KpKP13 Protein target profile

Phospholipase A1 bifunctional protein

Accession: KP13_01718

Gene: pldA AHE46978.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GGK3

Export view

Length 286

Pocket druggability (P2Rank · AlphaFold DB model) 0.909

Direct ligand evidence 0 51 total records

Functional annotation 2 EC 8 GO

Target summary

Promising target candidate with multiple supporting evidence streams.

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

Main supporting evidence

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: No hit
Gut microbiome similarity: 2.2% 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: 92.34 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) 0.909

Structure A0A0H3GGK3

Pocket Pocket 1

Druggability (FPocket) 0.67

Structure A0A0H3GGK3

Pocket Pocket 8

ColabFold model

P2Rank 0.903 · Pocket 1

FPocket 0.974 · Pocket 25

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 104 / 4744 genomes with a hit

Prevalence 2.2%

Sequence

Primary amino-acid sequence viewer.

MRISLACLVALCALPAGVMAQDASVHDKPAVRGSIIANLLQDHDNPFLLYPYESNYLLYTWTSDLNKEAIRSYDWAENARKDEVKFQLSLAFPLWRGILGDNSLLGASYTQKSWWQLSNSKESAPFRETNYEPQLFLGFATDYQFAGWTLRDIEMGYNHDSNGRSDPTSRSWNRLYARLMAQNGNWLVEVKPWYVVGNTDDNPDITKYMGYYRLKVGYQLGEAILSAQGQYNWNTGYGGAELGVSYPITKHVRAYTQIYSGYGESLIDYNFNQTRVGVGLMLNDLF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 8 GO

Subcellular localization

Localization: OuterMembrane

Enzyme Commission (EC)

Gene Ontology (GO)

GO:0004620 Catalysis of the hydrolysis of a glycerophospholipid.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
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:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
GO:0005509 Binding to a calcium ion (Ca2+).
GO:0008970 Catalysis of the reaction: a 1,2-diacyl-sn-glycero-3-phospholipid + H2O = a 2-acyl-sn-glycero-3-phospholipid + a fatty acid + H+. Note that the substrate has a diacyl group attached to the glycerol group.
GO:0004623 A glycerophospholipase activity that cleaves the fatty acid attached to the sn-2 position of the glycerol group of a glycerophospholipid. Substrates include phosphatidylcholine, phosphatidylethanolamine, choline plasmalogen and phosphatides.
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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

34 records

Show feature table

Start	End	DB	Term	Name
37	285	SUPERFAMILY	SSF56931	Outer membrane phospholipase A (OMPLA)
37	285	InterPro	IPR036541	Phospholipase A1 superfamily
47	277	CDD	cd00541	OMPLA
47	277	InterPro	IPR003187	Phospholipase A1
41	282	Pfam	PF02253	Phospholipase A1
41	282	InterPro	IPR003187	Phospholipase A1
1	20	Phobius	SIGNAL_PEPTIDE	Signal peptide region
30	286	Gene3D	G3DSA:2.40.230.10	Phospholipase A1
30	286	InterPro	IPR036541	Phospholipase A1 superfamily
1	2	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
24	286	PANTHER	PTHR40457	PHOSPHOLIPASE A1
24	286	InterPro	IPR003187	Phospholipase A1
153	167	PRINTS	PR01486	Bacterial phospholipase A1 protein signature
153	167	InterPro	IPR003187	Phospholipase A1
123	142	PRINTS	PR01486	Bacterial phospholipase A1 protein signature
123	142	InterPro	IPR003187	Phospholipase A1
233	250	PRINTS	PR01486	Bacterial phospholipase A1 protein signature
233	250	InterPro	IPR003187	Phospholipase A1
100	116	PRINTS	PR01486	Bacterial phospholipase A1 protein signature
100	116	InterPro	IPR003187	Phospholipase A1
200	218	PRINTS	PR01486	Bacterial phospholipase A1 protein signature
200	218	InterPro	IPR003187	Phospholipase A1
168	186	PRINTS	PR01486	Bacterial phospholipase A1 protein signature
168	186	InterPro	IPR003187	Phospholipase A1
255	275	PRINTS	PR01486	Bacterial phospholipase A1 protein signature
255	275	InterPro	IPR003187	Phospholipase A1
78	95	PRINTS	PR01486	Bacterial phospholipase A1 protein signature
78	95	InterPro	IPR003187	Phospholipase A1
30	286	FunFam	G3DSA:2.40.230.10:FF:000001	Phospholipase A(1)
1	20	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
21	286	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
15	20	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	22	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
3	14	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic 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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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

