Protein profile

VK055_5105

tonB-dependent siderophore receptor family protein

Genome: KpATCC43816

Gene: AIK83631.1 iroN Structure source: AlphaFold + ColabFold UniProt A4GZE7

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Amino acids 689

Annotations 7

Features 17

PDB binders 14

Druggability 0.842

Overview

Basic information about this protein and its source genome.

Accession: VK055_5105
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK83631.1 iroN
Status: annotated
Amino acids: 689
Structure source: AlphaFold + ColabFold

GO:0015343 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(out) + H+(out) = siderophore-iron(in) + H+(in). GO:0038023 Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response. 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:0015891 The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0042912 Enables the transfer of a colicin from one side of a membrane to the other. Colicins are a group of antibiotics produced by E. coli and related species that are encoded by a group of naturally occurring plasmids, e.g. Col E1. 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).

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 (%): 45.679
Localization: OuterMembrane
ColabFold pLDDT: 95.33

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 0.842

Structure A4GZE7

Pocket Pocket 5

P2Rank 0.968

Structure A4GZE7

Pocket Pocket 1

ColabFold model

FPocket 0.494 · Pocket 3

P2Rank 0.968 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 99 / 4744 genomes with a hit

Normalized 0.021

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0015343 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: siderophore-iron(out) + H+(out) = siderophore-iron(in) + H+(in).
GO:0038023 Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
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:0015891 The directed movement of siderophores, low molecular weight Fe(III)-chelating substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GO:0042912 Enables the transfer of a colicin from one side of a membrane to the other. Colicins are a group of antibiotics produced by E. coli and related species that are encoded by a group of naturally occurring plasmids, e.g. Col E1.
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
672	689	ProSitePatterns	PS01156	TonB-dependent receptor proteins signature 2.
672	689	InterPro	IPR010917	TonB-dependent receptor, conserved site
14	689	PANTHER	PTHR30069	TONB-DEPENDENT OUTER MEMBRANE RECEPTOR
14	689	InterPro	IPR039426	TonB-dependent receptor-like
224	687	Pfam	PF00593	TonB dependent receptor
224	687	InterPro	IPR000531	TonB-dependent receptor-like, beta-barrel
14	128	Pfam	PF07715	TonB-dependent Receptor Plug Domain
14	128	InterPro	IPR012910	TonB-dependent receptor, plug domain
1	133	Gene3D	G3DSA:2.170.130.10	-
1	133	InterPro	IPR037066	TonB-dependent receptor, plug domain superfamily
139	689	FunFam	G3DSA:2.40.170.20:FF:000002	Colicin I TonB-dependent receptor
15	689	NCBIfam	TIGR01783	TonB-dependent siderophore receptor
15	689	InterPro	IPR010105	TonB-dependent siderophore receptor
4	689	SUPERFAMILY	SSF56935	Porins
139	689	Gene3D	G3DSA:2.40.170.20	-
139	689	InterPro	IPR036942	TonB-dependent receptor-like, beta-barrel domain superfamily
14	689	CDD	cd01347	ligand_gated_channel

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_A4GZE7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_5105	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
5				0.842
7				0.827
4				0.68
1				0.542

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	28.96	0.928
2	11.21	0.601
3	10.76	0.578
4	10.16	0.547
5	7.55	0.397

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
3				0.494
8				0.41

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	29.11	0.929
2	19.58	0.841
3	7.35	0.384
4	6.16	0.306
5	5.6	0.269

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.

