Protein profile

KP13_12038

Lipopolysaccharide export system permease protein lptF

Genome: KpKP13

Gene: lptF ANJ86634.1 Structure source: Experimental + AlphaFold + ColabFold UniProt A0A1Y0Q3P9

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Amino acids 365

Annotations 4

Features 25

PDB binders 12

Druggability 0.511

Overview

Basic information about this protein and its source genome.

Accession: KP13_12038
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: lptF ANJ86634.1
Status: annotated
Amino acids: 365
Structure source: Experimental + AlphaFold + ColabFold

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter. GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GO:0015920 The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide.

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 (%): 87.945
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 83.86

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 0.511

Structure A0A1Y0Q3P9

Pocket Pocket 7

P2Rank 0.438

Structure A0A1Y0Q3P9

Pocket Pocket 1

ColabFold model

FPocket 0.46 · Pocket 27

P2Rank 0.424 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 128 / 4744 genomes with a hit

Normalized 0.027

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
GO:0015920 The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records

Show feature table

Start	End	DB	Term	Name
290	295	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
17	39	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
97	119	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
349	365	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
59	76	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
54	76	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
40	58	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
328	347	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	15	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
296	316	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
317	327	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
328	348	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
16	39	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
296	313	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
5	345	Pfam	PF03739	Lipopolysaccharide export system permease LptF/LptG
5	345	InterPro	IPR005495	Permease LptG/LptF-related
2	348	NCBIfam	TIGR04407	LPS export ABC transporter permease LptF
2	348	InterPro	IPR030922	LPS export ABC transporter permease LptF
77	96	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
266	289	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
97	119	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
267	289	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	349	PANTHER	PTHR33529	SLR0882 PROTEIN-RELATED
1	349	InterPro	IPR005495	Permease LptG/LptF-related
120	265	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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

1 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 7EFO	X-ray	20.00 Å	-	—	PDBe RCSB PDBj File	Viewing
AlphaFold AF_A0A1Y0Q3P9	AlphaFold	—	—	full sequence	—	Loaded
ColabFold KP13_12038	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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	12.03	0.636
2	10.03	0.539
3	6.91	0.356
4	5.57	0.267
5	3.86	0.15

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
16				0.248
8				0.028
2				0.0
36				0.0

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	9.51	0.438
2	3.48	0.101
3	2.17	0.042
4	2.12	0.04

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.

62 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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
JSG	7EFO Open crystal	2975.2 Da LogP 7.73 TPSA 1029.6	4 viol.	✓ Clean	`CCCCCCCCCCCCCC(=O)O[C@H](CCCCCCCCCCC)CC(=O)O[C@…`

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
AE3	6MJP	Q9KP75	134.2 Da LogP 0.03 TPSA 38.7	✓ Ro5	✓ Clean	`CCOCCOCCO`
ANP	6S8G	P0AFA1	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
AOV	6MHZ	P0AF98	544.2 Da LogP -3.05 TPSA 299.4	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
DCQ	6S8N	P0AFA1	322.4 Da LogP 4.49 TPSA 52.6	✓ Ro5	Alert	`CCCCCCCCCCC1=C(C(=O)C(=C(C1=O)OC)OC)C`
JU7	6MJP	Q9KP75	346.5 Da LogP 1.33 TPSA 99.4	✓ Ro5	✓ Clean	`C1CCC(CC1)CCCCCCO[C@H]2[C@@H]([C@H]([C@@H]([C@H…`
L0W	6S8N	P0AFA1	1814.4 Da LogP 21.50 TPSA 394.5	4 viol.	✓ Clean	`CCCCCCCCCCCCCC(=O)O[C@H](CCCCCCCCCCC)CC(=O)O[C@…`
LMD	6S8G	P0AFA1	538.7 Da LogP 0.33 TPSA 178.5	3 viol.	✓ Clean	`CCCCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](…`
LMN	6S8N	P0AFA1	1005.2 Da LogP -1.68 TPSA 357.1	3 viol.	✓ Clean	`CCCCCCCCCCC(CCCCCCCCCC)(CO[C@@H]1[C@@H]([C@@H](…`
LMT	6S8N	P0AFA1	510.6 Da LogP -0.45 TPSA 178.5	3 viol.	✓ Clean	`CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…`
MA4	6MJP	Q9KP75	508.6 Da LogP -0.84 TPSA 178.5	3 viol.	✓ Clean	`C1CCC(CC1)CCCCCCO[C@H]2[C@@H]([C@H]([C@@H]([C@H…`
PGT	6MI7	P0AF98	751.0 Da LogP 10.67 TPSA 148.8	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)O[C@@H](COC(=O)CCCCCCCCCC…`

