Protein profile

KP13_00356

Peptidase E

Genome: KpKP13

Gene: AHE46905.1 pepE Structure source: AlphaFold + ColabFold UniProt A0A060VEX5

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Amino acids 229

Annotations 5

Features 12

PDB binders 0

Druggability 0.365

Overview

Basic information about this protein and its source genome.

Accession: KP13_00356
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46905.1 pepE
Status: annotated
Amino acids: 229
Structure source: AlphaFold + ColabFold

3.4.13.21

GO:0016805 Catalysis of the hydrolysis of a dipeptide. GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. GO:0008236 Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.73

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 0.365

Structure A0A060VEX5

Pocket Pocket 4

P2Rank 0.549

Structure A0A060VEX5

Pocket Pocket 1

ColabFold model

FPocket 0.449 · Pocket 4

P2Rank 0.519 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 32 / 4744 genomes with a hit

Normalized 0.007

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)

3.4.13.21

Gene Ontology (GO)

GO:0016805 Catalysis of the hydrolysis of a dipeptide.
GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
GO:0008236 Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
2	215	CDD	cd03146	GAT1_Peptidase_E
2	215	InterPro	IPR005320	Peptidase S51
1	215	Hamap	MF_00510	Peptidase E [pepE].
1	215	InterPro	IPR023172	Peptidase S51, dipeptidase E
1	229	FunFam	G3DSA:3.40.50.880:FF:000007	Peptidase E
1	220	SUPERFAMILY	SSF52317	Class I glutamine amidotransferase-like
1	220	InterPro	IPR029062	Class I glutamine amidotransferase-like
3	205	Pfam	PF03575	Peptidase family S51
3	205	InterPro	IPR005320	Peptidase S51
8	210	PANTHER	PTHR20842	PROTEASE S51 ALPHA-ASPARTYL DIPEPTIDASE
1	229	Gene3D	G3DSA:3.40.50.880	-
1	229	InterPro	IPR029062	Class I glutamine amidotransferase-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_A0A060VEX5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00356	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
4				0.365

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				7.72	0.408

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				0.449

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				5.97	0.293
2				2.14	0.05

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.

45 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.

No PDB ligands found through similar proteins.

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
ZINC1709621	0.600	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)N[C@@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1709622	0.600	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CC(=O)N[C@@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1709623	0.600	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)N[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1709624	0.600	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CC(=O)N[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1575288	0.560	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC1575289	0.560	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC1575290	0.560	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC1575291	0.560	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC5131760	0.560	237.2 Da LogP -0.94 TPSA 137.9	✓ Ro5	✓ Clean	`N[C@@H](CS[C@@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC5131761	0.560	237.2 Da LogP -0.94 TPSA 137.9	✓ Ro5	✓ Clean	`N[C@H](CS[C@@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC5131922	0.560	237.2 Da LogP -0.94 TPSA 137.9	✓ Ro5	✓ Clean	`N[C@@H](CS[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC5131923	0.560	237.2 Da LogP -0.94 TPSA 137.9	✓ Ro5	✓ Clean	`N[C@H](CS[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC2123927	0.538	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)[C@@H](N)CC(=O)O)C(=O)O`
ZINC2560978	0.538	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)C[C@H](N)C(=O)O)C(=O)O`
ZINC1730666	0.524	208.2 Da LogP -1.46 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CSC[C@H](N)C(=O)O)C(=O)O`
ZINC1730667	0.524	208.2 Da LogP -1.46 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CSC[C@H](N)C(=O)O)C(=O)O`
ZINC1730669	0.524	208.2 Da LogP -1.46 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CSC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055005	0.524	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007	0.524	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010	0.524	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC100655912	0.519	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)N[C@H](…`
ZINC100655916	0.519	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)N[C@@H]…`
ZINC255993703	0.519	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)N[C@H](…`
ZINC4533843	0.519	363.3 Da LogP -3.21 TPSA 233.4	1 viol.	✓ Clean	`N[C@@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@…`
ZINC4533848	0.519	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@…`
ZINC4533853	0.519	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)N[C@@H]…`
ZINC1555366	0.500	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1555367	0.500	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555369	0.500	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1577651	0.500	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577652	0.500	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577653	0.500	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@H](CC(=O)O)C(=O)O`
ZINC1720127	0.500	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1720128	0.500	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720130	0.500	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC22923898	0.500	307.3 Da LogP -3.04 TPSA 199.3	1 viol.	✓ Clean	`N[C@@H](CN[C@@H](CN[C@@H](CC(=O)O)C(=O)O)C(=O)O…`
ZINC22923905	0.500	307.3 Da LogP -3.04 TPSA 199.3	1 viol.	✓ Clean	`N[C@@H](CN[C@H](CN[C@@H](CC(=O)O)C(=O)O)C(=O)O)…`
ZINC22930737	0.500	307.3 Da LogP -3.04 TPSA 199.3	1 viol.	✓ Clean	`N[C@H](CN[C@H](CN[C@@H](CC(=O)O)C(=O)O)C(=O)O)C…`
ZINC23355305	0.500	307.3 Da LogP -3.04 TPSA 199.3	1 viol.	✓ Clean	`N[C@H](CN[C@@H](CN[C@@H](CC(=O)O)C(=O)O)C(=O)O)…`
ZINC2384839	0.500	232.2 Da LogP -0.99 TPSA 129.7	✓ Ro5	✓ Clean	`CC(C)[C@H](NC(=O)[C@@H](N)CC(=O)O)C(=O)O`
ZINC2560328	0.500	239.1 Da LogP 1.53 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](CC(C(F)(F)F)C(F)(F)F)C(=O)O`
ZINC3623257	0.500	202.2 Da LogP -0.85 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](C/C=C/C[C@@H](N)C(=O)O)C(=O)O`
ZINC4348166	0.500	239.1 Da LogP 1.53 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](CC(C(F)(F)F)C(F)(F)F)C(=O)O`
ZINC4580672	0.500	202.2 Da LogP -0.85 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](C/C=C/C[C@H](N)C(=O)O)C(=O)O`
ZINC4580676	0.500	202.2 Da LogP -0.85 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](C/C=C/C[C@@H](N)C(=O)O)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.