Protein profile

KP13_01206

Putative glycerophosphoryl diester phosphodiesterase

Genome: KpKP13

Gene: AHE46575.1 Structure source: AlphaFold + ColabFold UniProt A0A486CX06
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Amino acids 276
Annotations 4
Features 9
PDB binders 2
Druggability 0.456

Overview

Basic information about this protein and its source genome.

Accession
KP13_01206
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46575.1
Status
annotated
Amino acids
276
Structure source
AlphaFold + ColabFold
EC
3.1.4.46
GO
GO:0008081 Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group. GO:0006629 The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. GO:0008889 Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
37.879
Human E-value
1.16e-07
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.92

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 0.456
Structure A0A486CX06
Pocket Pocket 4
P2Rank 0.788
Structure A0A486CX06
Pocket Pocket 1
ColabFold model
FPocket 0.098 · Pocket 2
P2Rank 0.687 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 3 / 4744 genomes with a hit
Normalized 0.001

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0008081 Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
  • GO:0006629 The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
  • GO:0008889 Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

9 records
Show feature table
Start End DB Term Name
18 139 Pfam PF03009 Glycerophosphoryl diester phosphodiesterase family
18 139 InterPro IPR030395 Glycerophosphodiester phosphodiesterase domain
13 260 ProSiteProfiles PS51704 GP-PDE domain profile.
13 260 InterPro IPR030395 Glycerophosphodiester phosphodiesterase domain
13 227 PANTHER PTHR46211 GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
15 265 SUPERFAMILY SSF51695 PLC-like phosphodiesterases
15 265 InterPro IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily
11 236 Gene3D G3DSA:3.20.20.190 Phosphatidylinositol (PI) phosphodiesterase
11 236 InterPro IPR017946 PLC-like phosphodiesterase, TIM beta/alpha-barrel 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

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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_A0A486CX06
AlphaFold — — full sequence — Viewing
ColabFold KP13_01206
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 0.456
1 0.358
8 0.296

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 14.42 0.722
2 1.8 0.034
3 1.3 0.014

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.

52 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
G3P
5T9B
P37965 172.1 Da LogP -1.55 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@H](COP(=O)(O)O)O)O
PE4
3MZ2
A6LIT8 354.4 Da LogP 0.11 TPSA 84.8 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCO

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.