Protein profile

KP13_01743

Xaa-Pro dipeptidase

Genome: KpKP13

Gene: AHE46954.1 pepQ Structure source: AlphaFold + ColabFold UniProt A0A0H3GGM3
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Amino acids 443
Annotations 8
Features 16
PDB binders 5
Druggability 0.76

Overview

Basic information about this protein and its source genome.

Accession
KP13_01743
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46954.1 pepQ
Status
annotated
Amino acids
443
Structure source
AlphaFold + ColabFold
EC
3.4.13.9
GO
GO:0016795 Catalysis of the hydrolysis of a phosphoric triester. 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:0046872 Binding to a metal ion. GO:0008235 Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of 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:0102009 Catalysis of the reaction: H2O + a dipeptide with proline at the C-terminal = L-proline + a standard alpha amino acid.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
33.218
Human E-value
9.09e-37
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.96

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 0.76
Structure A0A0H3GGM3
Pocket Pocket 1
P2Rank 0.771
Structure A0A0H3GGM3
Pocket Pocket 1
ColabFold model
FPocket 0.828 · Pocket 27
P2Rank 0.786 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 114 / 4744 genomes with a hit
Normalized 0.024

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0016795 Catalysis of the hydrolysis of a phosphoric triester.
  • 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:0046872 Binding to a metal ion.
  • GO:0008235 Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of 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:0102009 Catalysis of the reaction: H2O + a dipeptide with proline at the C-terminal = L-proline + a standard alpha amino acid.
  • 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.

16 records
Show feature table
Start End DB Term Name
168 430 Pfam PF00557 Metallopeptidase family M24
168 430 InterPro IPR000994 Peptidase M24
1 159 FunFam G3DSA:3.40.350.10:FF:000002 Xaa-Pro dipeptidase
16 438 PANTHER PTHR43226 XAA-PRO AMINOPEPTIDASE 3
163 438 SUPERFAMILY SSF55920 Creatinase/aminopeptidase
163 438 InterPro IPR036005 Creatinase/aminopeptidase-like
161 443 FunFam G3DSA:3.90.230.10:FF:000006 Xaa-Pro dipeptidase
167 438 CDD cd01087 Prolidase
1 443 Hamap MF_01279 Xaa-Pro dipeptidase [pepQ].
1 443 InterPro IPR022846 Xaa-Pro dipeptidase
335 347 ProSitePatterns PS00491 Aminopeptidase P and proline dipeptidase signature.
335 347 InterPro IPR001131 Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site
161 443 Gene3D G3DSA:3.90.230.10 Creatinase/methionine aminopeptidase superfamily
161 443 InterPro IPR036005 Creatinase/aminopeptidase-like
1 159 Gene3D G3DSA:3.40.350.10 -
1 159 InterPro IPR029149 Creatinase/Aminopeptidase P/Spt16, N-terminal

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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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_A0A0H3GGM3
AlphaFold — — full sequence — Viewing
ColabFold KP13_01743
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
1 0.76
3 0.3
26 0.285

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 13.63 0.693
2 2.12 0.049
3 1.35 0.016
4 1.05 0.006

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.

57 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
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
GOA
3L24
Q44238 76.1 Da LogP -0.94 TPSA 57.5 ✓ Ro5 ✓ Clean C(C(=O)O)O
M44
3L7G
Q44238 180.2 Da LogP 1.08 TPSA 61.4 ✓ Ro5 ✓ Clean CC(C)NP(=O)(NC(C)C)O
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

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.