Protein profile

VK055_4930

tonB dependent receptor family protein

Genome: KpATCC43816

Gene: AIK83456.1 Structure source: AlphaFold + ColabFold UniProt W8UHH6

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Amino acids 639

Annotations 3

Features 17

PDB binders 13

Druggability 0.943

Overview

Basic information about this protein and its source genome.

Accession: VK055_4930
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK83456.1
Status: annotated
Amino acids: 639
Structure source: AlphaFold + ColabFold

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:0015344 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(ferrioxamine)(out) + H+(out) = siderophore-iron(ferrioxamine)(in) + H+(in). GO:0044718 The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, from one side of a membrane to the other, by means of some agent such as a transporter or pore.

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 (%): 34.459
Localization: OuterMembrane
ColabFold pLDDT: 91.79

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 0.943

Structure W8UHH6

Pocket Pocket 39

P2Rank 0.953

Structure W8UHH6

Pocket Pocket 1

ColabFold model

FPocket 0.744 · Pocket 1

P2Rank 0.962 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 38 / 4744 genomes with a hit

Normalized 0.008

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

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:0015344 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(ferrioxamine)(out) + H+(out) = siderophore-iron(ferrioxamine)(in) + H+(in).
GO:0044718 The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, from one side of a membrane to the other, by means of some agent such as a transporter or pore.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
31	639	CDD	cd01347	ligand_gated_channel
7	138	Gene3D	G3DSA:2.170.130.10	-
7	138	InterPro	IPR037066	TonB-dependent receptor, plug domain superfamily
622	639	ProSitePatterns	PS01156	TonB-dependent receptor proteins signature 2.
622	639	InterPro	IPR010917	TonB-dependent receptor, conserved site
191	220	MobiDBLite	mobidb-lite	consensus disorder prediction
144	639	Gene3D	G3DSA:2.40.170.20	-
144	639	InterPro	IPR036942	TonB-dependent receptor-like, beta-barrel domain superfamily
6	138	FunFam	G3DSA:2.170.130.10:FF:000004	Colicin I TonB-dependent receptor
12	639	SUPERFAMILY	SSF56935	Porins
200	638	Pfam	PF00593	TonB dependent receptor
200	638	InterPro	IPR000531	TonB-dependent receptor-like, beta-barrel
7	639	PANTHER	PTHR30069	TONB-DEPENDENT OUTER MEMBRANE RECEPTOR
7	639	InterPro	IPR039426	TonB-dependent receptor-like
25	133	Pfam	PF07715	TonB-dependent Receptor Plug Domain
25	133	InterPro	IPR012910	TonB-dependent receptor, plug domain
193	208	MobiDBLite	mobidb-lite	consensus disorder prediction

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_W8UHH6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_4930	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
39				0.943
14				0.864
48				0.344

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	26.01	0.91
2	12.6	0.656
3	6.66	0.338
4	5.54	0.265
5	5.25	0.245

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
1				0.744
24				0.28

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	31.07	0.937
2	15.26	0.75
3	7.57	0.399
4	6.8	0.348
5	5.94	0.292

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.

63 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
8SW	5NC3	Q05098	692.6 Da LogP -1.77 TPSA 296.0	3 viol.	Alert	`C#CCNC(=O)C(CNC(=O)C(CNC(=O)CNC(=O)c1cccc(c1O)O…`
8T2	5NC4	Q05098	624.6 Da LogP 1.95 TPSA 237.8	2 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)NCCCC[C@@H](C(=O)NCCCCNC(=…`
95B	5NR2	Q05098	418.4 Da LogP 1.29 TPSA 176.4	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)NCCCC[C@@H](C(=O)O)NC(=O)c…`
C8E	5FR8	D0C8V9	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
EB4	6I2J	Q05098	669.6 Da LogP -0.74 TPSA 287.6	3 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)N[C@H]2COC(=O)[C@H](COC(=O…`
HEX	2GSK	P06129	86.2 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCC`
LDA	2GSK	P06129	229.4 Da LogP 4.48 TPSA 23.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[N+](C)(C)[O-]`
LP5	6Q5E	Q05098	711.9 Da LogP 4.91 TPSA 212.3	2 viol.	✓ Clean	`CCCCCCCCCCC[C@H](CC(=O)N[C@@H]1[C@H]([C@@H]([C@…`
MPG	2GUF	P06129	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCCCOC(=O)[C@@H](CO)O`
MTN	3RGM	P06129	264.4 Da LogP 1.82 TPSA 57.3	✓ Ro5	✓ Clean	`CC1(C=C(C(N1[O])(C)C)CSS(=O)(=O)C)C`
OCT	2GSK	P06129	114.2 Da LogP 3.37 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCC`
OES	2HDF	P17315	206.4 Da LogP 2.09 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@@](=O)CCO`
OWT	6Y47	Q05098	963.0 Da LogP 1.10 TPSA 299.6	3 viol.	Alert	`CC(=O)NCC1CN(C(=O)O1)c2ccc(c(c2)F)N3CCN(CC3)C(=…`

