Protein profile

KP13_02173

Xaa-Pro aminopeptidase

Genome: KpKP13

Gene: AHE42743.1 pepP Structure source: AlphaFold + ColabFold UniProt A0A0H3GXD1

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Amino acids 438

Annotations 5

Features 23

PDB binders 5

Druggability 0.191

Overview

Basic information about this protein and its source genome.

Accession: KP13_02173
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42743.1 pepP
Status: annotated
Amino acids: 438
Structure source: AlphaFold + ColabFold

3.4.11.9

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. 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 (%): 39.259
Human E-value: 9.95e-24
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 54.167
DEG E-value: 7.95e-172
Localization: Cytoplasmic
ColabFold pLDDT: 98.38

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 0.191

Structure A0A0H3GXD1

Pocket Pocket 3

P2Rank 0.73

Structure A0A0H3GXD1

Pocket Pocket 1

ColabFold model

FPocket 0.166 · Pocket 19

P2Rank 0.697 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 133 / 4744 genomes with a hit

Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

3.4.11.9

Gene Ontology (GO)

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
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.

23 records

Show feature table

Start	End	DB	Term	Name
1	171	Gene3D	G3DSA:3.40.350.10	-
1	171	InterPro	IPR029149	Creatinase/Aminopeptidase P/Spt16, N-terminal
2	434	PANTHER	PTHR43226	XAA-PRO AMINOPEPTIDASE 3
182	411	Pfam	PF00557	Metallopeptidase family M24
182	411	InterPro	IPR000994	Peptidase M24
348	360	ProSitePatterns	PS00491	Aminopeptidase P and proline dipeptidase signature.
348	360	InterPro	IPR001131	Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site
1	136	SMART	SM01011	AMP_N_2
1	136	InterPro	IPR007865	Aminopeptidase P, N-terminal
253	269	PRINTS	PR00599	Methionine aminopeptidase-1 signature
253	269	InterPro	IPR001714	Peptidase M24, methionine aminopeptidase
370	382	PRINTS	PR00599	Methionine aminopeptidase-1 signature
370	382	InterPro	IPR001714	Peptidase M24, methionine aminopeptidase
175	433	SUPERFAMILY	SSF55920	Creatinase/aminopeptidase
175	433	InterPro	IPR036005	Creatinase/aminopeptidase-like
173	438	FunFam	G3DSA:3.90.230.10:FF:000002	Xaa-Pro aminopeptidase 3
8	126	Pfam	PF05195	Aminopeptidase P, N-terminal domain
8	126	InterPro	IPR007865	Aminopeptidase P, N-terminal
2	174	SUPERFAMILY	SSF53092	Creatinase/prolidase N-terminal domain
2	174	InterPro	IPR029149	Creatinase/Aminopeptidase P/Spt16, N-terminal
179	419	CDD	cd01087	Prolidase
173	438	Gene3D	G3DSA:3.90.230.10	Creatinase/methionine aminopeptidase superfamily
173	438	InterPro	IPR036005	Creatinase/aminopeptidase-like

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_A0A0H3GXD1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02173	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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	12.52	0.654
2	1.91	0.039
3	1.71	0.03
4	1.69	0.029

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	10.77	0.578
2	1.84	0.035
3	1.59	0.025
4	1.25	0.012

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.

55 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…`
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).

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
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`
ZINC1569729	0.593	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](C)C(=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.