Protein profile

KP13_01609

KHG/KDPG aldolase

Genome: KpKP13

Gene: eda AHE43868.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVF4
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Amino acids 213
Annotations 3
Features 15
PDB binders 4
Druggability 0.94

Overview

Basic information about this protein and its source genome.

Accession
KP13_01609
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
eda AHE43868.1
Status
annotated
Amino acids
213
Structure source
AlphaFold + ColabFold
EC
4.1.2.14
GO
GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. GO:0008675 Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate 6-phosphate = pyruvate + D-glyceraldehyde 3-phosphate.

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 (%)
57.843
DEG E-value
5.23e-77
Localization
Cytoplasmic
ColabFold pLDDT
98.31

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 0.94
Structure A0A0H3GVF4
Pocket Pocket 1
P2Rank 0.21
Structure A0A0H3GVF4
Pocket Pocket 1
ColabFold model
FPocket 0.484 · Pocket 5
P2Rank 0.392 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 137 / 4744 genomes with a hit
Normalized 0.029

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

2
  • GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
  • GO:0008675 Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate 6-phosphate = pyruvate + D-glyceraldehyde 3-phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
9 210 NCBIfam TIGR01182 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase
9 210 InterPro IPR000887 KDPG/KHG aldolase
9 203 Pfam PF01081 KDPG and KHG aldolase
9 203 InterPro IPR000887 KDPG/KHG aldolase
27 204 CDD cd00452 KDPG_aldolase
27 204 InterPro IPR000887 KDPG/KHG aldolase
3 210 SUPERFAMILY SSF51569 Aldolase
129 142 ProSitePatterns PS00160 KDPG and KHG aldolases Schiff-base forming residue.
129 142 InterPro IPR031338 KDPG/KHG aldolase, active site 2
1 213 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 213 InterPro IPR013785 Aldolase-type TIM barrel
5 212 PANTHER PTHR30246 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE
5 212 InterPro IPR000887 KDPG/KHG aldolase
40 49 ProSitePatterns PS00159 KDPG and KHG aldolases active site.
40 49 InterPro IPR031337 KDPG/KHG aldolase, active site 1

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_A0A0H3GVF4
AlphaFold — — full sequence — Viewing
ColabFold KP13_01609
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
1 0.94
2 0.628

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 3.77 0.145

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.

54 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
3PG
5XSF
Q00384 186.1 Da LogP -1.46 TPSA 124.3 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)OP(=O)(O)O
3PY
5XSF
Q00384 104.1 Da LogP -1.37 TPSA 74.6 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)O
PVO
6OVI
Q5ZYF2 106.1 Da LogP -1.23 TPSA 77.8 ✓ Ro5 ✓ Clean CC(C(=O)O)(O)O
PYR
1EUA
P0A955 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.