KpATCC43816 Protein target profile

periplasmic serine peptidase DegS

Accession: VK055_3843

Gene: degS AIK82393.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GY66
Length 352
Pocket druggability (P2Rank · AlphaFold DB model) 0.169
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 6 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 (%)
36.875 Lower values reduce human off-target concern.
Human E-value
1.45e-18
Gut microbiome similarity
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
86.08 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
86.39 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) 0.169
Structure A0A0H3GY66
Pocket Pocket 1
Druggability (FPocket) 0.322
Structure A0A0H3GY66
Pocket Pocket 2
ColabFold model
P2Rank 0.103 · Pocket 1
FPocket 0.421 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 142 / 4744 genomes with a hit
Prevalence 3.0%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MPGKLLRSVLIGLLVGGLLLALMPSLRQWQLAPTTQNDTADDSPASYNAAVRRAAPAVVNVYNRALNSTSHNQLTLGSGVIMDQRGYILTNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPVIPINPKRTPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIRGYIGISGREIAPLHAQGGGIDQIQGIVVNDVAPDGPAAQAGIRANDVIISVNDKPAVSALETMDQVAEIRPGSEIPVVIMRDDKKITLHIAVQEYPATN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • 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).
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0005515 Binding to a protein.
  • GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0006515 The chemical reactions and pathways resulting in the breakdown of misfolded or attenuated proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

44 records
Show feature table
Start End DB Term Name
28 138 Gene3D G3DSA:2.40.10.10 -
28 138 InterPro IPR043504 Peptidase S1, PA clan, chymotrypsin-like fold
86 98 PRINTS PR00834 HtrA/DegQ protease family signature
86 98 InterPro IPR001940 Peptidase S1C
107 127 PRINTS PR00834 HtrA/DegQ protease family signature
107 127 InterPro IPR001940 Peptidase S1C
148 172 PRINTS PR00834 HtrA/DegQ protease family signature
148 172 InterPro IPR001940 Peptidase S1C
294 306 PRINTS PR00834 HtrA/DegQ protease family signature
294 306 InterPro IPR001940 Peptidase S1C
205 222 PRINTS PR00834 HtrA/DegQ protease family signature
205 222 InterPro IPR001940 Peptidase S1C
183 200 PRINTS PR00834 HtrA/DegQ protease family signature
183 200 InterPro IPR001940 Peptidase S1C
41 347 PANTHER PTHR22939 SERINE PROTEASE FAMILY S1C HTRA-RELATED
139 253 FunFam G3DSA:2.40.10.10:FF:000001 Periplasmic serine protease DegS
1 31 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
245 337 ProSiteProfiles PS50106 PDZ domain profile.
245 337 InterPro IPR001478 PDZ domain
237 343 SUPERFAMILY SSF50156 PDZ domain-like
237 343 InterPro IPR036034 PDZ superfamily
254 344 Pfam PF13180 PDZ domain
254 344 InterPro IPR001478 PDZ domain
1 27 Phobius SIGNAL_PEPTIDE Signal peptide region
28 352 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
254 341 CDD cd00987 PDZ_serine_protease
23 27 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
254 336 SMART SM00228 pdz_new
254 336 InterPro IPR001478 PDZ domain
4 349 NCBIfam TIGR02038 outer membrane-stress sensor serine endopeptidase DegS
4 349 InterPro IPR011783 Peptidase S1C, DegS
5 24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
44 251 SUPERFAMILY SSF50494 Trypsin-like serine proteases
44 251 InterPro IPR009003 Peptidase S1, PA clan
255 351 Gene3D G3DSA:2.30.42.10 -
255 351 InterPro IPR036034 PDZ superfamily
28 138 FunFam G3DSA:2.40.10.10:FF:000009 Serine endoprotease DegS, periplasmic
185 347 Pfam PF02163 Peptidase family M50
185 347 InterPro IPR008915 Peptidase M50
9 22 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
139 254 Gene3D G3DSA:2.40.10.10 -
139 254 InterPro IPR043504 Peptidase S1, PA clan, chymotrypsin-like fold
77 212 Pfam PF13365 Trypsin-like peptidase 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
0.169
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.141
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.124
Likely same site as FPocket 3 3.5 Å 11 shared residues 85% of smaller site
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.053
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2
0.322
Show in viewer
Surrounding area
Pocket 2 FPocket #3
0.219
Likely same site as P2Rank 3 3.5 Å 11 shared residues 85% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:123-123 Charge relay system
UniProt: Active site:198-198 Charge relay system
UniProt: Active site:93-93 Charge relay system
UniProt: Binding site:181-181
UniProt: Binding site:256-261
UniProt: Binding site:348-348
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_A0A0H3GY66
AlphaFold DB full sequence Viewing
ColabFold VK055_3843
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CXS PDB via homolog 221.3 Da · LogP 1.19 · TPSA 66.4 Open detail RCSB PDB
DFP PDB via homolog Detail RCSB PDB
PMS PDB via homolog Detail RCSB PDB
ZINC2004372 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC38364153 ZINC proposed compound · Tanimoto 0.926 Detail ZINC

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
CXS RCSB PDB A0A5P8YL96 221.3 Da LogP 1.19 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCCS(=O)(=O)O
DFP RCSB PDB P0C0V0 166.2 Da LogP 2.23 TPSA 35.5 ✓ Ro5 ✓ Clean CC(C)OP(=O)OC(C)C
PMS RCSB PDB O06291 172.2 Da LogP 1.07 TPSA 54.4 ✓ Ro5 ✓ Clean c1ccc(cc1)CS(=O)(=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.

Cross-references

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