Protein target profile

KP13_01605

Protease 2

Genome: KpKP13 Gene: ptrB AHE43872.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A060VSQ4
Length 675
Pocket druggability 0.163
Direct ligand evidence 0 154 total records
Functional annotation 1 EC 3 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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 (%)
27.022 Lower values reduce human off-target concern.
Human E-value
7.06e-48
Gut microbiome similarity
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
42.127 Higher values support similarity to known essential genes.
DEG E-value
2.6700000000000002e-117 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Unknown

Structure confidence

ColabFold pLDDT
96.63 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.163
Structure A0A060VSQ4
Pocket Pocket 46
P2Rank 0.678
Structure A0A060VSQ4
Pocket Pocket 1
ColabFold model
FPocket 0.651 · Pocket 1
P2Rank 0.661 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 113 / 4744 genomes with a hit
Prevalence 2.4%

Cross-references

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

Chemistry

ChEMBL CHEMBL189620 ChEMBL CHEMBL97152 ChEMBL CHEMBL95698 ChEMBL CHEMBL318284 ChEMBL CHEMBL318630 ChEMBL ZPR ChEMBL CHEMBL302654 ChEMBL CHEMBL65284 ChEMBL CHEMBL99305 ChEMBL CHEMBL291393 ChEMBL CHEMBL22766 ChEMBL CHEMBL63745 ChEMBL CHEMBL2333024 ChEMBL CHEMBL289651 ChEMBL CHEMBL65338 ChEMBL CHEMBL62580 ChEMBL CHEMBL4464623 ChEMBL CHEMBL1086968 ChEMBL CHEMBL217802 ChEMBL CHEMBL1243373 ChEMBL CHEMBL2333023 ChEMBL CHEMBL217244 ChEMBL CHEMBL304644 ChEMBL CHEMBL387444 ChEMBL CHEMBL387050 ChEMBL CHEMBL1079410 ChEMBL CHEMBL476508 ChEMBL CHEMBL65109 ChEMBL CHEMBL4451993 ChEMBL CHEMBL476950 ChEMBL CHEMBL66257 ChEMBL CHEMBL443836 ChEMBL CHEMBL216410 ChEMBL CHEMBL2333025 ChEMBL CHEMBL308073 ChEMBL CHEMBL63045 ChEMBL CHEMBL2024671 ChEMBL CHEMBL273161 ChEMBL CHEMBL66258 ChEMBL CHEMBL335796 ChEMBL CHEMBL477998 ChEMBL CHEMBL385419 ChEMBL CHEMBL100213 ChEMBL CHEMBL478199 ChEMBL CHEMBL64240 ChEMBL CHEMBL139862 ChEMBL CHEMBL5723333 ChEMBL CHEMBL62960 ChEMBL CHEMBL3233847 ChEMBL CHEMBL216376 ChEMBL CHEMBL422281 ChEMBL CHEMBL269822 ChEMBL CHEMBL262241 ChEMBL CHEMBL342718 ChEMBL CHEMBL515786 ChEMBL CHEMBL478844 ChEMBL CHEMBL1079579 ChEMBL CHEMBL5282548 ChEMBL CHEMBL138674 ChEMBL CHEMBL478843 ChEMBL CHEMBL516746 ChEMBL CHEMBL518279 ChEMBL CHEMBL63133 ChEMBL CHEMBL217753 ChEMBL CHEMBL423002 ChEMBL CHEMBL1173095 ChEMBL CHEMBL312332 ChEMBL CHEMBL476949 ChEMBL CHEMBL477776 ChEMBL CHEMBL478446 ChEMBL CHEMBL477338 ChEMBL CHEMBL311364 ChEMBL CHEMBL478610 ChEMBL CHEMBL515168 ChEMBL CHEMBL79002 ChEMBL CHEMBL136325 ChEMBL CHEMBL303066 ChEMBL CHEMBL99237 ChEMBL CHEMBL63994 ChEMBL CHEMBL209940 ChEMBL CHEMBL478609 ChEMBL CHEMBL63537 ChEMBL CHEMBL516744 ChEMBL CHEMBL292302 ChEMBL CHEMBL476943 ChEMBL CHEMBL78935 ChEMBL CHEMBL217754 ChEMBL CHEMBL477775 ChEMBL CHEMBL341749 ChEMBL CHEMBL514397 ChEMBL CHEMBL2333022 ChEMBL CHEMBL416866 ChEMBL CHEMBL477337 ChEMBL CHEMBL2159745 ChEMBL CHEMBL514385 ChEMBL CHEMBL65373 ChEMBL CHEMBL67279 ChEMBL CHEMBL23089 ChEMBL CHEMBL2332622 ChEMBL CHEMBL217056

Sequence

Primary amino-acid sequence viewer.

