Protein profile

PA5505

TonB-dependent receptor

Genome: NC_002516.2

Gene: PA5505 Structure source: Experimental + AlphaFold UniProt Q9HT68

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Amino acids 260

Annotations 1

Features 19

PDB binders 1

Druggability 0.646

Overview

Basic information about this protein and its source genome.

Accession: PA5505
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5505
Status: annotated
Amino acids: 260
Structure source: Experimental + AlphaFold

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: CytoplasmicMembrane

Selected Druggability evidence

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 0.646

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
106	210	Gene3D	G3DSA:3.40.190.10	-
25	260	Pfam	PF03180	NlpA lipoprotein
25	260	InterPro	IPR004872	Lipoprotein NlpA family
1	21	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
4	16	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	21	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
17	21	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
26	258	Gene3D	G3DSA:3.40.190.10	-
25	258	CDD	cd13597	PBP2_lipoprotein_Tp32
45	259	NCBIfam	TIGR00363	MetQ/NlpA family lipoprotein
45	259	InterPro	IPR004872	Lipoprotein NlpA family
22	260	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
6	260	PANTHER	PTHR30429	D-METHIONINE-BINDING LIPOPROTEIN METQ
6	260	InterPro	IPR004872	Lipoprotein NlpA family
1	21	Phobius	SIGNAL_PEPTIDE	Signal peptide region
25	260	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
1	260	PIRSF	PIRSF002854	MetQ
1	260	InterPro	IPR004872	Lipoprotein NlpA family

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 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 4K3F	X-ray	1.60 Å	A	91.9% 22-260	PDBe RCSB PDBj File	Viewing
AlphaFold PA5505	AlphaFold	—	—	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
4				0.646
1				0.637

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				3.1	0.104
2				3.08	0.103

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				0.493
2				0.283

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
PE4	3UP9	A7BBB2	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`

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
ZINC5650743	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
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`
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`
ZINC5859031	0.688	294.4 Da LogP 1.13 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCC`
ZINC1674993	0.640	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSCCSCC[C@H](N)C(=O)O)C(=O)O`
ZINC1674994	0.640	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSCCSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1674996	0.640	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCSCCSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1644613	0.619	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC1529407	0.615	222.3 Da LogP -1.07 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSC[C@@H](N)C(=O)O)C(=O)O`
ZINC1532680	0.615	222.3 Da LogP -1.07 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSC[C@H](N)C(=O)O)C(=O)O`
ZINC1708207	0.615	222.3 Da LogP -1.07 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCSC[C@H](N)C(=O)O)C(=O)O`
ZINC1708208	0.615	222.3 Da LogP -1.07 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1605257	0.613	280.4 Da LogP 0.39 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CCSC)C(=O)O`
ZINC1605258	0.613	280.4 Da LogP 0.39 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@H](N)CCSC)C(=O)O`
ZINC1605259	0.613	280.4 Da LogP 0.39 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@H](CCSC)C(=O)O`
ZINC1605260	0.613	280.4 Da LogP 0.39 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)N[C@H](CCSC)C(=O)O`
ZINC2384801	0.613	220.3 Da LogP -0.34 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](C)C(=O)O`
ZINC4556875	0.613	220.3 Da LogP -0.34 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)N[C@@H](C)C(=O)O`
ZINC4556876	0.613	220.3 Da LogP -0.34 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)N[C@H](C)C(=O)O`
ZINC4556877	0.613	220.3 Da LogP -0.34 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@H](C)C(=O)O`
ZINC1580161	0.600	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.600	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.600	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.600	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	0.600	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.600	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	0.600	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC2555269	0.591	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
ZINC1569523	0.581	206.3 Da LogP -0.73 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)NCC(=O)O`
ZINC1593212	0.581	206.3 Da LogP -0.73 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)NCC(=O)O`
ZINC4974293	0.579	280.4 Da LogP 1.08 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCOCCOCCOCC`
ZINC2384813	0.576	236.3 Da LogP -1.37 TPSA 112.7	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CO)C(=O)O`
ZINC2384835	0.576	264.3 Da LogP -0.89 TPSA 129.7	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC2390943	0.576	248.3 Da LogP 0.29 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@H](C(=O)O)C(C)C`
ZINC4557150	0.576	236.3 Da LogP -1.37 TPSA 112.7	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@H](CO)C(=O)O`
ZINC4899465	0.576	411.6 Da LogP 0.63 TPSA 121.5	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CCSC)C(=O)N[C@@H](CCSC…`
ZINC64219373	0.576	411.6 Da LogP 0.63 TPSA 121.5	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CCSC)C(=O)N[C@H](CCSC)…`
ZINC11755051	0.567	204.3 Da LogP 0.94 TPSA 46.3	✓ Ro5	✓ Clean	`CCN(CC)C(=O)[C@@H](N)CCSC`
ZINC57358674	0.567	205.3 Da LogP 1.41 TPSA 52.3	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)OC(C)(C)C`
ZINC57933694	0.567	205.3 Da LogP 1.41 TPSA 52.3	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)OC(C)(C)C`
ZINC62725402	0.567	204.3 Da LogP 0.94 TPSA 46.3	✓ Ro5	✓ Clean	`CCN(CC)C(=O)[C@H](N)CCSC`
ZINC101772322	0.565	434.7 Da LogP 4.76 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC14881140	0.565	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
ZINC58631420	0.565	422.6 Da LogP 3.22 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC95784968	0.565	450.7 Da LogP 4.00 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`

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.