Protein profile

PA5161

dTDP-D-glucose 4,6-dehydratase

Genome: NC_002516.2

Gene: PA5161 rmlB Structure source: AlphaFold UniProt Q9HU24
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Amino acids 352
Annotations 6
Features 13
PDB binders 3
Druggability 0.842

Overview

Basic information about this protein and its source genome.

Accession
PA5161
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA5161 rmlB
Status
annotated
Amino acids
352
Structure source
AlphaFold
EC
4.2.1.46
GO
GO:0008460 Catalysis of the reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O. GO:0019305 The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate. GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0009225 The cellular chemical reactions and pathways involving nucleotide-sugars, any nucleotide-carbohydrate in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
34.036
Human E-value
5.32e-62
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.842
Structure –
Pocket –

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:0008460 Catalysis of the reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O.
  • GO:0019305 The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate.
  • GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0009225 The cellular chemical reactions and pathways involving nucleotide-sugars, any nucleotide-carbohydrate in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
1 335 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
1 335 InterPro IPR036291 NAD(P)-binding domain superfamily
2 343 PANTHER PTHR43000 DTDP-D-GLUCOSE 4,6-DEHYDRATASE-RELATED
200 332 Gene3D G3DSA:3.90.25.10 -
4 324 Pfam PF16363 GDP-mannose 4,6 dehydratase
4 324 InterPro IPR016040 NAD(P)-binding domain
3 322 Gene3D G3DSA:3.40.50.720 -
3 337 NCBIfam TIGR01181 dTDP-glucose 4,6-dehydratase
3 337 InterPro IPR005888 dTDP-glucose 4,6-dehydratase
1 333 CDD cd05246 dTDP_GD_SDR_e
1 333 InterPro IPR005888 dTDP-glucose 4,6-dehydratase
146 174 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature.
146 174 InterPro IPR020904 Short-chain dehydrogenase/reductase, 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.

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Structural evidence

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA5161
AlphaFold — — full sequence — Viewing
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
2 0.842

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.

53 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
DAU
1KEU
P26391 564.3 Da LogP -3.46 TPSA 276.8 3 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…
TDX
1KEP
Q8GIP9 534.3 Da LogP -2.82 TPSA 256.5 3 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…
TYD
1KEW
P26391 402.2 Da LogP -1.28 TPSA 197.6 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…

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.