Protein profile

PA0796

2-methylisocitrate lyase

Genome: NC_002516.2

Gene: prpB PA0796 Structure source: Experimental + AlphaFold UniProt Q9I5E2
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Amino acids 298
Annotations 5
Features 15
PDB binders 5
Druggability 0.42

Overview

Basic information about this protein and its source genome.

Accession
PA0796
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
prpB PA0796
Status
annotated
Amino acids
298
Structure source
Experimental + AlphaFold
EC
4.1.3.30
GO
GO:0000287 Binding to a magnesium (Mg) ion. GO:0046421 Catalysis of the reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate. GO:0019629 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of propionate that occurs in the 2-methylcitrate cycle. 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
No hit
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 0.42
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0046421 Catalysis of the reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate.
  • GO:0019629 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of propionate that occurs in the 2-methylcitrate cycle.
  • 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.

15 records
Show feature table
Start End DB Term Name
4 295 Hamap MF_01939 2-methylisocitrate lyase [prpB].
4 295 InterPro IPR012695 2-methylisocitrate lyase
2 297 Gene3D G3DSA:3.20.20.60 -
2 297 InterPro IPR040442 Pyruvate kinase-like domain superfamily
123 128 ProSitePatterns PS00161 Isocitrate lyase signature.
123 128 InterPro IPR018523 Isocitrate lyase/phosphorylmutase, conserved site
8 292 SUPERFAMILY SSF51621 Phosphoenolpyruvate/pyruvate domain
8 292 InterPro IPR015813 Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
12 255 CDD cd00377 ICL_PEPM
12 255 InterPro IPR039556 ICL/PEPM domain
9 293 NCBIfam TIGR02317 methylisocitrate lyase
9 293 InterPro IPR012695 2-methylisocitrate lyase
4 287 PANTHER PTHR42905 PHOSPHOENOLPYRUVATE CARBOXYLASE
4 297 FunFam G3DSA:3.20.20.60:FF:000009 2-methylisocitrate lyase
19 256 Pfam PF13714 Phosphoenolpyruvate phosphomutase

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 6T5M
X-ray 1.76 Å A,B,C,D
100.0% 1-298
PDBe RCSB PDBj File
Viewing
PDB 6T4V
X-ray 1.81 Å A,B,C,D
100.0% 1-298
PDBe RCSB PDBj File
Loaded
AlphaFold PA0796
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
9 0.42
1 0.4

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 10.14 0.545
2 3.57 0.132
3 0.69 0.001

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.

53 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
PYR
6T5M 1.76 Å Open crystal
88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=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.