MTLHGDTRIDNYYWLRDDERARPDVLEYLHAENAYGKQVMDSQLSLQERLLKEIIDRIPQREVSAPYSKNGFRYRQVYEPGCEYAIYQRQSVLKEEWDEWEILLDANQRAAKSEFYTLGGLGIAPNNQLMAVAEDYLSRRQYGLRFCDLSNGEWYPEILENVTSGFAWSNDSRFVWYVRKHPTTLLPYQVWRHTVGTPAQSDALVYEEKDETFYVSVHKTTSQQFVVIYLSSATTSEVLLLNAELPDAEPVCFLPRRKDHEYSLDHYQHAFYLRSNREGKNFGLYRTVLRDEEQWTTLIPPRHDVMLEGFTLFTDWLVVEERQRGLTSLRQINRKTREVVGIAFDDPAYVTWLAYNPEPETSRLRYGYSSMTTPDTLFELDMDTGERRVIKQQEVKGLDTSCYQSEHLWVTARDGVEVPVSLVYHREHFRKGSNPLLVYGYGSYGESIDADFSASRLSLLNRGFVYAIAHVRGGGELGQQWYEDGKFLCKKNTFNDYLDVCDALLAQGYGDPRLCYGMGGSAGGMLMGVAVNERPELFHGVIAQVPFVDVVTTMLDETIPLTTGEFEEWGNPQDETYYHYMKSYSPYDGVRAQAYPHMLVTTGLHDSQVQYWEPAKWVAKLRELKTDDNLLLLCTDMDSGHGGKSGRFKSYEGVALEYAFFIALAQGTLPGKAAV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • 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:0004252 Catalysis of the hydrolysis of internal, alpha-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).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
351 661 FunFam G3DSA:3.40.50.1820:FF:000005 Prolyl endopeptidase
3 663 PANTHER PTHR11757 PROTEASE FAMILY S9A OLIGOPEPTIDASE
403 644 SUPERFAMILY SSF53474 alpha/beta-Hydrolases
403 644 InterPro IPR029058 Alpha/Beta hydrolase fold
452 664 Pfam PF00326 Prolyl oligopeptidase family
452 664 InterPro IPR001375 Peptidase S9, prolyl oligopeptidase, catalytic domain
10 662 Gene3D G3DSA:3.40.50.1820 alpha/beta hydrolase
10 662 InterPro IPR029058 Alpha/Beta hydrolase fold
435 453 PRINTS PR00862 Prolyl oligopeptidase serine protease (S9A) signature
435 453 InterPro IPR002470 Peptidase S9A, prolyl oligopeptidase
595 617 PRINTS PR00862 Prolyl oligopeptidase serine protease (S9A) signature
595 617 InterPro IPR002470 Peptidase S9A, prolyl oligopeptidase
461 485 PRINTS PR00862 Prolyl oligopeptidase serine protease (S9A) signature
461 485 InterPro IPR002470 Peptidase S9A, prolyl oligopeptidase
489 508 PRINTS PR00862 Prolyl oligopeptidase serine protease (S9A) signature
489 508 InterPro IPR002470 Peptidase S9A, prolyl oligopeptidase
519 539 PRINTS PR00862 Prolyl oligopeptidase serine protease (S9A) signature
519 539 InterPro IPR002470 Peptidase S9A, prolyl oligopeptidase
577 592 PRINTS PR00862 Prolyl oligopeptidase serine protease (S9A) signature
577 592 InterPro IPR002470 Peptidase S9A, prolyl oligopeptidase
1 396 SUPERFAMILY SSF50993 Peptidase/esterase 'gauge' domain
2 393 Pfam PF02897 Prolyl oligopeptidase, N-terminal beta-propeller domain
2 393 InterPro IPR023302 Peptidase S9A, N-terminal domain
61 394 Gene3D G3DSA:2.130.10.120 -

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

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.678
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Surrounding area
Site 2 P2Rank #2
0.535
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Surrounding area
Site 3 P2Rank #3
0.407
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Surrounding area
Site 4 P2Rank #4
0.356
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Surrounding area
Site 5 P2Rank #5
0.287
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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_A0A060VSQ4
AlphaFold DB full sequence Viewing
ColabFold KP13_01605
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.

154 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 104 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
15P PDB via homolog 1529.8 Da · LogP 0.17 · TPSA 334.1 Open detail RCSB PDB
552 PDB via homolog Detail RCSB PDB
BKO PDB via homolog Detail RCSB PDB
SPM PDB via homolog Detail RCSB PDB
CHEMBL189620 ChEMBL via homolog · pchembl 10.70 (~0.0 nM) 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
15P RCSB PDB Q9X6R4 1529.8 Da LogP 0.17 TPSA 334.1 2 viol. ✓ Clean COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO…
552 RCSB PDB P48147 389.8 Da LogP 2.81 TPSA 64.4 ✓ Ro5 ✓ Clean c1cc(ccc1COC2=NC(=C3C=C[C@H](N3C2=O)C(=O)N4CCCC…
BKO RCSB PDB A0A1X9T5X9 466.6 Da LogP 3.51 TPSA 70.1 ✓ Ro5 ✓ Clean c1ccc(cc1)/C=C/c2ccccc2OCCCC(=O)N3CC(CC3C(=O)N4…
SPM RCSB PDB B3VI58 202.3 Da LogP -0.36 TPSA 76.1 ✓ Ro5 ✓ Clean C(CCNCCCN)CNCCCN

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.