Protein profile

KP13_05561

Phosphoglycerate transport system sensor protein pgtB

Genome: KpKP13

Gene: AHE44567.1 pgtB Structure source: AlphaFold + ColabFold UniProt A0A0H3GTK9

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Amino acids 664

Annotations 6

Features 41

PDB binders 3

Druggability 0.967

Overview

Basic information about this protein and its source genome.

Accession: KP13_05561
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44567.1 pgtB
Status: annotated
Amino acids: 664
Structure source: AlphaFold + ColabFold

2.7.13.3

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0000155 Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response. GO:0007165 The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 83.02

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 0.967

Structure A0A0H3GTK9

Pocket Pocket 59

P2Rank 0.87

Structure A0A0H3GTK9

Pocket Pocket 1

ColabFold model

FPocket 0.708 · Pocket 54

P2Rank 0.939 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 24 / 4744 genomes with a hit

Normalized 0.005

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)

2.7.13.3

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0000155 Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
GO:0007165 The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

Sequence Features

Domain/signature hits from InterPro and related databases.

41 records

Show feature table

Start	End	DB	Term	Name
419	506	Gene3D	G3DSA:1.10.287.130	-
1	403	PIRSF	PIRSF037119	HK_PgtB
1	403	InterPro	IPR017116	Signal transduction histidine kinase, PgtB
398	661	PIRSF	PIRSF037119	HK_PgtB
398	661	InterPro	IPR017116	Signal transduction histidine kinase, PgtB
439	507	SUPERFAMILY	SSF47384	Homodimeric domain of signal transducing histidine kinase
439	507	InterPro	IPR036097	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily
553	659	SMART	SM00387	HKATPase_4
553	659	InterPro	IPR003594	Histidine kinase/HSP90-like ATPase
558	655	CDD	cd00075	HATPase
510	655	SUPERFAMILY	SSF55874	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
510	655	InterPro	IPR036890	Histidine kinase/HSP90-like ATPase superfamily
29	33	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
360	412	ProSiteProfiles	PS50885	HAMP domain profile.
360	412	InterPro	IPR003660	HAMP domain
1	16	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
15	37	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
441	507	CDD	cd00082	HisKA
441	507	InterPro	IPR003661	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
553	657	Pfam	PF02518	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
553	657	InterPro	IPR003594	Histidine kinase/HSP90-like ATPase
317	418	Gene3D	G3DSA:6.10.340.10	-
360	412	SMART	SM00304	HAMP_11
445	508	Pfam	PF00512	His Kinase A (phospho-acceptor) domain
445	508	InterPro	IPR003661	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
34	333	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
357	408	Pfam	PF00672	HAMP domain
357	408	InterPro	IPR003660	HAMP domain
331	353	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
17	28	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
397	434	Coils	Coil	Coil
107	647	PANTHER	PTHR43065	SENSOR HISTIDINE KINASE
1	33	Phobius	SIGNAL_PEPTIDE	Signal peptide region
443	511	SMART	SM00388	HisKA_10
443	511	InterPro	IPR003661	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
515	662	Gene3D	G3DSA:3.30.565.10	-
515	662	InterPro	IPR036890	Histidine kinase/HSP90-like ATPase superfamily
334	357	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
358	664	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
450	659	ProSiteProfiles	PS50109	Histidine kinase domain profile.
450	659	InterPro	IPR005467	Histidine kinase domain

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_A0A0H3GTK9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05561	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
59				0.967
32				0.305

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	9.02	0.483
2	5.5	0.262
3	2.96	0.096
4	2.08	0.047
5	0.98	0.005

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
54				0.708
45				0.545

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	13.07	0.673
2	9.66	0.519
3	1.19	0.01
4	1.07	0.007

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.