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
ZINC100014200	1.000	494.7 Da LogP 4.02 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC100070166	1.000	290.4 Da LogP 3.17 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCO`
ZINC100310628	1.000	478.7 Da LogP 4.78 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC100365196	1.000	302.5 Da LogP 4.71 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCO`
ZINC101772322	1.000	434.7 Da LogP 4.76 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC103600921	1.000	466.7 Da LogP 3.24 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC14880431	1.000	378.6 Da LogP 3.20 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC14881140	1.000	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
ZINC16051619	1.000	350.5 Da LogP 2.42 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCOCCO`
ZINC1849937	1.000	201.4 Da LogP 3.70 TPSA 23.1	✓ Ro5	✓ Clean	`CCCCCCCCCC[N+](C)(C)[O-]`
ZINC2008702	1.000	243.4 Da LogP 4.87 TPSA 23.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC[N+](C)(C)[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-]`
ZINC2584424	1.000	218.3 Da LogP 2.37 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCO`
ZINC4521877	1.000	234.3 Da LogP 1.61 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCO`
ZINC5273610	1.000	322.4 Da LogP 1.64 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCOCCOCCO`
ZINC58538366	1.000	392.6 Da LogP 3.59 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC58631420	1.000	422.6 Da LogP 3.22 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC59441819	1.000	318.5 Da LogP 3.95 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCO`
ZINC59622400	1.000	274.4 Da LogP 3.93 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCO`
ZINC71788551	1.000	334.5 Da LogP 3.19 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCO`
ZINC71788564	1.000	262.4 Da LogP 2.39 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCO`
ZINC71788567	1.000	406.6 Da LogP 3.98 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC8214594	1.000	362.6 Da LogP 3.97 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC88260008	1.000	390.6 Da LogP 4.75 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC95784968	1.000	450.7 Da LogP 4.00 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC95863931	1.000	464.7 Da LogP 4.39 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC1849711	0.950	202.3 Da LogP 3.14 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCO`
ZINC1850542	0.950	216.4 Da LogP 3.53 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCOCCO`
ZINC2555269	0.950	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
ZINC59660505	0.950	244.4 Da LogP 4.31 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCO`
ZINC8437287	0.950	230.4 Da LogP 3.92 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCO`
ZINC85733754	0.950	258.4 Da LogP 4.70 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCO`
ZINC1644613	0.810	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC3650087	0.805	418.4 Da LogP 1.29 TPSA 176.4	1 viol.	Alert	`O=C(NCCCC[C@H](NC(=O)c1cccc(O)c1O)C(=O)O)c1cccc…`
ZINC59545536	0.773	258.4 Da LogP 4.70 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCCO`
ZINC95831576	0.773	230.4 Da LogP 3.92 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCCCO`
ZINC1627284	0.700	214.4 Da LogP 4.94 TPSA 9.2	✓ Ro5	✓ Clean	`CCCCCCCOCCCCCCC`
ZINC2564179	0.700	214.4 Da LogP 4.94 TPSA 9.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCCCCC`
ZINC4102415	0.682	404.4 Da LogP 1.20 TPSA 159.3	1 viol.	Alert	`O=C(NCCCC[C@@H](CO)NC(=O)c1cccc(O)c1O)c1cccc(O)…`
ZINC95933635	0.636	228.3 Da LogP -1.14 TPSA 74.6	✓ Ro5	✓ Clean	`O=[S@@](CCO)CCC[S@@](=O)CCO`
ZINC95933636	0.636	228.3 Da LogP -1.14 TPSA 74.6	✓ Ro5	✓ Clean	`O=[S@@](CCO)CCC[S@](=O)CCO`
ZINC95933637	0.636	228.3 Da LogP -1.14 TPSA 74.6	✓ Ro5	✓ Clean	`O=[S@](CCO)CCC[S@](=O)CCO`
ZINC100019020	0.607	290.5 Da LogP 4.13 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[S@@](=O)CCC(=O)O`
ZINC100019023	0.607	290.5 Da LogP 4.13 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[S@](=O)CCC(=O)O`
ZINC100245876	0.607	262.4 Da LogP 3.35 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC[S@@](=O)CCC(=O)O`
ZINC100246022	0.607	262.4 Da LogP 3.35 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC[S@@](=O)CCCCC(=O)O`
ZINC100246029	0.607	262.4 Da LogP 3.35 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC[S@](=O)CCCCC(=O)O`
ZINC17357184	0.607	234.4 Da LogP 2.57 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC[S@@](=O)CCC(=O)O`
ZINC17357186	0.607	234.4 Da LogP 2.57 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC[S@](=O)CCC(=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.