Protein profile

KP13_01856

3-methyl-2-oxobutanoate hydroxymethyltransferase

Genome: KpKP13

Gene: AHE46296.1 panB Structure source: AlphaFold + ColabFold UniProt A0A0H3GMQ9
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Amino acids 263
Annotations 6
Features 16
PDB binders 2
Druggability 0.545

Overview

Basic information about this protein and its source genome.

Accession
KP13_01856
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46296.1 panB
Status
annotated
Amino acids
263
Structure source
AlphaFold + ColabFold
EC
2.1.2.11
GO
GO:0003864 Catalysis of the reaction: 5,10-methylenetetrahydrofolate + 3-methyl-2-oxobutanoate = tetrahydrofolate + 2-dehydropantoate. GO:0015940 The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods. 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0000287 Binding to a magnesium (Mg) ion.

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 (%)
67.681
DEG E-value
1.01e-130
Localization
Cytoplasmic
ColabFold pLDDT
97.83

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 0.545
Structure A0A0H3GMQ9
Pocket Pocket 1
P2Rank 0.877
Structure A0A0H3GMQ9
Pocket Pocket 1
ColabFold model
FPocket 0.769 · Pocket 2
P2Rank 0.868 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 200 / 4744 genomes with a hit
Normalized 0.042

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:0003864 Catalysis of the reaction: 5,10-methylenetetrahydrofolate + 3-methyl-2-oxobutanoate = tetrahydrofolate + 2-dehydropantoate.
  • GO:0015940 The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0000287 Binding to a magnesium (Mg) ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
6 256 CDD cd06557 KPHMT-like
6 256 InterPro IPR003700 Ketopantoate hydroxymethyltransferase
2 262 PANTHER PTHR20881 3-METHYL-2-OXOBUTANOATE HYDROXYMETHYLTRANSFERASE
2 262 InterPro IPR003700 Ketopantoate hydroxymethyltransferase
1 263 FunFam G3DSA:3.20.20.60:FF:000003 3-methyl-2-oxobutanoate hydroxymethyltransferase
4 262 SUPERFAMILY SSF51621 Phosphoenolpyruvate/pyruvate domain
4 262 InterPro IPR015813 Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
1 263 NCBIfam TIGR00222 3-methyl-2-oxobutanoate hydroxymethyltransferase
1 263 InterPro IPR003700 Ketopantoate hydroxymethyltransferase
4 257 Pfam PF02548 Ketopantoate hydroxymethyltransferase
4 257 InterPro IPR003700 Ketopantoate hydroxymethyltransferase
1 262 Gene3D G3DSA:3.20.20.60 -
1 262 InterPro IPR040442 Pyruvate kinase-like domain superfamily
4 262 Hamap MF_00156 3-methyl-2-oxobutanoate hydroxymethyltransferase [panB].
4 262 InterPro IPR003700 Ketopantoate hydroxymethyltransferase
1 263 PIRSF PIRSF000388 PanB

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_A0A0H3GMQ9
AlphaFold — — full sequence — Viewing
ColabFold KP13_01856
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 0.545
3 0.029
4 0.0
6 0.0

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 26.96 0.877
2 7.69 0.342
3 3.81 0.119

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.

2 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
KIV
1O68
Q9JZW6 116.1 Da LogP 0.30 TPSA 54.4 ✓ Ro5 ✓ Clean CC(C)C(=O)C(=O)O
KPL
1M3U
P31057 146.1 Da LogP -0.34 TPSA 74.6 ✓ Ro5 ✓ Clean CC(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.