Protein profile

VK055_5026

6-phosphogluconate dehydrogenase

Genome: KpATCC43816

Gene: AIK83552.1 gnd Structure source: Experimental + ColabFold UniProt A0A0J9WZ66
Amino acids 468
Annotations 6
Features 37
PDB binders 7
Druggability 0.687

Overview

Basic information about this protein and its source genome.

Accession
VK055_5026
Gene
AIK83552.1 gnd
Status
annotated
Amino acids
468
Structure source
Experimental + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
58.163
Human E-value
7.21e-76
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
86.141
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.99

Selected Druggability evidence

PDB experimental structure

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 0.687
Structure 2ZYG
Pocket Pocket 23
P2Rank 0.331
Structure 2ZYG
Pocket Pocket 1
ColabFold model
FPocket 0.625 · Pocket 17
P2Rank 0.409 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 637 / 4744 genomes with a hit
Normalized 0.134

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:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
  • 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:0004616 Catalysis of the reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH + H+.
  • GO:0006098 The metabolic process in which glucose-6-phosphate is oxidized to form carbon dioxide (CO2) and ribulose 5-phosphate, coupled to reduction of NADP+ to NADPH; ribulose 5-P then enters a series of reactions that can yield biosynthetic precursors (ribose-5-phosphate and erythrose-4-phosphate) and glycolytic intermediates (fructose-6-phosphate and glyceraldehyde-3-phosphate).
  • GO:0019521 The chemical reactions and pathways involving D-gluconate, the anion of D-gluconic acid, the aldonic acid derived from glucose.

Sequence Features

Domain/signature hits from InterPro and related databases.

37 records
Show feature table
Start End DB Term Name
181 434 FunFam G3DSA:1.10.1040.10:FF:000002 6-phosphogluconate dehydrogenase, decarboxylating
5 174 Pfam PF03446 NAD binding domain of 6-phosphogluconate dehydrogenase
5 174 InterPro IPR006115 6-phosphogluconate dehydrogenase, NADP-binding
181 434 Gene3D G3DSA:1.10.1040.10 -
181 434 InterPro IPR013328 6-phosphogluconate dehydrogenase, domain 2
2 180 FunFam G3DSA:3.40.50.720:FF:000007 6-phosphogluconate dehydrogenase, decarboxylating
179 466 Pfam PF00393 6-phosphogluconate dehydrogenase, C-terminal domain
179 466 InterPro IPR006114 6-phosphogluconate dehydrogenase, C-terminal
435 468 FunFam G3DSA:1.20.5.320:FF:000001 6-phosphogluconate dehydrogenase, decarboxylating
253 265 ProSitePatterns PS00461 6-phosphogluconate dehydrogenase signature.
253 265 InterPro IPR006184 6-phosphogluconate-binding site
4 173 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
4 173 InterPro IPR036291 NAD(P)-binding domain superfamily
177 467 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like
177 467 InterPro IPR008927 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
435 468 Gene3D G3DSA:1.20.5.320 -
1 180 Gene3D G3DSA:3.40.50.720 -
1 468 PIRSF PIRSF000109 6PGD
1 468 InterPro IPR006113 6-phosphogluconate dehydrogenase, decarboxylating
3 467 PANTHER PTHR11811 6-PHOSPHOGLUCONATE DEHYDROGENASE
3 467 InterPro IPR006183 6-phosphogluconate dehydrogenase
179 467 SMART SM01350 6PGD_2
179 467 InterPro IPR006114 6-phosphogluconate dehydrogenase, C-terminal
5 467 NCBIfam TIGR00873 decarboxylating NADP(+)-dependent phosphogluconate dehydrogenase
5 467 InterPro IPR006113 6-phosphogluconate dehydrogenase, decarboxylating
66 95 PRINTS PR00076 6-phosphogluconate dehydrogenase signature
66 95 InterPro IPR006183 6-phosphogluconate dehydrogenase
168 196 PRINTS PR00076 6-phosphogluconate dehydrogenase signature
168 196 InterPro IPR006183 6-phosphogluconate dehydrogenase
249 276 PRINTS PR00076 6-phosphogluconate dehydrogenase signature
249 276 InterPro IPR006183 6-phosphogluconate dehydrogenase
4 27 PRINTS PR00076 6-phosphogluconate dehydrogenase signature
4 27 InterPro IPR006183 6-phosphogluconate dehydrogenase
119 144 PRINTS PR00076 6-phosphogluconate dehydrogenase signature
119 144 InterPro IPR006183 6-phosphogluconate dehydrogenase
356 378 PRINTS PR00076 6-phosphogluconate dehydrogenase signature
356 378 InterPro IPR006183 6-phosphogluconate 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

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 2ZYG
X-ray 2.10 Å A,B
100.0% 1-468
Viewing
ColabFold VK055_5026
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
60 0.458
63 0.347
4 0.219

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 19.12 0.835
2 12.79 0.662
3 10.4 0.559
4 6.54 0.331
5 6.36 0.32

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.

61 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
2AM P00349 347.2 Da LogP -1.86 TPSA 186.1 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
3PG P52209 186.1 Da LogP -1.46 TPSA 124.3 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)OP(=O)(O)O
6PG P00350 276.1 Da LogP -3.38 TPSA 185.0 1 viol. ✓ Clean C([C@H]([C@H]([C@@H]([C@H](C(=O)O)O)O)O)O)OP(=O…
8HS P52209 271.2 Da LogP -0.88 TPSA 134.6 ✓ Ro5 ✓ Clean CC1(O[C@@H]([C@@H](O1)C(=O)NO)COP(=O)(O)O)C
ATR P00350 507.2 Da LogP -1.63 TPSA 279.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
NBP P00349 822.3 Da LogP -2.77 TPSA 367.6 3 viol. ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P…
POP P00349 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.