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
ZINC100053689	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H]…`
ZINC100053691	1.000	496.6 Da LogP -0.84 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCCO[C@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC1501015302	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC2039285652	1.000	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](C…`
ZINC2039285653	1.000	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](C…`
ZINC2039285654	1.000	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](C…`
ZINC2039285655	1.000	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](C…`
ZINC2053493146	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H]…`
ZINC2053493147	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H]…`
ZINC2053493148	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H]…`
ZINC2053493149	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H]…`
ZINC238809244	1.000	510.6 Da LogP -0.45 TPSA 178.5	3 viol.	✓ Clean	`CCCCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C…`
ZINC238809245	1.000	510.6 Da LogP -0.45 TPSA 178.5	3 viol.	✓ Clean	`CCCCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C…`
ZINC252695223	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC252695224	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC252695225	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC252695226	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC2575028	1.000	322.4 Da LogP 4.49 TPSA 52.6	✓ Ro5	Alert	`CCCCCCCCCCC1=C(C)C(=O)C(OC)=C(OC)C1=O`
ZINC5650743	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC58649715	1.000	496.6 Da LogP -0.84 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC59978443	1.000	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H](…`
ZINC6403917	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC66157001	1.000	468.5 Da LogP -1.62 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H]…`
ZINC70669940	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC70669941	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC70669942	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC70669943	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC77311968	1.000	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H]…`
ZINC83433913	1.000	426.5 Da LogP -2.79 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H](CO…`
ZINC85482724	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC86002923	1.000	426.5 Da LogP -2.79 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCO[C@@H]1O[C@H](CO)[C@H](O[C@H]2O[C@H](CO)…`
ZINC14881288	0.857	494.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](OCCCCC…`
ZINC100034925	0.811	348.5 Da LogP 1.72 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC100050848	0.811	376.5 Da LogP 2.50 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](…`
ZINC100056252	0.811	334.5 Da LogP 1.33 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[…`
ZINC100622854	0.811	348.5 Da LogP 1.72 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCO[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](O…`
ZINC100622858	0.811	348.5 Da LogP 1.72 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCO[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](O…`
ZINC100622862	0.811	348.5 Da LogP 1.72 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC100623033	0.811	334.5 Da LogP 1.33 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCO[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](O)…`
ZINC118906329	0.811	348.5 Da LogP 1.72 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O)[C@@H](O)[…`
ZINC118911500	0.811	278.3 Da LogP -0.23 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCO[C@H]1O[C@H](CO)[C@H](O)[C@@H](O)[C@@H]…`
ZINC15609263	0.811	306.4 Da LogP 0.55 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@…`
ZINC1849674	0.811	292.4 Da LogP 0.16 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCO[C@H]1O[C@@H](CO)[C@H](O)[C@@H](O)[C@@…`
ZINC40165555	0.811	292.4 Da LogP 0.16 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H…`
ZINC53683291	0.811	292.4 Da LogP 0.16 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCO[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]…`
ZINC58563863	0.811	292.4 Da LogP 0.16 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]…`
ZINC66122924	0.811	292.4 Da LogP 0.16 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H…`
ZINC71788562	0.811	292.4 Da LogP 0.16 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O)[C@H](O)[C@…`
ZINC76945547	0.811	292.4 Da LogP 0.16 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCO[C@@H]1O[C@H](CO)[C@H](O)[C@@H](O)[C@@…`
ZINC95713698	0.811	348.5 Da LogP 1.72 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](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.