KpATCC43816 Protein target profile

antimicrobial peptide resistance and lipid A acylation PagP family protein

Accession: VK055_1877

Gene: AIK80483.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GPV4

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Length 172

Pocket druggability (P2Rank · AlphaFold DB model) 0.9

Direct ligand evidence 0 51 total records

Functional annotation 1 EC 3 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.90, FPocket 0.89). Use the 3D pocket comparison to verify whether they identify the same site. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.89. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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: 2.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 83.766 Higher values support similarity to known essential genes.
DEG E-value: 4.14e-101 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 88.36 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) 0.9

Structure A0A0H3GPV4

Pocket Pocket 1

Druggability (FPocket) 0.894

Structure A0A0H3GPV4

Pocket Pocket 10

ColabFold model

P2Rank 0.928 · Pocket 1

FPocket 0.846 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 93 / 4744 genomes with a hit

Prevalence 2.0%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSGNASASFSSTLSEGYHTLSNNVAQTWNEPEHYDLYVPAITWHARFAYDKEKTDKYNERPWGAGFGVSRWDEKGNWHGLYLMAFKDSFNKWEPIGGYGWEKTWRPLTDQNFHLGLGYTLGVTARDNWNYIPIPVILPLASIGYGPATFQMTYIPGTYNNGNVYFAWARIQF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Subcellular localization

Localization: OuterMembrane

Enzyme Commission (EC)

2.3.1.251

Gene Ontology (GO)

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:0016409 Catalysis of the transfer of a palmitoyl (CH3-[CH2]14-CO-) group to an acceptor molecule.
GO:0009245 The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

8 records

Show feature table

Start	End	DB	Term	Name
13	172	Gene3D	G3DSA:2.40.160.20	-
12	172	FunFam	G3DSA:2.40.160.20:FF:000002	Lipid A palmitoyltransferase PagP
23	169	Pfam	PF07017	Antimicrobial peptide resistance and lipid A acylation protein PagP
23	169	InterPro	IPR009746	Llipid A acylation PagP
18	172	SUPERFAMILY	SSF56925	OMPA-like
18	172	InterPro	IPR011250	Outer membrane protein/outer membrane enzyme PagP, beta-barrel
1	172	Hamap	MF_00837	Lipid A palmitoyltransferase PagP [pagP].
1	172	InterPro	IPR009746	Llipid A acylation PagP

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

0.9

Likely same site as FPocket 15 4.1 Å 12 shared residues 100% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.231

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Surrounding area

Pocket 3 P2Rank #3

0.097

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Surrounding area

Pocket 4 P2Rank #4

0.028

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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 #10

0.894

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Surrounding area

Pocket 2 FPocket #15

0.372

Likely same site as P2Rank 1 4.1 Å 12 shared residues 100% of smaller site

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Surrounding area

Pocket 3 FPocket #7

0.366

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Surrounding area

Residue sets

UniProt: Active site:106-106

UniProt: Active site:107-107

UniProt: Active site:63-63

UniProt: Site:177-177 Role in the phospholipid gating

UniProt: Site:72-72 Role in lipopolysaccharide recognition

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.928

Likely same site as FPocket 1 0.5 Å 26 shared residues 93% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.181

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Surrounding area

Pocket 3 P2Rank #3

0.062

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Surrounding area

Pocket 4 P2Rank #4

0.038

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Surrounding area

Residue sets

UniProt: Active site:106-106

UniProt: Active site:107-107

UniProt: Active site:63-63

UniProt: Site:177-177 Role in the phospholipid gating

UniProt: Site:72-72 Role in lipopolysaccharide recognition

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_A0A0H3GPV4	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_1877	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 2 records from similar proteins

Structural ligands 2 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 49 similarity-based ZINC candidates

