KpKP13 Protein target profile

Oligopeptidase A

Accession: KP13_00308

Gene: prlC AHE42217.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GZT5
Length 680
Pocket druggability (P2Rank · AlphaFold DB model) 0.997
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 (%)
41.436 Lower values reduce human off-target concern.
Human E-value
2.25e-36
Gut microbiome similarity
4.0% 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
96.65 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) 0.997
Structure A0A0H3GZT5
Pocket Pocket 1
Druggability (FPocket) 0.84
Structure A0A0H3GZT5
Pocket Pocket 2
ColabFold model
P2Rank 0.997 · Pocket 1
FPocket 0.83 · Pocket 23
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 188 / 4744 genomes with a hit
Prevalence 4.0%

Sequence

Primary amino-acid sequence viewer.

MTNPLLTPFSLPPFSAIKPEHVVPAVTKALEDCRAAVESAVAHGAPYSWENLCQPLAEVDDVLGRIFSPVSHLNSVKNSPELREAYEQTLPLLSEYSTWVGQHEGLYKAYRDLRDGDNYATLNTAQKKAVDNALRDFELSGIGLPPEAQKRYGEIAARLSELGNQYSNNVLDATMGWNKLVTDVADLAGMPESALAAAQAQAQAKEQEGYLLTLDIPSYLPVMTYCDNQALREEMYRAYSTRASDQGPNAGKWDNSPVMAEILALRHELAQLLGFDSYAYKSLATKMAKDPQQVLDFLTDLAKRARPQGEKELAQLRAFAKAEFGVDELQPWDIAYYSEKQKQHLYSISDEQLRPYFPENKAVSGLFEVVKRIYGITAKERTDVDVWHPEVRFFELYDEHNELRGSFYLDLYAREHKRGGAWMDDCVGQMRKLDGSLQKPVAYLTCNFNRPVNGKPALFTHDEVITLFHEFGHGLHHMLTRIDTAGVSGISGVPWDAVELPSQFMENWCWEPEALAFISGHYETGEPLPQELLEKMLAAKNYQAAMFILRQLEFGLFDFRLHAEYKPEQGAKILETLAEIKKQVAVVPGPTWGRFPHAFSHIFAGGYAAGYYSYLWADVLAADAFSRFEEEGIFNRETGQSFLDNILSRGGSEEPMELFKRFRGREPQLDAMLEHYGIKG

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:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in 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.
  • GO:0008233 Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
  • GO:0008237 Catalysis of the hydrolysis of peptide bonds 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:0046872 Binding to a metal ion.
  • GO:0006518 The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
358 508 Gene3D G3DSA:3.40.390.10 Collagenase (Catalytic Domain)
358 508 InterPro IPR024079 Metallopeptidase, catalytic domain superfamily
3 679 PANTHER PTHR11804 PROTEASE M3 THIMET OLIGOPEPTIDASE-RELATED
3 679 InterPro IPR045090 Peptidase M3A/M3B
358 508 FunFam G3DSA:3.40.390.10:FF:000009 Oligopeptidase A
20 678 CDD cd06456 M3A_DCP
20 678 InterPro IPR034005 Peptidyl-dipeptidase DCP
1 677 SUPERFAMILY SSF55486 Metalloproteases ("zincins"), catalytic domain
150 673 Gene3D G3DSA:1.10.1370.10 Neurolysin, domain 3
150 673 InterPro IPR024077 Neurolysin/Thimet oligopeptidase, domain 2
222 677 Pfam PF01432 Peptidase family M3
222 677 InterPro IPR001567 Peptidase M3A/M3B catalytic domain
35 147 Pfam PF19310 Neurolysin/Thimet oligopeptidase, N-terminal domain
35 147 InterPro IPR045666 Oligopeptidase A, N-terminal domain

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
0.997
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Surrounding area
Pocket 2 P2Rank #2
0.869
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Surrounding area
Pocket 3 P2Rank #3
0.46
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Surrounding area
Pocket 4 P2Rank #4
0.387
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Surrounding area
Pocket 5 P2Rank #5
0.293
Likely same site as FPocket 37 0.9 Å 8 shared residues 100% of smaller site
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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 #2
0.84 Unusual size
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Surrounding area
Pocket 2 FPocket #37
0.398
Likely same site as P2Rank 5 0.9 Å 8 shared residues 100% of smaller site
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Surrounding area
Pocket 3 FPocket #44
0.22 Unusual size
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Surrounding area
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_A0A0H3GZT5
AlphaFold DB full sequence Viewing
ColabFold KP13_00308
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 2 0 loaded crystals
Measured bioactivity 5 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0W2 PDB via homolog 525.1 Da · LogP 5.69 · TPSA 64.7 Open detail RCSB PDB
K26 PDB via homolog Detail RCSB PDB
DWT ChEMBL via homolog · pchembl 6.97 (~107.2 nM) Detail ChEMBL
CHEMBL5070123 ChEMBL via homolog · pchembl 6.00 (~1.0 µM) Detail ChEMBL
CHEMBL5079973 ChEMBL via homolog Detail ChEMBL

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
0W2 RCSB PDB P42676 525.1 Da LogP 5.69 TPSA 64.7 2 viol. ✓ Clean C[C@@H](C(=O)N1CC[C@@H](N1c2ccccc2F)c3ccccc3Cl)…
K26 RCSB PDB A0A1L1QK30 535.5 Da LogP 1.54 TPSA 185.3 2 viol. ✓ Clean CC[C@H](C)[C@@H](C(=O)N[C@@H](Cc1ccc(cc1)O)C(=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.