Protein profile

KP13_03351

putative bacterial antimicrobial peptide resistance protein PagP

Genome: KpKP13

Gene: pagP AHE45730.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GPV4

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Amino acids 189

Annotations 4

Features 15

PDB binders 2

Druggability 0.894

Overview

Basic information about this protein and its source genome.

Accession: KP13_03351
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: pagP AHE45730.1
Status: annotated
Amino acids: 189
Structure source: AlphaFold + ColabFold

2.3.1.251

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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 84.416
DEG E-value: 1.54e-101
Localization: OuterMembrane
ColabFold pLDDT: 86.95

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 0.894

Structure A0A0H3GPV4

Pocket Pocket 10

P2Rank 0.9

Structure A0A0H3GPV4

Pocket Pocket 1

ColabFold model

FPocket 0.858 · Pocket 4

P2Rank 0.922 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 91 / 4744 genomes with a hit

Normalized 0.019

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

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 Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
1	24	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
1	24	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
29	189	FunFam	G3DSA:2.40.160.20:FF:000002	Lipid A palmitoyltransferase PagP
35	189	SUPERFAMILY	SSF56925	OMPA-like
35	189	InterPro	IPR011250	Outer membrane protein/outer membrane enzyme PagP, beta-barrel
25	189	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
19	24	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	6	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
7	18	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
40	186	Pfam	PF07017	Antimicrobial peptide resistance and lipid A acylation protein PagP
40	186	InterPro	IPR009746	Llipid A acylation PagP
30	189	Gene3D	G3DSA:2.40.160.20	-
1	24	Phobius	SIGNAL_PEPTIDE	Signal peptide region
2	189	Hamap	MF_00837	Lipid A palmitoyltransferase PagP [pagP].
2	189	InterPro	IPR009746	Llipid A acylation PagP

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...

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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_A0A0H3GPV4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03351	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
10				0.894
15				0.372
7				0.366

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	Score	Probability
1	19.81	0.845
2	3.37	0.12
3	1.85	0.036
4	1.3	0.014

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
4				0.858

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	Score	Probability
1	24.1	0.895
2	2.79	0.086
3	2.28	0.057
4	1.07	0.007
5	1.02	0.006

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

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