Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: KP13_01414
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE47416.1
Status: annotated
Amino acids: 187
Structure source: AlphaFold + ColabFold

EC

3.1.4.4

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:0004630 A glycerophospholipase activity that cleaves the second phosphodiester bond between the phosphate and phospholipid, releasing a phosphatidic acid. GO:0016891 Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters. GO:0016042 The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. GO:0006793 The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 29.464
Human E-value: 6.74e-11
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Unknown
ColabFold pLDDT: 88.01

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 L0B968

Pocket Pocket 6

P2Rank 0.01

Structure L0B968

Pocket Pocket 1

ColabFold model

FPocket 0.348 · Pocket 2

P2Rank 0.049 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 7 / 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 5 GO

Enzyme Commission (EC)

1

3.1.4.4

Gene Ontology (GO)

5

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:0004630 A glycerophospholipase activity that cleaves the second phosphodiester bond between the phosphate and phospholipid, releasing a phosphatidic acid.
GO:0016891 Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
GO:0016042 The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
GO:0006793 The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
1	18	SignalP_EUK	SignalP-noTM	SignalP-noTM
38	179	CDD	cd09170	PLDc_Nuc
121	148	ProSiteProfiles	PS50035	Phospholipase D phosphodiesterase active site profile.
121	148	InterPro	IPR001736	Phospholipase D/Transphosphatidylase
1	23	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
5	16	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
54	177	Pfam	PF13091	PLD-like domain
54	177	InterPro	IPR025202	Phospholipase D-like domain
1	23	Phobius	SIGNAL_PEPTIDE	Signal peptide region
1	23	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
121	148	SMART	SM00155	pld_4
36	184	Gene3D	G3DSA:3.30.870.10	Endonuclease Chain A
24	187	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
17	23	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
36	183	PANTHER	PTHR43856	CARDIOLIPIN HYDROLASE
44	182	SUPERFAMILY	SSF56024	Phospholipase D/nuclease
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...

Legend High Medium Low

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_L0B968	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01414	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				0.348

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				1.28	0.013
2				0.92	0.004

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.

1 records

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
WO4	4GGK	Q5SWZ9	247.8 Da LogP -2.62 TPSA 80.3	✓ Ro5	✓ Clean	`[O-][W](=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).

No virtual-screening candidates for this protein.

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.

KP13_01414