Protein profile

VK055_2592

phosphopentomutase

Genome: KpATCC43816

Gene: deoB AIK81189.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GHY4
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Amino acids 407
Annotations 12
Features 20
PDB binders 4
Druggability 0.193

Overview

Basic information about this protein and its source genome.

Accession
VK055_2592
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
deoB AIK81189.1
Status
annotated
Amino acids
407
Structure source
AlphaFold + ColabFold
EC
5.4.2.7
GO
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0043094 Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells. GO:0008973 Catalysis of the reaction: D-ribose 1-phosphate = D-ribose 5-phosphate. Also converts 2-deoxy-alpha-D-ribose 1-phosphate into 2-deoxy-D-ribose 5-phosphate. GO:0046872 Binding to a metal ion. GO:0009117 The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates). GO:0000287 Binding to a magnesium (Mg) ion.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
43.276
DEG E-value
2.61e-95
Localization
Cytoplasmic
ColabFold pLDDT
96.82

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 0.193
Structure A0A0H3GHY4
Pocket Pocket 4
P2Rank 0.492
Structure A0A0H3GHY4
Pocket Pocket 1
ColabFold model
FPocket 0.59 · Pocket 2
P2Rank 0.491 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 204 / 4744 genomes with a hit
Normalized 0.043

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0043094 Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells.
  • GO:0008973 Catalysis of the reaction: D-ribose 1-phosphate = D-ribose 5-phosphate. Also converts 2-deoxy-alpha-D-ribose 1-phosphate into 2-deoxy-D-ribose 5-phosphate.
  • GO:0046872 Binding to a metal ion.
  • GO:0009117 The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0030145 Binding to a manganese ion (Mn).
  • GO:0006018 The chemical reactions and pathways resulting in the breakdown of deoxyribose 1-phosphate, the phosphorylated sugar 1-phospho-2-deoxyribose.
  • GO:0006015 The chemical reactions and pathways resulting in the formation of 5-phosphoribose 1-diphosphate, also known as 5-phosphoribosyl-1-pyrophosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
2 406 CDD cd16009 PPM
2 406 InterPro IPR010045 Phosphopentomutase
1 407 Hamap MF_00740 Phosphopentomutase [deoB].
1 407 InterPro IPR010045 Phosphopentomutase
2 398 Pfam PF01676 Metalloenzyme superfamily
2 398 InterPro IPR006124 Metalloenzyme
3 405 NCBIfam TIGR01696 phosphopentomutase
3 405 InterPro IPR010045 Phosphopentomutase
1 406 SUPERFAMILY SSF53649 Alkaline phosphatase-like
1 406 InterPro IPR017850 Alkaline-phosphatase-like, core domain superfamily
1 407 PIRSF PIRSF001491 Ppentomutase
3 406 Gene3D G3DSA:3.40.720.10 Alkaline Phosphatase, subunit A
3 406 InterPro IPR017850 Alkaline-phosphatase-like, core domain superfamily
115 235 FunFam G3DSA:3.30.70.1250:FF:000001 Phosphopentomutase
116 240 Gene3D G3DSA:3.30.70.1250 Phosphopentomutase
116 240 InterPro IPR024052 Phosphopentomutase DeoB cap domain superfamily
117 235 SUPERFAMILY SSF143856 DeoB insert domain-like
117 235 InterPro IPR024052 Phosphopentomutase DeoB cap domain superfamily
1 406 PANTHER PTHR21110 PHOSPHOPENTOMUTASE
1 406 InterPro IPR010045 Phosphopentomutase

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_A0A0H3GHY4
AlphaFold — — full sequence — Viewing
ColabFold VK055_2592
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 5.48 0.261
2 1.95 0.041

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
1X4
4LRE
Q818Z9 198.1 Da LogP -0.41 TPSA 96.2 ✓ Ro5 ✓ Clean C1C[C@H](O[C@@H]1COP(=O)(O)O)O
AZI
4N7T
Q8DTU0 42.0 Da LogP 0.87 TPSA 58.7 ✓ Ro5 Alert [N-]=[N+]=[N-]
G16
3OT9
Q818Z9 339.1 Da LogP -3.62 TPSA 206.3 1 viol. ✓ Clean C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[P@](=O)(…
HSX
3M8Z
Q818Z9 230.1 Da LogP -2.47 TPSA 136.7 ✓ Ro5 ✓ Clean C([C@@H]1[C@H]([C@H]([C@H](O1)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.