53 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
EMC	3A0W	Q9X180	229.7 Da LogP 0.97 TPSA 0.0	✓ Ro5	✓ Clean	`CC[Hg+]`
EMT	3A0W	Q9X180	382.8 Da LogP 2.91 TPSA 37.3	✓ Ro5	✓ Clean	`CC[Hg]Sc1ccccc1C(=O)O`
PG0	5UKV	P71815	120.1 Da LogP -0.36 TPSA 38.7	✓ Ro5	✓ Clean	`COCCOCCO`

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
ZINC1580161	1.000	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	1.000	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	1.000	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	1.000	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	1.000	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	1.000	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	1.000	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC575419714	0.727	312.4 Da LogP 0.42 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCSCCOCCOCCO`
ZINC115163232	0.700	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCCO`
ZINC258837490	0.700	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCCO`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1692489	0.688	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC3874716	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC4530388	0.688	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5178829	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5701172	0.688	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC5997861	0.688	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC575432150	0.667	344.4 Da LogP -0.89 TPSA 100.5	✓ Ro5	✓ Clean	`COCCOCCOCCS(=O)(=O)CCOCCOCCO`
ZINC1857524240	0.652	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`COCCNCCOCCOCCO`
ZINC5650743	0.600	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	0.600	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC116078641	0.583	222.2 Da LogP -0.80 TPSA 74.2	✓ Ro5	✓ Clean	`COC(=O)COCCOCCOCCO`
ZINC1857790631	0.583	280.3 Da LogP -0.39 TPSA 83.5	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCOCCO`
ZINC196151418	0.583	266.3 Da LogP -0.78 TPSA 83.5	✓ Ro5	✓ Clean	`COC(=O)COCCOCCOCCOCCO`
ZINC202958272	0.583	236.3 Da LogP -0.41 TPSA 74.2	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCO`
ZINC34111591	0.583	207.3 Da LogP -1.06 TPSA 62.2	✓ Ro5	✓ Clean	`COCCOCCN(CCO)CCO`
ZINC642881862	0.583	324.4 Da LogP -0.38 TPSA 92.7	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCOCCOCCO`
ZINC34764844	0.550	206.3 Da LogP 1.09 TPSA 36.9	✓ Ro5	✓ Clean	`CCCOCCOCCOCCOC`
ZINC5369059	0.548	274.3 Da LogP 3.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Sc1ccccc1C(=O)O`
ZINC1644613	0.545	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC1672344	0.545	230.3 Da LogP 3.54 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1Sc1ccccc1`
ZINC2675142	0.545	334.4 Da LogP 3.97 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1SCCSc1ccccc1C(=O)O`
ZINC2383745924	0.542	398.5 Da LogP -0.01 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCC(CO)COCCOCCOCCOC`
ZINC5059317	0.541	240.3 Da LogP 2.34 TPSA 74.6	✓ Ro5	✓ Clean	`CC[C@H](Sc1ccccc1C(=O)O)C(=O)O`
ZINC5059320	0.541	240.3 Da LogP 2.34 TPSA 74.6	✓ Ro5	✓ Clean	`CC[C@@H](Sc1ccccc1C(=O)O)C(=O)O`
ZINC7262012	0.541	210.3 Da LogP 3.28 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCSc1ccccc1C(=O)O`
ZINC3122032	0.529	256.2 Da LogP 1.01 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1SC(C(=O)O)C(=O)O`
ZINC2584162	0.528	210.3 Da LogP 3.13 TPSA 37.3	✓ Ro5	✓ Clean	`CC(C)CSc1ccccc1C(=O)O`
ZINC3375023	0.528	210.3 Da LogP 2.07 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CSc1ccccc1C(=O)O`
ZINC19263534	0.526	224.3 Da LogP 3.67 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCSc1ccccc1C(=O)O`
ZINC115086873	0.524	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC140264883	0.524	223.3 Da LogP -0.43 TPSA 72.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCON`
ZINC146143823	0.524	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC5024003	0.524	251.3 Da LogP -0.34 TPSA 72.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCN`
ZINC83253927	0.524	400.5 Da LogP 0.68 TPSA 73.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC83253930	0.524	224.3 Da LogP 0.61 TPSA 36.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCS`
ZINC90741447	0.524	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`

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.