Protein profile

PA5162

dTDP-4-dehydrorhamnose reductase

Genome: NC_002516.2

Gene: PA5162 rmlD Structure source: AlphaFold UniProt Q9HU23
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Amino acids 302
Annotations 7
Features 11
PDB binders 3
Druggability 0.804

Overview

Basic information about this protein and its source genome.

Accession
PA5162
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA5162 rmlD
Status
annotated
Amino acids
302
Structure source
AlphaFold
EC
1.1.1.133
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0008831 Catalysis of the reaction: dTDP-6-deoxy-L-mannose + NADP+ = dTDP-4-dehydro-6-deoxy-L-mannose + H+ + NADPH. 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:0009243 The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide. GO:0000271 The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
32.911
Human E-value
2.32e-18
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 0.804
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008831 Catalysis of the reaction: dTDP-6-deoxy-L-mannose + NADP+ = dTDP-4-dehydro-6-deoxy-L-mannose + H+ + NADPH.
  • 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:0009243 The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
  • GO:0000271 The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
159 286 Gene3D G3DSA:3.90.25.10 -
2 297 PANTHER PTHR10491 DTDP-4-DEHYDRORHAMNOSE REDUCTASE
2 297 InterPro IPR005913 dTDP-4-dehydrorhamnose reductase family
4 283 Gene3D G3DSA:3.40.50.720 -
1 296 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
1 296 InterPro IPR036291 NAD(P)-binding domain superfamily
3 296 Pfam PF04321 RmlD substrate binding domain
3 296 InterPro IPR029903 RmlD-like substrate binding domain
3 286 CDD cd05254 dTDP_HR_like_SDR_e
3 295 NCBIfam TIGR01214 dTDP-4-dehydrorhamnose reductase
3 295 InterPro IPR005913 dTDP-4-dehydrorhamnose reductase family

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 PA5162
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
1 0.804
2 0.282

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.

55 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
STL
2YDX
Q9NZL9 228.2 Da LogP 2.97 TPSA 60.7 ✓ Ro5 ✓ Clean c1cc(ccc1\C=C\c2cc(cc(c2)O)O)O
TRH
1KC3
P26392 548.3 Da LogP -2.43 TPSA 256.5 3 viol. ✓ Clean C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O[P@](=O)(O)…
TXP
2YDX
Q9NZL9 747.4 Da LogP -3.18 TPSA 364.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.