Protein profile

PA4088

aminotransferase

Genome: NC_002516.2

Gene: PA4088 Structure source: Experimental + AlphaFold UniProt Q9HWU0
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Amino acids 461
Annotations 4
Features 10
PDB binders 6
Druggability 0.642

Overview

Basic information about this protein and its source genome.

Accession
PA4088
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA4088
Status
annotated
Amino acids
461
Structure source
Experimental + AlphaFold
GO
GO:0042286 Catalysis of the reaction: (S)-4-amino-5-oxopentanoate = 5-aminolevulinate. 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:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
24.848
Human E-value
1.05e-07
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.642
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MDTTFGLDLARVETLFKRELRRFDELHPRSAQAYRENRRHWLYGAPLHWMQQWPGNCPLLVKEAQGARVTDIDGQQYVDFALGDSGAMFGHAQPAVADAIARQARRGSTLMLPTEDSLWVGAELARRFGLPYWQVTTSATDANRFVLRLCRMLSGRDKVVVFNCNYHGSVDESQVEFDAAGRMVPRAGVHPNGVRHATTTRLVEFNDLDALEAALAHGDVAAVLTEPFMTNVGMVPPAEGFHAGLRELTRRHDVALIIDETHTISCGPAGYSGAHGLEPDFFVLGKCIAGGIPSAVWGCSQAQAERIWAVLPHFRPGQAINHFGFGGTLAGNALQLAAMRATFAEVMTEDAYRHMFQLAAQLEAGVRATLEELRLPWHVTRIGARVEYLFMTHAPRNGGEAHHARNGLIEACLHLYLLNRGVLLTPFHNMALTCPATRAEDVELHDRLLRDCLGELLERPS

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0042286 Catalysis of the reaction: (S)-4-amino-5-oxopentanoate = 5-aminolevulinate.
  • 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:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
53 432 Pfam PF00202 Aminotransferase class-III
53 432 InterPro IPR005814 Aminotransferase class-III
93 351 Gene3D G3DSA:3.40.640.10 -
93 351 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
28 439 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
28 439 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
93 351 FunFam G3DSA:3.40.640.10:FF:000215 Probable aminotransferase
10 444 PANTHER PTHR43713 GLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE
45 455 SUPERFAMILY SSF53383 PLP-dependent transferases
45 455 InterPro IPR015424 Pyridoxal phosphate-dependent transferase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

2 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 5YKR
X-ray 1.44 Å A,B
100.0% 1-461
PDBe RCSB PDBj File
Viewing
PDB 5YKT
X-ray 1.57 Å A,B
100.0% 1-461
PDBe RCSB PDBj File
Loaded
AlphaFold PA4088
AlphaFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.642

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 20.37 0.854
2 17.59 0.805
3 8.6 0.46
4 5.78 0.281
5 4.96 0.224

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

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
PMP
5YKT 1.57 Å Open crystal
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.