Protein profile

PA5224

aminopeptidase

Genome: NC_002516.2

Gene: PA5224 pepP Structure source: Experimental + AlphaFold UniProt Q9HTW6

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Amino acids 444

Annotations 6

Features 18

PDB binders 6

Druggability 0.469

Overview

Basic information about this protein and its source genome.

Accession: PA5224
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5224 pepP
Status: annotated
Amino acids: 444
Structure source: Experimental + AlphaFold

3.4.11.9

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0004177 Catalysis of the hydrolysis of a single N-terminal amino acid residue from a polypeptide chain. GO:0030145 Binding to a manganese ion (Mn). GO:0070006 Catalysis of the hydrolysis of a single N-terminal amino acid residue from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 39.241
Human E-value: 1.39e-61
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

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 0.469

Structure –

Pocket –

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)

3.4.11.9

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0004177 Catalysis of the hydrolysis of a single N-terminal amino acid residue from a polypeptide chain.
GO:0030145 Binding to a manganese ion (Mn).
GO:0070006 Catalysis of the hydrolysis of a single N-terminal amino acid residue from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
4	138	SMART	SM01011	AMP_N_2
183	423	CDD	cd01087	Prolidase
177	437	SUPERFAMILY	SSF55920	Creatinase/aminopeptidase
177	437	InterPro	IPR036005	Creatinase/aminopeptidase-like
4	176	SUPERFAMILY	SSF53092	Creatinase/prolidase N-terminal domain
4	176	InterPro	IPR029149	Creatinase/Aminopeptidase P/Spt16, N-terminal
175	444	Gene3D	G3DSA:3.90.230.10	Creatinase/methionine aminopeptidase superfamily
175	444	InterPro	IPR036005	Creatinase/aminopeptidase-like
4	138	InterPro	IPR007865	Aminopeptidase P, N-terminal
1	173	Gene3D	G3DSA:3.40.350.10	-
1	173	InterPro	IPR029149	Creatinase/Aminopeptidase P/Spt16, N-terminal
184	414	Pfam	PF00557	Metallopeptidase family M24
184	414	InterPro	IPR000994	Peptidase M24
175	442	FunFam	G3DSA:3.90.230.10:FF:000002	Xaa-Pro aminopeptidase 3
3	438	PANTHER	PTHR43226	XAA-PRO AMINOPEPTIDASE 3
9	128	Pfam	PF05195	Aminopeptidase P, N-terminal domain
9	128	InterPro	IPR007865	Aminopeptidase P, N-terminal
1	173	FunFam	G3DSA:3.40.350.10:FF:000009	Xaa-Pro aminopeptidase

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 5WZE	X-ray	1.78 Å	A,B,C,D	100.0% 1-444	PDBe RCSB PDBj File	Viewing
AlphaFold PA5224	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
5				0.469
1				0.246
2				0.212

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	15.27	0.75
2	7.94	0.422
3	3.12	0.105
4	2.47	0.068
5	2.08	0.047

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				0.532

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.

58 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
01B	5X49	Q9NQH7	195.2 Da LogP 0.00 TPSA 83.5	✓ Ro5	✓ Clean	`c1ccc(cc1)C[C@H]([C@@H](C(=O)O)O)N`
12P	5X49	Q9NQH7	546.7 Da LogP -0.85 TPSA 142.0	2 viol.	✓ Clean	`C(COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO)O`
FLC	2BHA	P15034	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
JEF	6A9T	P40051	597.8 Da LogP 3.24 TPSA 118.3	2 viol.	✓ Clean	`C[C@@H](COC[C@@H](C)OC[C@@H](C)OC[C@H](C)OC[C@H…`
MH2	6QSC	P12955	71.9 Da LogP -0.56 TPSA 20.2	✓ Ro5	✓ Clean	`O[Mn+2]`
XPE	1WL6	P15034	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`C(COCCOCCOCCOCCOCCOCCOCCOCCOCCO)O`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL5429139	P12955	6.28	272.3 Da LogP 0.03 TPSA 92.9	✓ Ro5	✓ Clean	`CCCC[C@@H](N)[C@H](O)C(=O)N1CCC[C@H]1C(=O)OC`
CHEMBL5410658	P12955	6.04	385.5 Da LogP 0.42 TPSA 122.0	✓ Ro5	✓ Clean	`COC(=O)[C@H](CC(C)C)NC(=O)[C@@H]1CCCN1C(=O)[C@@…`

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
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC115086873	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC13354127	0.688	209.2 Da LogP 0.09 TPSA 72.5	✓ Ro5	✓ Clean	`COC(=O)[C@H](O)[C@@H](N)Cc1ccccc1`
ZINC13354130	0.688	209.2 Da LogP 0.09 TPSA 72.5	✓ Ro5	✓ Clean	`COC(=O)[C@@H](O)[C@@H](N)Cc1ccccc1`
ZINC137432264	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC140096846	0.677	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](CCc1ccccc1)[C@@H](O)C(=O)O`
ZINC140096989	0.677	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](CCc1ccccc1)[C@H](O)C(=O)O`
ZINC38867114	0.677	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](CCc1ccccc1)[C@H](O)C(=O)O`
ZINC38867116	0.677	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](CCc1ccccc1)[C@@H](O)C(=O)O`
ZINC60123716	0.667	223.3 Da LogP 0.48 TPSA 72.5	✓ Ro5	✓ Clean	`CCOC(=O)[C@@H](O)[C@@H](N)Cc1ccccc1`
ZINC144169243	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC2569682	0.647	251.3 Da LogP 1.26 TPSA 72.5	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@H](O)[C@@H](N)Cc1ccccc1`
ZINC2569683	0.647	251.3 Da LogP 1.26 TPSA 72.5	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@@H](O)[C@H](N)Cc1ccccc1`
ZINC575441396	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC2526314	0.625	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)[C@@H](O)CC(=O)O`
ZINC2598915	0.625	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1)[C@@H](O)CC(=O)O`
ZINC2598917	0.625	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)[C@H](O)CC(=O)O`
ZINC2598919	0.625	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1)[C@H](O)CC(=O)O`
ZINC34514743	0.615	240.3 Da LogP 2.13 TPSA 52.0	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)[C@@H](N)Cc1ccccc1`
ZINC1644613	0.611	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC258839852	0.611	276.3 Da LogP 0.61 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCC(F)(F)F`
ZINC167715346	0.600	266.3 Da LogP -0.18 TPSA 77.4	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCOCCCO`
ZINC34160867	0.600	222.3 Da LogP -0.20 TPSA 68.2	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCCO`
ZINC4899733	0.600	200.2 Da LogP -0.50 TPSA 72.6	✓ Ro5	✓ Clean	`COC(=O)[C@@H]1CCCN1C(=O)[C@H](C)N`

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.