64 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…`
BOG	6BPO	P75780	292.4 Da LogP 0.16 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)…`
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
ZINC100107878	1.000	262.5 Da LogP 3.65 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[S@@](=O)CCO`
ZINC14880337	1.000	206.4 Da LogP 2.09 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@](=O)CCO`
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`
ZINC2555269	0.950	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
ZINC100244447	0.826	276.5 Da LogP 4.04 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@@](=O)CCCCCCCO`
ZINC100244449	0.826	276.5 Da LogP 4.04 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@](=O)CCCCCCCO`
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…`
ZINC1593347	0.762	246.5 Da LogP 4.68 TPSA 17.1	✓ Ro5	✓ Clean	`CCCCCCCS(=O)CCCCCCC`
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)…`
ZINC71404858	0.676	458.5 Da LogP -4.58 TPSA 208.0	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OCCCOCCCO[C@H]2O[C@H](CO)[C@H](O…`
ZINC71404860	0.676	458.5 Da LogP -4.58 TPSA 208.0	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OCCCOCCCO[C@@H]2O[C@H](CO)[C@H](…`
ZINC71404862	0.676	458.5 Da LogP -4.58 TPSA 208.0	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](OCCCOCCCO[C@@H]2O[C@H](CO)[C@H]…`
ZINC13518823	0.667	208.2 Da LogP -2.18 TPSA 99.4	✓ Ro5	✓ Clean	`CCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O`
ZINC13533701	0.667	208.2 Da LogP -2.18 TPSA 99.4	✓ Ro5	✓ Clean	`CCO[C@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O`
ZINC13544857	0.667	208.2 Da LogP -2.18 TPSA 99.4	✓ Ro5	✓ Clean	`CCO[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O`
ZINC140959267	0.667	208.2 Da LogP -2.18 TPSA 99.4	✓ Ro5	✓ Clean	`CCO[C@H]1O[C@H](CO)[C@H](O)[C@@H](O)[C@@H]1O`
ZINC141629887	0.667	208.2 Da LogP -2.18 TPSA 99.4	✓ Ro5	✓ Clean	`CCO[C@@H]1O[C@H](CO)[C@H](O)[C@@H](O)[C@@H]1O`
ZINC5861418	0.667	208.2 Da LogP -2.18 TPSA 99.4	✓ Ro5	✓ Clean	`CCO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O`
ZINC35644405	0.658	336.4 Da LogP -0.38 TPSA 136.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCO[C@@H]1O[C@H](CO)[C@H](O)[C@H](O…`
ZINC95495932	0.657	237.3 Da LogP -2.85 TPSA 125.4	✓ Ro5	✓ Clean	`NCCCO[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O`
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`
ZINC257371379	0.619	396.4 Da LogP -2.15 TPSA 158.3	1 viol.	✓ Clean	`CCCCCCO[C@H]1O[C@@H](CO[C@@H]2OC[C@H](O)[C@H](O…`
ZINC257371380	0.619	396.4 Da LogP -2.15 TPSA 158.3	1 viol.	✓ Clean	`CCCCCCO[C@H]1O[C@@H](CO[C@@H]2OC[C@@H](O)[C@@H]…`
ZINC257371381	0.619	396.4 Da LogP -2.15 TPSA 158.3	1 viol.	✓ Clean	`CCCCCCO[C@H]1O[C@@H](CO[C@@H]2OC[C@H](O)[C@@H](…`
ZINC257371382	0.619	396.4 Da LogP -2.15 TPSA 158.3	1 viol.	✓ Clean	`CCCCCCO[C@H]1O[C@@H](CO[C@@H]2OC[C@@H](O)[C@H](…`
ZINC38308095	0.615	384.4 Da LogP -3.96 TPSA 178.5	2 viol.	✓ Clean	`CCCO[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[…`
ZINC34522850	0.611	250.3 Da LogP -1.15 TPSA 99.4	✓ Ro5	✓ Clean	`CC(C)CCO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]…`
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`
ZINC100245881	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`
ZINC8700292	0.605	248.3 Da LogP -1.23 TPSA 99.4	✓ Ro5	✓ Clean	`C=CCCCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O`
ZINC8700293	0.605	248.3 Da LogP -1.23 TPSA 99.4	✓ Ro5	✓ Clean	`C=CCCCO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O`
ZINC100302699	0.600	332.5 Da LogP 3.48 TPSA 65.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OCCOCCOCCO`
ZINC101013974	0.600	273.5 Da LogP 3.90 TPSA 44.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCN`
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`
ZINC44583812	0.600	380.6 Da LogP 3.49 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCCCCCCCCCCS`
ZINC44583816	0.600	468.7 Da LogP 3.52 TPSA 75.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCCCCCCCCCCS`

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.