Protein profile

PA0607

ribulose-phosphate 3-epimerase

Genome: NC_002516.2

Gene: rpe PA0607 Structure source: Experimental + AlphaFold UniProt Q9I5T1
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Amino acids 224
Annotations 9
Features 21
PDB binders 5
Druggability 0.753

Overview

Basic information about this protein and its source genome.

Accession
PA0607
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
rpe PA0607
Status
annotated
Amino acids
224
Structure source
Experimental + AlphaFold
EC
5.1.3.1
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:0004750 Catalysis of the reaction: D-ribulose 5-phosphate = D-xylulose 5-phosphate. GO:0046872 Binding to a metal ion. GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0019323 The chemical reactions and pathways resulting in the breakdown of a pentose, any monosaccharide with a chain of five carbon atoms in the molecule. GO:0009052 The branch of the pentose-phosphate shunt which does not involve oxidation reactions. It comprises a series of sugar phosphate interconversions, starting with ribulose 5-P and producing fructose 6-P and glyceraldehyde 3-P.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
39.459
Human E-value
2.14e-39
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 0.753
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MQPFAIAPSILSADFARLGEDVDKVLAAGADIVHFDVMDNHYVPNLTIGPMVCSALRKYGVSAPIDVHLMVSPVDRIIGDFIEAGATYITFHPEASQHIDRSLQLIRDGGCKAGLVFNPATPLEVLKYVMDKVDMVLLMSVNPGFGGQKFIPGTLDKLREARALIDASGREIRLEIDGGVNVKNIREIAAAGADTFVAGSAIFNAPDYAEVIRAMHAELAQAHQ

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004750 Catalysis of the reaction: D-ribulose 5-phosphate = D-xylulose 5-phosphate.
  • GO:0046872 Binding to a metal ion.
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0019323 The chemical reactions and pathways resulting in the breakdown of a pentose, any monosaccharide with a chain of five carbon atoms in the molecule.
  • GO:0009052 The branch of the pentose-phosphate shunt which does not involve oxidation reactions. It comprises a series of sugar phosphate interconversions, starting with ribulose 5-P and producing fructose 6-P and glyceraldehyde 3-P.
  • 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:0016857 Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
1 222 FunFam G3DSA:3.20.20.70:FF:000004 Ribulose-phosphate 3-epimerase
136 158 ProSitePatterns PS01086 Ribulose-phosphate 3-epimerase family signature 2.
136 158 InterPro IPR000056 Ribulose-phosphate 3-epimerase-like
6 216 CDD cd00429 RPE
6 216 InterPro IPR000056 Ribulose-phosphate 3-epimerase-like
4 217 SUPERFAMILY SSF51366 Ribulose-phoshate binding barrel
4 217 InterPro IPR011060 Ribulose-phosphate binding barrel
33 47 ProSitePatterns PS01085 Ribulose-phosphate 3-epimerase family signature 1.
33 47 InterPro IPR000056 Ribulose-phosphate 3-epimerase-like
6 203 Pfam PF00834 Ribulose-phosphate 3 epimerase family
6 203 InterPro IPR000056 Ribulose-phosphate 3-epimerase-like
6 216 NCBIfam TIGR01163 ribulose-phosphate 3-epimerase
6 216 InterPro IPR026019 Ribulose-phosphate 3-epimerase
1 224 PIRSF PIRSF001461 RPE
1 224 InterPro IPR026019 Ribulose-phosphate 3-epimerase
1 223 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 223 InterPro IPR013785 Aldolase-type TIM barrel
5 223 PANTHER PTHR11749 RIBULOSE-5-PHOSPHATE-3-EPIMERASE
5 223 InterPro IPR000056 Ribulose-phosphate 3-epimerase-like
3 218 Hamap MF_02227 Ribulose-phosphate 3-epimerase [rpe].
3 218 InterPro IPR026019 Ribulose-phosphate 3-epimerase

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 7U5Y
X-ray 2.55 Å A,B,C,D,E,F
100.0% 1-224
PDBe RCSB PDBj File
Viewing
AlphaFold PA0607
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
2 0.753

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 13.47 0.687

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
5RP
3OVQ
Q96AT9 230.1 Da LogP -2.62 TPSA 144.5 ✓ Ro5 ✓ Clean C([C@H]([C@H](C(=O)CO)O)O)OP(=O)(O)O
5SP
3OVR
Q96AT9 230.1 Da LogP -2.62 TPSA 144.5 ✓ Ro5 ✓ Clean C([C@H]([C@@H](C(=O)CO)O)O)OP(=O)(O)O
DX5
2FLI
Q9A1H8 232.1 Da LogP -2.83 TPSA 147.7 1 viol. ✓ Clean C([C@@H]([C@H]([C@@H](COP(=O)(O)O)O)O)O)O
S6P
3CTL
P32719 262.2 Da LogP -3.47 TPSA 167.9 1 viol. ✓ Clean C([C@@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)…
XPE
3OVP
Q96AT9 458.5 Da LogP -0.88 TPSA 123.5 1 viol. ✓ Clean C(COCCOCCOCCOCCOCCOCCOCCOCCOCCO)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.