Protein profile

PA2624

isocitrate dehydrogenase

Genome: NC_002516.2

Gene: idh PA2624 Structure source: Experimental + AlphaFold UniProt Q9I0L4
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Amino acids 741
Annotations 6
Features 8
PDB binders 5
Druggability 0.788

Overview

Basic information about this protein and its source genome.

Accession
PA2624
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
idh PA2624
Status
annotated
Amino acids
741
Structure source
Experimental + AlphaFold
EC
1.1.1.42
GO
GO:0004450 Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH. GO:0046872 Binding to a metal ion. GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. GO:0006097 A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate. GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Unknown

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 0.788
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0004450 Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH.
  • GO:0046872 Binding to a metal ion.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • GO:0006097 A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
  • GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

Sequence Features

Domain/signature hits from InterPro and related databases.

8 records
Show feature table
Start End DB Term Name
4 740 PANTHER PTHR36999 ISOCITRATE DEHYDROGENASE [NADP]
4 740 InterPro IPR004436 Isocitrate dehydrogenase NADP-dependent, monomeric
5 740 SUPERFAMILY SSF53659 Isocitrate/Isopropylmalate dehydrogenase-like
6 738 Pfam PF03971 Monomeric isocitrate dehydrogenase
6 738 InterPro IPR004436 Isocitrate dehydrogenase NADP-dependent, monomeric
1 741 PIRSF PIRSF009407 IDH_monmr
1 741 InterPro IPR004436 Isocitrate dehydrogenase NADP-dependent, monomeric
4 740 NCBIfam TIGR00178 NADP-dependent isocitrate dehydrogenase

3D Structure

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

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Structural evidence

1 + 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 6G3U
X-ray 2.71 Å A,B
99.5% 5-741
PDBe RCSB PDBj File
Viewing
AlphaFold PA2624
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
2 0.788
4 0.54
15 0.244

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 48.35 0.978
2 19.27 0.837
3 5.11 0.234
4 3.51 0.129
5 2.92 0.093

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.

11 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
AKG
6G3U 2.71 Å Open crystal
146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=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.