Protein profile

KP13_00351

Isocitrate lyase

Genome: KpKP13

Gene: AHE46910.1 aceA Structure source: AlphaFold + ColabFold UniProt A0A0H3GHC8
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Amino acids 439
Annotations 7
Features 20
PDB binders 9
Druggability 0.795

Overview

Basic information about this protein and its source genome.

Accession
KP13_00351
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46910.1 aceA
Status
annotated
Amino acids
439
Structure source
AlphaFold + ColabFold
EC
4.1.3.1
GO
GO:0019752 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). 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:0004451 Catalysis of the reaction: isocitrate = glyoxylate + succinate. GO:0046872 Binding to a metal ion. 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
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
67.824
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.89

Selected Druggability evidence

AlphaFold / UniProt model

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 0.795
Structure A0A0H3GHC8
Pocket Pocket 9
P2Rank 0.638
Structure A0A0H3GHC8
Pocket Pocket 1
ColabFold model
FPocket 0.79 · Pocket 30
P2Rank 0.587 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 203 / 4744 genomes with a hit
Normalized 0.043

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0019752 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
  • 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:0004451 Catalysis of the reaction: isocitrate = glyoxylate + succinate.
  • GO:0046872 Binding to a metal ion.
  • 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.

20 records
Show feature table
Start End DB Term Name
7 439 PANTHER PTHR21631 ISOCITRATE LYASE/MALATE SYNTHASE
7 439 InterPro IPR006254 Isocitrate lyase
13 260 NCBIfam TIGR01346 isocitrate lyase
13 260 InterPro IPR006254 Isocitrate lyase
261 439 NCBIfam TIGR01346 isocitrate lyase
261 439 InterPro IPR006254 Isocitrate lyase
5 439 PIRSF PIRSF001362 ICL
5 439 InterPro IPR006254 Isocitrate lyase
58 373 CDD cd00377 ICL_PEPM
58 373 InterPro IPR039556 ICL/PEPM domain
6 439 FunFam G3DSA:3.20.20.60:FF:000005 Isocitrate lyase
9 422 SUPERFAMILY SSF51621 Phosphoenolpyruvate/pyruvate domain
9 422 InterPro IPR015813 Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
5 422 Gene3D G3DSA:3.20.20.60 -
5 422 InterPro IPR040442 Pyruvate kinase-like domain superfamily
262 439 Pfam PF00463 Isocitrate lyase family
262 439 InterPro IPR006254 Isocitrate lyase
13 260 Pfam PF00463 Isocitrate lyase family
198 203 ProSitePatterns PS00161 Isocitrate lyase signature.
198 203 InterPro IPR018523 Isocitrate lyase/phosphorylmutase, conserved site

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

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GHC8
AlphaFold — — full sequence — Viewing
ColabFold KP13_00351
ColabFold — — 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 0.795
7 0.682
3 0.254
1 0.216

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 10.64 0.571
2 2.25 0.056
3 1.78 0.033

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.

66 records

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
3NP
6C4A
P9WKK7 119.1 Da LogP -0.26 TPSA 80.4 ✓ Ro5 ✓ Clean C(C[N+](=O)[O-])C(=O)O
GLV
1F8I
P9WKK7 74.0 Da LogP -0.73 TPSA 54.4 ✓ Ro5 ✓ Clean C(=O)C(=O)O
ICT
6LRT
A9WDE7 192.1 Da LogP -1.39 TPSA 132.1 ✓ Ro5 ✓ Clean C([C@@H]([C@H](C(=O)O)O)C(=O)O)C(=O)O
MLA
3OQ8
Q2YQA0 104.1 Da LogP -0.45 TPSA 74.6 ✓ Ro5 ✓ Clean C(C(=O)O)C(=O)O
OXD
6VB9
P9WKK7 90.0 Da LogP -0.84 TPSA 74.6 ✓ Ro5 ✓ Clean C(=O)(C(=O)O)O
PYR
1IGW
P0A9G6 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
SIN
1F8I
P9WKK7 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
U9S
6WSI
P9WKK7 132.1 Da LogP -1.08 TPSA 87.1 ✓ Ro5 ✓ Clean [C@@H]1([C@H](O1)C(=O)O)C(=O)O
VGX
5DQL
P9WKK7 118.1 Da LogP -0.98 TPSA 74.6 ✓ Ro5 ✓ Clean C(CO)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.