Protein profile

KP13_01944

L-ribulose-5-phosphate 4-epimerase

Genome: KpKP13

Gene: araD AHE46383.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GMG9
Export view
Amino acids 231
Annotations 7
Features 15
PDB binders 2
Druggability 0.405

Overview

Basic information about this protein and its source genome.

Accession
KP13_01944
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
araD AHE46383.1
Status
annotated
Amino acids
231
Structure source
AlphaFold + ColabFold
EC
5.1.3.4
GO
GO:0019572 The chemical reactions and pathways resulting in the breakdown of L-arabinose, the L-enantiomer of arabino-pentose. GO:0008270 Binding to a zinc ion (Zn). GO:0019569 The chemical reactions and pathways resulting in the breakdown of L-arabinose into D-xylulose 5-phosphate. GO:0008742 Catalysis of the reaction: L-ribulose 5-phosphate = D-xylulose 5-phosphate. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0016832 Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.71

Selected Druggability evidence

AlphaFold / UniProt model

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 0.405
Structure A0A0H3GMG9
Pocket Pocket 4
P2Rank 0.583
Structure A0A0H3GMG9
Pocket Pocket 1
ColabFold model
FPocket 0.646 · Pocket 1
P2Rank 0.538 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1225 / 4744 genomes with a hit
Normalized 0.258

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:0019572 The chemical reactions and pathways resulting in the breakdown of L-arabinose, the L-enantiomer of arabino-pentose.
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0019569 The chemical reactions and pathways resulting in the breakdown of L-arabinose into D-xylulose 5-phosphate.
  • GO:0008742 Catalysis of the reaction: L-ribulose 5-phosphate = D-xylulose 5-phosphate.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0016832 Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
8 195 Pfam PF00596 Class II Aldolase and Adducin N-terminal domain
8 195 InterPro IPR001303 Class II aldolase/adducin N-terminal
1 231 Gene3D G3DSA:3.40.225.10 -
1 231 InterPro IPR036409 Class II aldolase/adducin N-terminal domain superfamily
1 231 FunFam G3DSA:3.40.225.10:FF:000001 L-ribulose-5-phosphate 4-epimerase UlaF
1 231 NCBIfam TIGR00760 L-ribulose-5-phosphate 4-epimerase
1 231 InterPro IPR004661 L-ribulose-5-phosphate 4-epimerase
1 231 Hamap MF_00989 L-ribulose-5-phosphate 4-epimerase [araD].
1 231 InterPro IPR033748 L-ribulose-5-phosphate 4-epimerase AraD
2 230 PANTHER PTHR22789 FUCULOSE PHOSPHATE ALDOLASE
3 223 CDD cd00398 Aldolase_II
7 198 SMART SM01007 Aldolase_II_2
7 198 InterPro IPR001303 Class II aldolase/adducin N-terminal
1 223 SUPERFAMILY SSF53639 AraD/HMP-PK domain-like
1 223 InterPro IPR036409 Class II aldolase/adducin N-terminal domain superfamily

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

Loading 3D structure...

Legend High Medium Low

Structural evidence

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GMG9
AlphaFold — — full sequence — Viewing
ColabFold KP13_01944
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
4 0.405

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 6.97 0.36
2 6.69 0.34
3 1.13 0.008
4 1.03 0.006

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.

2 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
13P
1E47
P0AB87 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)COP(=O)(O)O)O
PGH
4FUA
P0AB87 171.0 Da LogP -1.40 TPSA 116.1 ✓ Ro5 ✓ Clean C(C(=O)NO)OP(=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.