Protein target profile

VK055_3645

4-aminobutyrate transaminase

Genome: KpATCC43816 Gene: AIK82200.1 gabT2 3D evidence: Experimental + ColabFold model Metabolism 1 reaction UniProt A0A0H3GYJ5
Length 421
Pocket druggability 0.076
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 56 total records
Functional annotation 0 EC 7 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
Hit
Human identity (%)
33.103 Lower values reduce human off-target concern.
Human E-value
2.79e-15
Gut microbiome similarity
2.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
46.963 Higher values support similarity to known essential genes.
DEG E-value
1.11e-135 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
98.33 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 0.076
Structure 6WJ8
Pocket Pocket 7
P2Rank 0.225
Structure 6WJ8
Pocket Pocket 1
ColabFold model
FPocket 0.26 · Pocket 21
P2Rank 0.417 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 121 / 4744 genomes with a hit
Prevalence 2.6%

Cross-references

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

Structure

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 95.4% of genes in this genome.

Relative network centrality 95.4% more central than 95.4% of genes in this genome
Chokepoint Not a chokepoint
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.

MKSSELNQRRQQATPRGVGVMCNYFVEKAENATLWDIEGNEVIDFAAGIAVLNTGHRHPKVVAAVADQLQAFTHTAYQIVPYESYVSLAERINDLAPIDGPAKTAFFTTGAEAVENAVKIARAYTGRPGLITFGGGFHGRTFMTMALTGKVAPYKIGFGPFPGSVYHGVYPNAAHGVTTADALKSLERIFKADIAPDQVAAIILEPIQGEGGFNVAPADFMQALRDLCDTHGILLIADEVQTGFARTGKLFAMQHYEVKPDLMTMAKSLAGGFPLSGVVGRAEVMDAPAPGGLGGTYAGNPLAVAAAHAVLDVIAEEQLCQRAEQLGSHLQEVLNQARATCPAIVDVRGRGSMVAVEFNDPQTGEPSPEFTRQVQQKAQENGLLLLSCGVYGNVIRFLYPLTIPDTQFSKALDILARVLKS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • 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:0009448 The chemical reactions and pathways involving gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms.
  • GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
  • GO:0003867 OBSOLETE. Catalysis of the reaction: 4-aminobutanoate + amino group acceptor = succinate semialdehyde + amino acid.
  • 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:0034386 Catalysis of the reaction: 2-oxoglutarate + 4-aminobutanoate = L-glutamate + succinate semialdehyde.
  • GO:0042802 Binding to an identical protein or proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
125 421 PIRSF PIRSF000521 Transaminase_4ab_Lys_Orn
125 421 InterPro IPR005814 Aminotransferase class-III
1 128 PIRSF PIRSF000521 Transaminase_4ab_Lys_Orn
1 128 InterPro IPR005814 Aminotransferase class-III
235 272 ProSitePatterns PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.
235 272 InterPro IPR005814 Aminotransferase class-III
5 415 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
5 415 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
58 317 FunFam G3DSA:3.40.640.10:FF:000013 4-aminobutyrate aminotransferase
20 419 Pfam PF00202 Aminotransferase class-III
20 419 InterPro IPR005814 Aminotransferase class-III
23 420 SUPERFAMILY SSF53383 PLP-dependent transferases
23 420 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
6 419 CDD cd00610 OAT_like
6 419 InterPro IPR005814 Aminotransferase class-III
58 317 Gene3D G3DSA:3.40.640.10 -
58 317 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
8 420 NCBIfam TIGR00700 4-aminobutyrate--2-oxoglutarate transaminase
8 420 InterPro IPR004632 4-aminobutyrate aminotransferase, bacterial
23 420 PANTHER PTHR11986 AMINOTRANSFERASE CLASS III

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

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

Site 1 P2Rank #1
0.225
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Surrounding area
Site 2 P2Rank #2
0.184
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Surrounding area
Site 3 P2Rank #3
0.181
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Surrounding area
Site 4 P2Rank #4
0.016
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Surrounding area
Site 5 P2Rank #5
0.01
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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 6WJ8
X-ray 2.59 Å A,B,C,D
100.0% 1-421
Viewing
ColabFold VK055_3645
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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ABU PDB via homolog 103.1 Da · LogP -0.19 · TPSA 63.3 Open detail RCSB PDB
IK2 PDB via homolog Detail RCSB PDB
PLZ PDB via homolog Detail RCSB PDB
PMP PDB via homolog Detail RCSB PDB
SSN PDB via homolog Detail RCSB PDB

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
ABU RCSB PDB A1R958 103.1 Da LogP -0.19 TPSA 63.3 ✓ Ro5 ✓ Clean C(CC(=O)O)CN
IK2 RCSB PDB P22256 322.2 Da LogP -0.19 TPSA 158.4 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNOCC(=O)O)O
PLZ RCSB PDB Q8NT35 334.3 Da LogP 0.66 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNCCCC(=O)O)O
PMP RCSB PDB P22256 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
SSN RCSB PDB A0QQ04 102.1 Da LogP 0.05 TPSA 54.4 ✓ Ro5 ✓ Clean C(CC(=O)O)C=O
TAR RCSB PDB D0CCF6 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@H]([C@@H](C(=O)O)O)(C(=O)O)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.