Protein profile

KP13_02167

Ribose-5-phosphate isomerase A

Genome: KpKP13

Gene: AHE42737.1 rpiA Structure source: AlphaFold + ColabFold UniProt A0A0H3GXD5
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Amino acids 219
Annotations 5
Features 17
PDB binders 4
Druggability 0.176

Overview

Basic information about this protein and its source genome.

Accession
KP13_02167
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42737.1 rpiA
Status
annotated
Amino acids
219
Structure source
AlphaFold + ColabFold
EC
5.3.1.6
GO
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:0004751 Catalysis of the reaction: aldehydo-D-ribose 5-phosphate = D-ribulose 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:0006014 The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
37.054
Human E-value
8.580000000000001e-31
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
95.89
DEG E-value
4.92e-152
Localization
Cytoplasmic
ColabFold pLDDT
97.72

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 0.176
Structure A0A0H3GXD5
Pocket Pocket 1
P2Rank 0.438
Structure A0A0H3GXD5
Pocket Pocket 1
ColabFold model
FPocket 0.226 · Pocket 9
P2Rank 0.619 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 279 / 4744 genomes with a hit
Normalized 0.059

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • 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:0004751 Catalysis of the reaction: aldehydo-D-ribose 5-phosphate = D-ribulose 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:0006014 The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
125 196 FunFam G3DSA:3.30.70.260:FF:000004 Ribose-5-phosphate isomerase A
6 215 NCBIfam TIGR00021 ribose 5-phosphate isomerase A
6 215 InterPro IPR004788 Ribose 5-phosphate isomerase, type A
2 146 SUPERFAMILY SSF100950 NagB/RpiA/CoA transferase-like
2 146 InterPro IPR037171 NagB/RpiA transferase-like
3 217 Hamap MF_00170 Ribose-5-phosphate isomerase A [rpiA].
3 217 InterPro IPR020672 Ribose-5-phosphate isomerase, type A, subgroup
6 209 Gene3D G3DSA:3.40.50.1360 -
127 198 SUPERFAMILY SSF75445 D-ribose-5-phosphate isomerase (RpiA), lid domain
6 210 CDD cd01398 RPI_A
6 210 InterPro IPR004788 Ribose 5-phosphate isomerase, type A
6 137 FunFam G3DSA:3.40.50.1360:FF:000001 Ribose-5-phosphate isomerase A
49 213 Pfam PF06026 Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
49 213 InterPro IPR004788 Ribose 5-phosphate isomerase, type A
2 218 PANTHER PTHR11934 RIBOSE-5-PHOSPHATE ISOMERASE
2 218 InterPro IPR004788 Ribose 5-phosphate isomerase, type A
125 196 Gene3D G3DSA:3.30.70.260 -

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

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_A0A0H3GXD5
AlphaFold — — full sequence — Viewing
ColabFold KP13_02167
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 4.08 0.164

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.

54 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
4M8L
A4IYN5 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
ARF
4M8L
A4IYN5 45.0 Da LogP -0.90 TPSA 43.1 ✓ Ro5 ✓ Clean C(=O)N
FLC
4X84
Q9I6G1 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
R5P
3UW1
Q2SVL4 230.1 Da LogP -2.62 TPSA 144.5 ✓ Ro5 ✓ Clean C(C(C(C(C=O)O)O)O)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.