Protein profile

KP13_02697

Dihydroxy-acid dehydratase

Genome: KpKP13

Gene: AHE47015.1 ilvD Structure source: AlphaFold + ColabFold UniProt A0A0H3GGG0
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Amino acids 590
Annotations 10
Features 17
PDB binders 1
Druggability 0.38

Overview

Basic information about this protein and its source genome.

Accession
KP13_02697
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE47015.1 ilvD
Status
annotated
Amino acids
590
Structure source
AlphaFold + ColabFold
EC
4.2.1.9
GO
GO:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water. GO:0004160 Catalysis of the reaction: (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O. 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:0009082 The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two 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 (%)
74.788
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.03

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 0.38
Structure A0A0H3GGG0
Pocket Pocket 21
P2Rank 0.833
Structure A0A0H3GGG0
Pocket Pocket 1
ColabFold model
FPocket 0.718 · Pocket 33
P2Rank 0.672 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 700 / 4744 genomes with a hit
Normalized 0.148

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
  • GO:0004160 Catalysis of the reaction: (2R)-2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O.
  • 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:0009082 The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0009097 OBSOLETE. The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
  • GO:0009099 The chemical reactions and pathways resulting in the formation of valine, 2-amino-3-methylbutanoic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
1 584 Hamap MF_00012 Dihydroxy-acid dehydratase [ilvD].
1 584 InterPro IPR004404 Dihydroxy-acid dehydratase
96 106 ProSitePatterns PS00886 Dihydroxy-acid and 6-phosphogluconate dehydratases signature 1.
96 106 InterPro IPR020558 Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site
261 281 Coils Coil Coil
483 494 ProSitePatterns PS00887 Dihydroxy-acid and 6-phosphogluconate dehydratases signature 2.
483 494 InterPro IPR020558 Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site
1 584 NCBIfam TIGR00110 dihydroxy-acid dehydratase
395 546 FunFam G3DSA:3.50.30.80:FF:000001 Dihydroxy-acid dehydratase
395 584 SUPERFAMILY SSF52016 LeuD/IlvD-like
2 394 SUPERFAMILY SSF143975 IlvD/EDD N-terminal domain-like
2 394 InterPro IPR037237 IlvD/EDD, N-terminal domain
8 581 Pfam PF00920 Dehydratase family
8 581 InterPro IPR000581 Dihydroxy-acid/6-phosphogluconate dehydratase
395 546 Gene3D G3DSA:3.50.30.80 -
395 546 InterPro IPR042096 Dihydroxy-acid dehydratase, C-terminal
1 587 PANTHER PTHR43661 D-XYLONATE DEHYDRATASE

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_A0A0H3GGG0
AlphaFold — — full sequence — Viewing
ColabFold KP13_02697
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
21 0.38
24 0.273

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 15.21 0.749
2 1.93 0.04
3 1.54 0.023

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.