Protein profile

KP13_01610

Phosphogluconate dehydratase

Genome: KpKP13

Gene: edd AHE43867.1 Structure source: AlphaFold + ColabFold UniProt A0A2X3IFG5
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Amino acids 599
Annotations 9
Features 17
PDB binders 1
Druggability 0.725

Overview

Basic information about this protein and its source genome.

Accession
KP13_01610
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
edd AHE43867.1
Status
annotated
Amino acids
599
Structure source
AlphaFold + ColabFold
EC
4.2.1.12
GO
GO:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water. GO:0009255 A pathway that converts a carbohydrate to pyruvate and glyceraldehyde-3 phosphate by producing 6-phosphogluconate and then dehydrating it. 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:0004456 Catalysis of the reaction: 6-phospho-D-gluconate = 2-dehydro-3-deoxy-6-phospho-D-gluconate + H2O. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.

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 (%)
61.538
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.03

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 0.725
Structure A0A2X3IFG5
Pocket Pocket 29
P2Rank 0.952
Structure A0A2X3IFG5
Pocket Pocket 1
ColabFold model
FPocket 0.963 · Pocket 31
P2Rank 0.968 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 161 / 4744 genomes with a hit
Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
  • GO:0009255 A pathway that converts a carbohydrate to pyruvate and glyceraldehyde-3 phosphate by producing 6-phosphogluconate and then dehydrating it.
  • 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:0004456 Catalysis of the reaction: 6-phospho-D-gluconate = 2-dehydro-3-deoxy-6-phospho-D-gluconate + H2O.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0046872 Binding to a metal ion.
  • GO:0019521 The chemical reactions and pathways involving D-gluconate, the anion of D-gluconic acid, the aldonic acid derived from glucose.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
1 598 Hamap MF_02094 Phosphogluconate dehydratase [edd].
1 598 InterPro IPR004786 6-phosphogluconate dehydratase
2 598 NCBIfam TIGR01196 phosphogluconate dehydratase
2 598 InterPro IPR004786 6-phosphogluconate dehydratase
150 160 ProSitePatterns PS00886 Dihydroxy-acid and 6-phosphogluconate dehydratases signature 1.
150 160 InterPro IPR020558 Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site
501 512 ProSitePatterns PS00887 Dihydroxy-acid and 6-phosphogluconate dehydratases signature 2.
501 512 InterPro IPR020558 Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site
62 594 Pfam PF00920 Dehydratase family
62 594 InterPro IPR000581 Dihydroxy-acid/6-phosphogluconate dehydratase
415 564 Gene3D G3DSA:3.50.30.80 -
415 564 InterPro IPR042096 Dihydroxy-acid dehydratase, C-terminal
16 597 PANTHER PTHR43661 D-XYLONATE DEHYDRATASE
415 565 FunFam G3DSA:3.50.30.80:FF:000001 Dihydroxy-acid dehydratase
415 596 SUPERFAMILY SSF52016 LeuD/IlvD-like
3 414 SUPERFAMILY SSF143975 IlvD/EDD N-terminal domain-like
3 414 InterPro IPR037237 IlvD/EDD, N-terminal domain

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_A0A2X3IFG5
AlphaFold — — full sequence — Viewing
ColabFold KP13_01610
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
29 0.725

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 27.75 0.922
2 4.67 0.203
3 2.1 0.048
4 1.5 0.021
5 1.42 0.018

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.

1 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
FES
5J84
B5ZZ34 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1

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.