Protein profile

PA5454

oxidoreductase Rmd

Genome: NC_002516.2

Gene: rmd PA5454 Structure source: Experimental + AlphaFold UniProt Q9HTB6
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Amino acids 304
Annotations 7
Features 7
PDB binders 6
Druggability 0.735

Overview

Basic information about this protein and its source genome.

Accession
PA5454
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
rmd PA5454
Status
annotated
Amino acids
304
Structure source
Experimental + AlphaFold
EC
1.1.1.281
GO
GO:0033705 Catalysis of the reaction: GDP-6-deoxy-D-mannose + NAD(P)+ = GDP-4-dehydro-6-deoxy-D-mannose + NAD(P)H + H+. GO:0070402 Binding to the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions. 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:0019306 The chemical reactions and pathways resulting in the formation of GDP-D-rhamnose, a substance composed of rhamnose in glycosidic linkage with guanosine diphosphate. GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
36.735
Human E-value
9.25e-08
Gut microbiome off-target
hit
Essential (DEG)
N
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 0.735
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MTQRLFVTGLSGFVGKHLQAYLAAAHTPWALLPVPHRYDLLEPDSLGDLWPELPDAVIHLAGQTYVPEAFRDPARTLQINLLGTLNLLQALKARGFSGTFLYISSGDVYGQVAEAALPIHEELIPHPRNPYAVSKLAAESLCLQWGITEGWRVLVARPFNHIGPGQKDSFVIASAARQIARMKQGLQANRLEVGDIDVSRDFLDVQDVLSAYLRLLSHGEAGAVYNVCSGQEQKIRELIELLADIAQVELEIVQDPARMRRAEQRRVRGSHARLHDTTGWKPEITIKQSLRAILSDWESRVREE

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:0033705 Catalysis of the reaction: GDP-6-deoxy-D-mannose + NAD(P)+ = GDP-4-dehydro-6-deoxy-D-mannose + NAD(P)H + H+.
  • GO:0070402 Binding to the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
  • 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:0019306 The chemical reactions and pathways resulting in the formation of GDP-D-rhamnose, a substance composed of rhamnose in glycosidic linkage with guanosine diphosphate.
  • GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

7 records
Show feature table
Start End DB Term Name
167 291 Gene3D G3DSA:3.90.25.10 -
3 299 PANTHER PTHR43000 DTDP-D-GLUCOSE 4,6-DEHYDRATASE-RELATED
3 299 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
3 299 InterPro IPR036291 NAD(P)-binding domain superfamily
4 283 Gene3D G3DSA:3.40.50.720 -
36 291 Pfam PF16363 GDP-mannose 4,6 dehydratase
36 291 InterPro IPR016040 NAD(P)-binding domain

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

1 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 6X3B
X-ray 1.91 Å A,B,C,D
100.0% 1-304
PDBe RCSB PDBj File
Viewing
AlphaFold PA5454
AlphaFold — — 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 0.735

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 32.43 0.943
2 1.11 0.008
3 1.1 0.007

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.

56 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
POP
6X3B 1.91 Å Open crystal
176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(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.