Best available ligand signal

LDA PDB via homolog 229.4 Da · LogP 4.48 · TPSA 23.1 Open detail RCSB PDB

SDS PDB via homolog Detail RCSB PDB

ZINC1532179 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC1847701 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC1849937 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
LDA RCSB PDB	1THQ	P37001	229.4 Da LogP 4.48 TPSA 23.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[N+](C)(C)[O-]`
SDS RCSB PDB	3GP6	P37001	266.4 Da LogP 3.73 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOS(=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
ZINC1532179 ZINC	1.000	266.4 Da LogP 3.73 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOS(=O)(=O)O`
ZINC1847701 ZINC	1.000	238.3 Da LogP 2.95 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCCCOS(=O)(=O)O`
ZINC1849937 ZINC	1.000	201.4 Da LogP 3.70 TPSA 23.1	✓ Ro5	✓ Clean	`CCCCCCCCCC[N+](C)(C)[O-]`
ZINC2004468 ZINC	1.000	224.3 Da LogP 2.56 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCCOS(=O)(=O)O`
ZINC2008702 ZINC	1.000	243.4 Da LogP 4.87 TPSA 23.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC[N+](C)(C)[O-]`
ZINC2015925 ZINC	1.000	210.3 Da LogP 2.17 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCOS(=O)(=O)O`
ZINC2039372 ZINC	1.000	229.4 Da LogP 4.48 TPSA 23.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[N+](C)(C)[O-]`
ZINC2516963 ZINC	1.000	215.4 Da LogP 4.09 TPSA 23.1	✓ Ro5	✓ Clean	`CCCCCCCCCCC[N+](C)(C)[O-]`
ZINC2572139 ZINC	1.000	252.4 Da LogP 3.34 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCOS(=O)(=O)O`
ZINC43079016 ZINC	1.000	280.4 Da LogP 4.12 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOS(=O)(=O)O`
ZINC6845654 ZINC	1.000	294.5 Da LogP 4.51 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOS(=O)(=O)O`
ZINC111883998 ZINC	0.769	456.6 Da LogP 4.18 TPSA 100.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCOCCOCCOCCOS(=O)(=O)O`
ZINC95669525 ZINC	0.769	354.5 Da LogP 3.76 TPSA 82.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOS(=O)(=O)O`
ZINC95669590 ZINC	0.769	310.5 Da LogP 3.74 TPSA 72.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOS(=O)(=O)O`
ZINC95794047 ZINC	0.769	398.6 Da LogP 3.78 TPSA 91.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOS(=O)(=O)O`
ZINC100940389 ZINC	0.640	292.5 Da LogP 4.66 TPSA 43.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOS(C)(=O)=O`
ZINC1690886 ZINC	0.640	264.4 Da LogP 3.88 TPSA 43.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOS(C)(=O)=O`
ZINC2522557 ZINC	0.640	236.4 Da LogP 3.10 TPSA 43.4	✓ Ro5	✓ Clean	`CCCCCCCCCCOS(C)(=O)=O`
ZINC100019694 ZINC	0.625	238.3 Da LogP 2.64 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCCOS(=O)(=O)OCCCCC`
ZINC14591952 ZINC	0.607	210.3 Da LogP 2.02 TPSA 63.6	✓ Ro5	✓ Clean	`CC(C)CCCCCOS(=O)(=O)O`
ZINC1673414 ZINC	0.600	228.4 Da LogP 4.61 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[N+](C)(C)C`
ZINC1700269 ZINC	0.600	200.4 Da LogP 3.83 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCC[N+](C)(C)C`
ZINC100311579 ZINC	0.593	280.5 Da LogP 4.22 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCO[S@@](C)(=O)=S`
ZINC100311581 ZINC	0.593	280.5 Da LogP 4.22 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCO[S@](C)(=O)=S`
ZINC167961104 ZINC	0.593	224.4 Da LogP 2.65 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCO[S@@](C)(=O)=S`
ZINC167961220 ZINC	0.593	224.4 Da LogP 2.65 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCCO[S@](C)(=O)=S`
ZINC100304592 ZINC	0.576	351.5 Da LogP 3.62 TPSA 92.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)NCCOS(=O)(=O)O`
ZINC100315353 ZINC	0.556	358.5 Da LogP 2.84 TPSA 86.7	✓ Ro5	✓ Clean	`CCCCCS(=O)(=O)OCCCCOS(=O)(=O)CCCCC`
ZINC104242223 ZINC	0.552	322.5 Da LogP 4.59 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCS(=O)(=O)O`
ZINC1589373 ZINC	0.552	238.3 Da LogP 2.25 TPSA 63.6	✓ Ro5	✓ Clean	`CCCCCCCCOCCS(=O)(=O)O`
ZINC100991279 ZINC	0.548	314.5 Da LogP 4.38 TPSA 52.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)NCCCC[N+](C)(C)[O-]`
ZINC1670600 ZINC	0.545	201.4 Da LogP 3.08 TPSA 26.0	✓ Ro5	✓ Clean	`CCCCCCCCCC[N+](C)(C)N`
ZINC59314569 ZINC	0.545	229.4 Da LogP 3.86 TPSA 26.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[N+](C)(C)N`
ZINC104284322 ZINC	0.533	324.5 Da LogP 2.26 TPSA 101.6	✓ Ro5	✓ Clean	`NCCNCCCCCCCCCCCCOS(=O)(=O)O`
ZINC2031656 ZINC	0.520	210.3 Da LogP 1.86 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCOS(=O)(=O)OCCCC`
ZINC104334352 ZINC	0.519	330.5 Da LogP 2.06 TPSA 86.7	✓ Ro5	✓ Clean	`CCCCS(=O)(=O)OCCCCOS(=O)(=O)CCCC`
ZINC163821152 ZINC	0.516	272.4 Da LogP 3.21 TPSA 52.2	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)NCCC[N+](C)(C)[O-]`
ZINC53683257 ZINC	0.516	300.5 Da LogP 3.99 TPSA 52.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)NCCC[N+](C)(C)[O-]`
ZINC59660513 ZINC	0.516	308.4 Da LogP 3.34 TPSA 80.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOC(=O)CS(=O)(=O)O`
ZINC100019805 ZINC	0.500	292.5 Da LogP 4.97 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCS(=O)(=O)O`
ZINC112977758 ZINC	0.500	244.5 Da LogP 3.13 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCC[N+](C)(C)CCC[N+](C)(C)C`
ZINC1625794 ZINC	0.500	264.4 Da LogP 4.19 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCS(=O)(=O)O`
ZINC1651926 ZINC	0.500	250.4 Da LogP 3.80 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCS(=O)(=O)O`
ZINC1843748 ZINC	0.500	222.3 Da LogP 3.01 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCS(=O)(=O)O`
ZINC2515939 ZINC	0.500	236.4 Da LogP 3.41 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCS(=O)(=O)O`
ZINC2900787 ZINC	0.500	228.4 Da LogP 4.61 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCC[N+](CC)(CC)CC`
ZINC42921009 ZINC	0.500	278.5 Da LogP 4.58 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCS(=O)(=O)O`
ZINC60139895 ZINC	0.500	222.3 Da LogP 3.53 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCCCCCCCO[P@@H](=O)O`
ZINC80135680 ZINC	0.500	208.3 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCS(=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 A0A0H3GPV4