Protein profile

PA3540

GDP-mannose 6-dehydrogenase AlgD

Genome: NC_002516.2

Gene: PA3540 algD Structure source: Experimental + AlphaFold UniProt P11759
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Amino acids 436
Annotations 8
Features 32
PDB binders 5
Druggability 0.778

Overview

Basic information about this protein and its source genome.

Accession
PA3540
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3540 algD
Status
annotated
Amino acids
436
Structure source
Experimental + AlphaFold
EC
1.1.1.132
GO
GO:0047919 Catalysis of the reaction: GDP-alpha-D-mannose + H2O + 2 NAD+ = GDP-D-mannuronate + 3 H+ + 2 NADH. GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH. GO:0042121 The chemical reactions and pathways resulting in the formation of alginic acid, a hydrophilic polysaccharide occurring in, for example, the cell walls of brown algae (brown seaweeds). GO:0036460 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stress acting at the cell envelope. GO:0006970 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell. GO:0044010 A process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
33.929
Human E-value
1.84e-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 0.778
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0047919 Catalysis of the reaction: GDP-alpha-D-mannose + H2O + 2 NAD+ = GDP-D-mannuronate + 3 H+ + 2 NADH.
  • GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
  • GO:0042121 The chemical reactions and pathways resulting in the formation of alginic acid, a hydrophilic polysaccharide occurring in, for example, the cell walls of brown algae (brown seaweeds).
  • GO:0036460 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stress acting at the cell envelope.
  • GO:0006970 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell.
  • GO:0044010 A process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
  • GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
1 436 PIRSF PIRSF500135 GDPman_DH
1 436 InterPro IPR028358 GDP-mannose 6-dehydrogenase
16 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 16 SignalP_EUK SignalP-noTM SignalP-noTM
317 425 SMART SM00984 UDPG_MGDP_dh_C_a_2_a
317 425 InterPro IPR014027 UDP-glucose/GDP-mannose dehydrogenase, C-terminal
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
305 434 SUPERFAMILY SSF52413 UDP-glucose/GDP-mannose dehydrogenase C-terminal domain
305 434 InterPro IPR036220 UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily
235 436 FunFam G3DSA:3.40.50.720:FF:000664 GDP-mannose 6-dehydrogenase
1 202 Gene3D G3DSA:3.40.50.720 -
1 436 PIRSF PIRSF000124 UDPglc_GDPman_dh
1 436 InterPro IPR017476 UDP-glucose/GDP-mannose dehydrogenase
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
318 405 Pfam PF03720 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
318 405 InterPro IPR014027 UDP-glucose/GDP-mannose dehydrogenase, C-terminal
235 436 Gene3D G3DSA:3.40.50.720 -
1 190 Pfam PF03721 UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
1 190 InterPro IPR001732 UDP-glucose/GDP-mannose dehydrogenase, N-terminal
1 195 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
1 195 InterPro IPR036291 NAD(P)-binding domain superfamily
204 300 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like
204 300 InterPro IPR008927 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
21 436 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 410 NCBIfam TIGR03026 nucleotide sugar dehydrogenase
1 410 InterPro IPR017476 UDP-glucose/GDP-mannose dehydrogenase
1 404 PANTHER PTHR43750 UDP-GLUCOSE 6-DEHYDROGENASE TUAD
205 298 Pfam PF00984 UDP-glucose/GDP-mannose dehydrogenase family, central domain
205 298 InterPro IPR014026 UDP-glucose/GDP-mannose dehydrogenase, dimerisation
203 234 Gene3D G3DSA:1.20.5.170 -
4 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 202 FunFam G3DSA:3.40.50.720:FF:000573 GDP-mannose 6-dehydrogenase

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

3 + 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 1MV8
X-ray 1.55 Å A,B,C,D
100.0% 1-436
PDBe RCSB PDBj File
Viewing
PDB 1MUU
X-ray 2.02 Å A,B,C,D
100.0% 1-436
PDBe RCSB PDBj File
Loaded
PDB 1MFZ
X-ray 2.80 Å A,B,C,D
100.0% 1-436
PDBe RCSB PDBj File
Loaded
AlphaFold PA3540
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 0.778
2 0.211

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 13.66 0.695
2 10.82 0.581
3 9.3 0.499
4 8.31 0.443
5 3.74 0.143

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

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
GDX
1MFZ 2.80 Å Open crystal
619.3 Da LogP -4.54 TPSA 348.8 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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.