0.909

Show in viewer

Surrounding area

Pocket 2 P2Rank #2

0.041

Show in viewer

Surrounding area

Pocket 3 P2Rank #3

0.011

Show in viewer

Surrounding area

Pocket 4 P2Rank #4

0.008

Show in viewer

Surrounding area

Pocket 5 P2Rank #5

0.005

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #8

0.67

Show in viewer

Surrounding area

Pocket 2 FPocket #5

0.395

Show in viewer

Surrounding area

Pocket 3 FPocket #14

0.309

Show in viewer

Surrounding area

Residue sets

UniProt: Active site:159-159 Proton acceptor

UniProt: Active site:161-161 Nucleophile

UniProt: Binding site:123-123 in dimeric form

UniProt: Binding site:164-164 in dimeric form

UniProt: Binding site:169-169 in dimeric form

UniProt: Binding site:201-201 in dimeric form

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.903

Show in viewer

Surrounding area

Pocket 2 P2Rank #2

0.093

Likely same site as FPocket 25 4.8 Å 14 shared residues 100% of smaller site

Show in viewer

Surrounding area

Pocket 3 P2Rank #3

0.053

Show in viewer

Surrounding area

Pocket 4 P2Rank #4

0.021

Show in viewer

Surrounding area

Pocket 5 P2Rank #5

0.021

Show in viewer

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_A0A0H3GGK3	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_01718	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.

51 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 50 similarity-based ZINC candidates

