Protein profile
KP13_00960
Glycerophosphoryl diester phosphodiesterase
Genome: KpKP13
Overview
Basic information about this protein and its source genome.
- Accession
- KP13_00960
- Gene
- glpQ AHE43510.1
- Status
- annotated
- Amino acids
- 356
- Structure source
- AlphaFold + ColabFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 32.584
- Human E-value
- 4.6e-07
- Gut microbiome off-target
- hit
- Essential (DEG)
- N
- DEG identity (%)
- 0.0
- Localization
- Periplasmic
- ColabFold pLDDT
- 93.63
Selected Druggability evidence
AlphaFold / UniProt modelSelected 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.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
5- 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:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
- GO:0008889 Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.
- GO:0006071 The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 26 | 353 | FunFam | G3DSA:3.20.20.190:FF:000009 | Glycerophosphodiester phosphodiesterase, periplasmic |
| 33 | 347 | Pfam | PF03009 | Glycerophosphoryl diester phosphodiesterase family |
| 33 | 347 | InterPro | IPR030395 | Glycerophosphodiester phosphodiesterase domain |
| 1 | 25 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM |
| 15 | 353 | PANTHER | PTHR43620 | GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE |
| 29 | 352 | SUPERFAMILY | SSF51695 | PLC-like phosphodiesterases |
| 29 | 352 | InterPro | IPR017946 | PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily |
| 23 | 356 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 28 | 346 | CDD | cd08600 | GDPD_EcGlpQ_like |
| 15 | 22 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 28 | 352 | ProSiteProfiles | PS51704 | GP-PDE domain profile. |
| 28 | 352 | InterPro | IPR030395 | Glycerophosphodiester phosphodiesterase domain |
| 27 | 353 | Gene3D | G3DSA:3.20.20.190 | Phosphatidylinositol (PI) phosphodiesterase |
| 27 | 353 | InterPro | IPR017946 | PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily |
| 1 | 25 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM |
| 5 | 14 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. |
| 1 | 26 | SignalP_EUK | SignalP-noTM | SignalP-noTM |
| 1 | 22 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
| 1 | 4 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
3D Structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.
Loading 3D structure...
Structural evidence
0 + 2Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
AF_A0A0H3H0Y9
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_00960
|
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 |
|---|---|---|---|---|---|---|---|
| 2 | 0.642 |
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 | 23.54 | 0.89 | ||||||
| 2 | 1.83 | 0.035 | ||||||
| 3 | 1.48 | 0.02 | ||||||
| 4 | 0.91 | 0.004 |
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 |
|---|---|---|---|---|---|---|---|
| 1 | 0.686 |
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 | 25.62 | 0.908 | ||||||
| 2 | 2.05 | 0.045 | ||||||
| 3 | 1.96 | 0.041 | ||||||
| 4 | 0.99 | 0.005 |
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.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| G3P | P37965 | 172.1 Da LogP -1.55 TPSA 107.2 | ✓ Ro5 | ✓ Clean |
C([C@H](COP(=O)(O)O)O)O
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC1529618 | 0.739 | 246.2 Da LogP -2.17 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(OC[C@@H](O)CO)OC[C@H](O)CO
|
| ZINC1529620 | 0.739 | 246.2 Da LogP -2.17 TPSA 136.7 | ✓ Ro5 | ✓ Clean |
O=P(O)(OC[C@@H](O)CO)OC[C@@H](O)CO
|
| ZINC5975509 | 0.640 | 202.1 Da LogP -2.19 TPSA 127.5 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)OC[C@H](O)[C@H](O)CO
|
| ZINC2516111 | 0.593 | 262.2 Da LogP -3.47 TPSA 167.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO
|
| ZINC2522704 | 0.593 | 262.2 Da LogP -3.47 TPSA 167.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO
|
| ZINC3869812 | 0.593 | 262.2 Da LogP -3.47 TPSA 167.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO
|
| ZINC4095590 | 0.567 | 215.1 Da LogP -1.57 TPSA 122.2 | ✓ Ro5 | ✓ Clean |
NCCO[P@@](=O)(O)OC[C@H](O)CO
|
| ZINC4095591 | 0.567 | 215.1 Da LogP -1.57 TPSA 122.2 | ✓ Ro5 | ✓ Clean |
NCCO[P@@](=O)(O)OC[C@@H](O)CO
|
| ZINC1680142 | 0.533 | 212.1 Da LogP -0.34 TPSA 96.2 | ✓ Ro5 | ✓ Clean |
C=CCOC[C@@H](O)COP(=O)(O)O
|
| ZINC5426687 | 0.533 | 212.1 Da LogP -0.34 TPSA 96.2 | ✓ Ro5 | ✓ Clean |
C=CCOC[C@H](O)COP(=O)(O)O
|
| ZINC100067589 | 0.531 | 334.2 Da LogP -4.34 TPSA 197.4 | 1 viol. | ✓ Clean |
O=[P@@](O)(OC[C@H](O)CO)O[C@H]1[C@H](O)[C@@H](O…
|
| ZINC100620818 | 0.531 | 334.2 Da LogP -4.34 TPSA 197.4 | 1 viol. | ✓ Clean |
O=[P@@](O)(OC[C@H](O)CO)O[C@H]1[C@@H](O)[C@@H](…
|
| ZINC1532714 | 0.515 | 258.2 Da LogP -0.82 TPSA 96.2 | ✓ Ro5 | ✓ Clean |
C[N+](C)(C)CCO[P@@](=O)(O)OC[C@H](O)CO
|
| ZINC1842903 | 0.515 | 258.2 Da LogP -0.82 TPSA 96.2 | ✓ Ro5 | ✓ Clean |
C[N+](C)(C)CCO[P@](=O)(O)OC[C@@H](O)CO
|
| ZINC1529626 | 0.500 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC1532567 | 0.500 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC1532851 | 0.500 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC30320708 | 0.500 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C(CO)[C@@H](O)[C@H](O)COP(=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.