KpKP13 Protein target profile

Glycerophosphoryl diester phosphodiesterase

Accession: KP13_00960

Gene: AHE43510.1 glpQ 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H0Y9

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Length 356

Pocket druggability (P2Rank · AlphaFold DB model) 0.933

Direct ligand evidence 0 19 total records

Functional annotation 1 EC 5 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Moderate predicted binding pocket FPocket selected-pocket score 0.64. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.93. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 1 structural and 0 bioactivity records.

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target: Hit
Human identity (%): 32.584 Lower values reduce human off-target concern.
Human E-value: 4.6e-07
Gut microbiome similarity: 2.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 93.63 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.933

Structure A0A0H3H0Y9

Pocket Pocket 1

Druggability (FPocket) 0.642

Structure A0A0H3H0Y9

Pocket Pocket 2

ColabFold model

P2Rank 0.941 · Pocket 1

FPocket 0.686 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 130 / 4744 genomes with a hit

Prevalence 2.7%

Sequence

Primary amino-acid sequence viewer.

MKMKLTALMSGMILSSSALCFSATAADKMVIAHRGASGYLPEHTLPAKAMAYAQGAEYLEQDLVMTKDDRLVVLHDHYLDRVTDVAQRFPQRARQDGRFYAIDFTLAEIKSLKFTEGFEPKNGKNVQTYPGRFPMGKSDFRIHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAASTLKVLKEYGYTSKQDKVYLQCFDANELKRIKNELEPKMGMDLNLVQLIAYTDWNETQQKQADGKWVNYSYDWMFKPGAMAQIAQYADGIGPDYHMLVAEGSKPGAVKLTAMVKEAHASHLQVHPYTVRADQLPEYATNVNQLYDVLYNQAGVDGLFTDFPDKAVQFLDAKH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization: Periplasmic

Enzyme Commission (EC)

3.1.4.46

Gene Ontology (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: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 domains and features

Domain and signature matches imported from InterPro and related databases.

19 records

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; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low

How colors and pocket overlays are used

Uniform protein color marks the displayed model as a single molecular object.

Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.

Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.

'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.

'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.

'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.933

Likely same site as FPocket 2 4.9 Å 18 shared residues 82% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.073

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Surrounding area

Pocket 3 P2Rank #3

0.06

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Surrounding area

Pocket 4 P2Rank #4

0.014

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Surrounding area

Pocket 5 P2Rank #5

0.011

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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #2

0.642 Unusual size

Likely same site as P2Rank 1 4.9 Å 18 shared residues 82% of smaller site

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Surrounding area

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.941

Likely same site as FPocket 1 5.1 Å 16 shared residues 73% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.132

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Surrounding area

Pocket 3 P2Rank #3

0.065

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Surrounding area

Pocket 4 P2Rank #4

0.019

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Surrounding area

Pocket 5 P2Rank #5

0.017

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Surrounding area

All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold DB AF_A0A0H3H0Y9	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_00960	ColabFold	—	—	full sequence	—	Loaded

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.

19 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 18 similarity-based ZINC candidates

Best available ligand signal

G3P PDB via homolog 172.1 Da · LogP -1.55 · TPSA 107.2 Open detail RCSB PDB

ZINC1529618 ZINC proposed compound · Tanimoto 0.739 Detail ZINC

ZINC1529620 ZINC proposed compound · Tanimoto 0.739 Detail ZINC

ZINC5975509 ZINC proposed compound · Tanimoto 0.640 Detail ZINC

ZINC2516111 ZINC proposed compound · Tanimoto 0.593 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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 RCSB PDB	5T9B	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	0.567	215.1 Da LogP -1.57 TPSA 122.2	✓ Ro5	✓ Clean	`NCCO[P@@](=O)(O)OC[C@H](O)CO`
ZINC4095591 ZINC	0.567	215.1 Da LogP -1.57 TPSA 122.2	✓ Ro5	✓ Clean	`NCCO[P@@](=O)(O)OC[C@@H](O)CO`
ZINC1680142 ZINC	0.533	212.1 Da LogP -0.34 TPSA 96.2	✓ Ro5	✓ Clean	`C=CCOC[C@@H](O)COP(=O)(O)O`
ZINC5426687 ZINC	0.533	212.1 Da LogP -0.34 TPSA 96.2	✓ Ro5	✓ Clean	`C=CCOC[C@H](O)COP(=O)(O)O`
ZINC100067589 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3H0Y9