Best available ligand signal

HDS PDB via homolog 306.5 Da · LogP 5.36 · TPSA 54.4 Open detail RCSB PDB

ZINC100019805 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC1625794 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC1651926 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC1843748 ZINC proposed compound · Tanimoto 1.000 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
HDS RCSB PDB	1QD6	P0A921	306.5 Da LogP 5.36 TPSA 54.4	1 viol.	✓ Clean	`CCCCCCCCCCCCCCCCS(=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
ZINC100019805 ZINC	1.000	292.5 Da LogP 4.97 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCS(=O)(=O)O`
ZINC1625794 ZINC	1.000	264.4 Da LogP 4.19 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCS(=O)(=O)O`
ZINC1651926 ZINC	1.000	250.4 Da LogP 3.80 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCS(=O)(=O)O`
ZINC1843748 ZINC	1.000	222.3 Da LogP 3.01 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCS(=O)(=O)O`
ZINC2515939 ZINC	1.000	236.4 Da LogP 3.41 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCS(=O)(=O)O`
ZINC42921009 ZINC	1.000	278.5 Da LogP 4.58 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCS(=O)(=O)O`
ZINC80135680 ZINC	1.000	208.3 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCS(=O)(=O)O`
ZINC5113156 ZINC	0.722	246.3 Da LogP 0.32 TPSA 108.7	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCCCS(=O)(=O)O`
ZINC1763010 ZINC	0.667	218.3 Da LogP -0.46 TPSA 108.7	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCS(=O)(=O)O`
ZINC14880434 ZINC	0.654	336.6 Da LogP 4.26 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[N+](C)(C)CCCS(=O)(=O)O`
ZINC2384686 ZINC	0.654	280.5 Da LogP 2.70 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC[N+](C)(C)CCCS(=O)(=O)O`
ZINC58541260 ZINC	0.654	308.5 Da LogP 3.48 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC[N+](C)(C)CCCS(=O)(=O)O`
ZINC20231719 ZINC	0.619	234.4 Da LogP 3.56 TPSA 34.1	✓ Ro5	✓ Clean	`CCCCCCS(=O)(=O)CCCCCC`
ZINC2166283 ZINC	0.619	262.5 Da LogP 4.34 TPSA 34.1	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCCCCC`
ZINC104242223 ZINC	0.615	322.5 Da LogP 4.59 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCS(=O)(=O)O`
ZINC1589373 ZINC	0.615	238.3 Da LogP 2.25 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCOCCS(=O)(=O)O`
ZINC1595574 ZINC	0.591	234.4 Da LogP 3.56 TPSA 34.1	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCCC`
ZINC1595597 ZINC	0.591	220.4 Da LogP 3.17 TPSA 34.1	✓ Ro5	✓ Clean	`CCCCCCCCCCS(C)(=O)=O`
ZINC5225211 ZINC	0.579	204.2 Da LogP -0.85 TPSA 108.7	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCS(=O)(=O)O`
ZINC1690090 ZINC	0.571	206.4 Da LogP 2.78 TPSA 34.1	✓ Ro5	✓ Clean	`CCCCCS(=O)(=O)CCCCC`
ZINC59471161 ZINC	0.565	265.4 Da LogP 2.73 TPSA 80.4	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCS(=O)(=O)O`
ZINC100310228 ZINC	0.560	334.6 Da LogP 4.87 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCS(=O)(=O)CCO`
ZINC101020164 ZINC	0.560	292.5 Da LogP 3.70 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCS(=O)(=O)CCCO`
ZINC1732769 ZINC	0.560	222.3 Da LogP 1.75 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCO`
ZINC98008412 ZINC	0.560	250.4 Da LogP 2.53 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCCCO`
ZINC98008415 ZINC	0.560	236.4 Da LogP 2.14 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCCO`
ZINC2895764 ZINC	0.533	279.4 Da LogP 2.13 TPSA 83.5	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)NCCS(=O)(=O)O`
ZINC59696283 ZINC	0.533	363.6 Da LogP 4.47 TPSA 83.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)NCCS(=O)(=O)O`
ZINC95669587 ZINC	0.533	308.4 Da LogP 3.34 TPSA 80.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OCCS(=O)(=O)O`
ZINC1593660 ZINC	0.520	221.4 Da LogP 2.24 TPSA 37.4	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)N(C)C`
ZINC1602586 ZINC	0.520	207.3 Da LogP 1.90 TPSA 46.2	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)NC`
ZINC97977037 ZINC	0.520	278.5 Da LogP 4.27 TPSA 43.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCS(=O)(=O)OC`
ZINC100311643 ZINC	0.519	292.4 Da LogP 3.41 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCS(=O)(=O)CC(=O)O`
ZINC1583652 ZINC	0.519	264.4 Da LogP 2.63 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCCCCCS(=O)(=O)CC(=O)O`
ZINC20519776 ZINC	0.519	208.3 Da LogP 1.07 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCS(=O)(=O)CC(=O)O`
ZINC43352221 ZINC	0.519	236.3 Da LogP 1.85 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CC(=O)O`
ZINC116083549 ZINC	0.517	224.3 Da LogP 1.00 TPSA 80.7	✓ Ro5	✓ Clean	`CCOC(=O)CCCCCS(=O)(=O)O`
ZINC100025293 ZINC	0.516	262.4 Da LogP 1.50 TPSA 60.9	✓ Ro5	✓ Clean	`CCCCN1C=CN(CCCCS(=O)(=O)O)C1`
ZINC100304321 ZINC	0.516	349.5 Da LogP 4.03 TPSA 74.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)N(C)CCS(=O)(=O)O`
ZINC59684305 ZINC	0.516	321.5 Da LogP 3.25 TPSA 74.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)N(C)CCS(=O)(=O)O`
ZINC103008613 ZINC	0.500	249.4 Da LogP 3.07 TPSA 46.2	✓ Ro5	✓ Clean	`CCCCCCCCCNS(=O)(=O)CCC`
ZINC1550780 ZINC	0.500	235.3 Da LogP 1.25 TPSA 77.2	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CC(N)=O`
ZINC1602573 ZINC	0.500	222.3 Da LogP 2.71 TPSA 43.4	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)OCC`
ZINC1723787 ZINC	0.500	204.3 Da LogP 2.91 TPSA 34.1	✓ Ro5	✓ Clean	`C=CS(=O)(=O)CCCCCCCC`
ZINC1847701 ZINC	0.500	238.3 Da LogP 2.95 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCCCOS(=O)(=O)O`
ZINC2004468 ZINC	0.500	224.3 Da LogP 2.56 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCCOS(=O)(=O)O`
ZINC2015925 ZINC	0.500	210.3 Da LogP 2.17 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCOS(=O)(=O)O`
ZINC2865194 ZINC	0.500	221.4 Da LogP 1.72 TPSA 60.2	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCN`
ZINC2895765 ZINC	0.500	223.3 Da LogP 0.57 TPSA 83.5	✓ Ro5	✓ Clean	`CCCCCC(=O)NCCS(=O)(=O)O`
ZINC39317991 ZINC	0.500	290.4 Da LogP 0.34 TPSA 118.0	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCOCCCCS(=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 A0A0H3GGK3