KpKP13 Protein target profile

Xaa-Pro dipeptidase

Accession: KP13_01743

Gene: pepQ AHE46954.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GGM3
Length 443
Pocket druggability (P2Rank · AlphaFold DB model) 0.771
Direct ligand evidence 0 57 total records
Functional annotation 1 EC 7 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
33.218 Lower values reduce human off-target concern.
Human E-value
9.09e-37
Gut microbiome similarity
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
96.96 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.771
Structure A0A0H3GGM3
Pocket Pocket 1
Druggability (FPocket) 0.76
Structure A0A0H3GGM3
Pocket Pocket 1
ColabFold model
P2Rank 0.786 · Pocket 1
FPocket 0.828 · Pocket 27
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 114 / 4744 genomes with a hit
Prevalence 2.4%

Sequence

Primary amino-acid sequence viewer.

MESLAALYKNHIVTLQERTRDVLARFQMDALLIHSGELVNVFLDDHPYPFKVNPQFKAWVPVTQVPNCWLLVDGVNKPKLWFYLPVDYWHNVEPLPTSFWTEEIDVIALPKADGIGSQLPAARGNIGYIGPVPERALGLGIAADKINPKGVIDYLHYYRAYKTDYELACMREAQKSAVNGHRAAYEAFQSGMSEFDINQAYLTATGHRDTDVPYSNIVALNEHASVLHYTKLDHRAPAEMRSFLLDAGAEYNGYAADLTRTWAAHGDNDFAHLIKDVNDEQQALISTMKAGTSYIDYHIQFHQRIAKLLRKHQLVTDMSEEAMVENDLTGPFMPHGIGHPLGLQVHDVAGFMQDDTGTHLAAPSKYPYLRCTRIIEPRMVLTIEPGIYFIESLLAPWREGPFSKHFNWQKIDAMKPFGGIRIEDNVVIHENSIENMTRDLKLA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Cytoplasmic

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 domains and features

Domain and signature matches imported 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; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.771
Likely same site as FPocket 1 7.7 Å 17 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.112
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Surrounding area
Pocket 3 P2Rank #3
0.043
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Surrounding area
Pocket 4 P2Rank #4
0.019
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Surrounding area
Pocket 5 P2Rank #5
0.01
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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1
0.76 Unusual size
Likely same site as P2Rank 1 7.7 Å 17 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #3
0.3
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Surrounding area
Pocket 3 FPocket #26
0.285
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Surrounding area
Residue sets
UniProt: Binding site:246-246
UniProt: Binding site:257-257
UniProt: Binding site:339-339
UniProt: Binding site:384-384
UniProt: Binding site:423-423
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GGM3
AlphaFold DB full sequence Viewing
ColabFold KP13_01743
ColabFold full sequence Loaded

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
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 2 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
FLC PDB via homolog 189.1 Da · LogP -5.25 · TPSA 140.6 Open detail RCSB PDB
GOA PDB via homolog Detail RCSB PDB
M44 PDB via homolog Detail RCSB PDB
MH2 PDB via homolog Detail RCSB PDB
XPE PDB via homolog Detail RCSB PDB

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 RCSB PDB 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 RCSB PDB Q44238 76.1 Da LogP -0.94 TPSA 57.5 ✓ Ro5 ✓ Clean C(C(=O)O)O
M44 RCSB PDB Q44238 180.2 Da LogP 1.08 TPSA 61.4 ✓ Ro5 ✓ Clean CC(C)NP(=O)(NC(C)C)O
MH2 RCSB PDB P12955 71.9 Da LogP -0.56 TPSA 20.2 ✓ Ro5 ✓ Clean O[Mn+2]
XPE RCSB PDB 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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.