_3623
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.

22 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 18 similarity-based ZINC candidates
Best available ligand signal
AKG PDB via homolog 146.1 Da · LogP -0.50 · TPSA 91.7 Open detail RCSB PDB
DCS PDB via homolog Detail RCSB PDB
PGU PDB via homolog Detail RCSB PDB
PMP PDB via homolog Detail RCSB PDB
ZINC1532708 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
AKG RCSB PDB
1MDX
Q8ZNF3 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
DCS RCSB PDB
1MDZ
Q8ZNF3 333.2 Da LogP -0.78 TPSA 150.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CONC2=O)O
PGU RCSB PDB
2OGA
Q9ZGH4 378.3 Da LogP 0.11 TPSA 186.5 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCC(=O)O)C(=O…
PMP RCSB PDB
6EWR
A0A0H2URM1 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)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.

Sequence

UniProt A0A0H3GUE5

Pathways

KEGG R07659 BioCyc RXN0-1863