Protein target profile

KP13_32154

ATP-dependent Clp protease proteolytic subunit ClpP

Genome: KpKP13 Gene: AHE46016.1 clpP 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GKH6
Length 175
Pocket druggability 0.576
Direct ligand evidence 0 155 total records
Functional annotation 1 EC 7 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 (%)
55.975 Lower values reduce human off-target concern.
Human E-value
3.74e-64
Gut microbiome similarity
87.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
71.023 Higher values support similarity to known essential genes.
DEG E-value
4.9699999999999995e-95 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.51 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 0.576
Structure A0A0H3GKH6
Pocket Pocket 1
P2Rank 0.103
Structure A0A0H3GKH6
Pocket Pocket 1
ColabFold model
FPocket 0.435 · Pocket 6
P2Rank 0.046 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 4152 / 4744 genomes with a hit
Prevalence 87.5%

Cross-references

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

Chemistry

ChEMBL CHEMBL4303616 ChEMBL CHEMBL4297310 ChEMBL CHEMBL5572211 ChEMBL CHEMBL5597011 ChEMBL CHEMBL5596220 ChEMBL CHEMBL5597441 ChEMBL CHEMBL4549588 ChEMBL CHEMBL5170429 ChEMBL CHEMBL5176506 ChEMBL CHEMBL5194447 ChEMBL CHEMBL5283010 ChEMBL CHEMBL5287429 ChEMBL CHEMBL5290620 ChEMBL CHEMBL5596597 ChEMBL CHEMBL5173519 ChEMBL CHEMBL5180553 ChEMBL CHEMBL5597008 ChEMBL CHEMBL5598515 ChEMBL CHEMBL5275131 ChEMBL CHEMBL5426567 ChEMBL CHEMBL5597414 ChEMBL CHEMBL5205960 ChEMBL CHEMBL5191392 ChEMBL CHEMBL4579446 ChEMBL CHEMBL5197418 ChEMBL CHEMBL5595943 ChEMBL CHEMBL5196310 ChEMBL CHEMBL3763937 ChEMBL CHEMBL5597713 ChEMBL CHEMBL5598503 ChEMBL CHEMBL4536651 ChEMBL CHEMBL4582486 ChEMBL CHEMBL5193179 ChEMBL CHEMBL5596563 ChEMBL CHEMBL5597740 ChEMBL CHEMBL4593456 ChEMBL CHEMBL5185111 ChEMBL CHEMBL4542946 ChEMBL CHEMBL5190079 ChEMBL CHEMBL3342324 ChEMBL CHEMBL5170508 ChEMBL CHEMBL5172282 ChEMBL CHEMBL5196543 ChEMBL CHEMBL4530326 ChEMBL CHEMBL4549148 ChEMBL CHEMBL4551784 ChEMBL CHEMBL4537982 ChEMBL CHEMBL4548354 ChEMBL CHEMBL4553929 ChEMBL CHEMBL5176285 ChEMBL CHEMBL5206788 ChEMBL CHEMBL5596404 ChEMBL CHEMBL4532810 ChEMBL CHEMBL4536048 ChEMBL CHEMBL4561696 ChEMBL CHEMBL4562037 ChEMBL CHEMBL4586300 ChEMBL CHEMBL4515327 ChEMBL CHEMBL4528926 ChEMBL CHEMBL5193731 ChEMBL CHEMBL5195731 ChEMBL CHEMBL4515648 ChEMBL CHEMBL4536809 ChEMBL CHEMBL3765324 ChEMBL CHEMBL4466041 ChEMBL CHEMBL4528556 ChEMBL CHEMBL5181406 ChEMBL CHEMBL5287669 ChEMBL CHEMBL4555286 ChEMBL CHEMBL4562804 ChEMBL CHEMBL4566150 ChEMBL CHEMBL5191962 ChEMBL CHEMBL5206329 ChEMBL CHEMBL5596606 ChEMBL CHEMBL4549693 ChEMBL CHEMBL4591519 ChEMBL CHEMBL5179264 ChEMBL CHEMBL5401730 ChEMBL CHEMBL5172475 ChEMBL CHEMBL4525304 ChEMBL CHEMBL4538112 ChEMBL CHEMBL4557275 ChEMBL CHEMBL5590920 ChEMBL CHEMBL4448860 ChEMBL CHEMBL4549864 ChEMBL CHEMBL4551942 ChEMBL CHEMBL4567848 ChEMBL CHEMBL5174896 ChEMBL CHEMBL5183001 ChEMBL CHEMBL5199237 ChEMBL CHEMBL5568993 ChEMBL CHEMBL5566864 ChEMBL CHEMBL5598320 ChEMBL CHEMBL4577962 ChEMBL CHEMBL5639722 ChEMBL CHEMBL4546432 ChEMBL CHEMBL4650311 ChEMBL CHEMBL5185632 ChEMBL CHEMBL4444802 ChEMBL CHEMBL4483092

Sequence

Primary amino-acid sequence viewer.

MYSRLLKERVIFLTGQVEDHMANLIVAQMLFLEAENPEKDIYLYINSPGGVITAGMSIYDTMQFIKPDVSTICMGQAASMGAFLLTAGAKGKRFCLPNSRVMIHQPLGGYQGQATDIEIHAREILKVKGRMNELMAHHTGQSLEQIERDTERDRFLSAAEAVEYGLVDSILTHRN

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:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0004176 Catalysis of the hydrolysis of peptide bonds, driven by ATP hydrolysis.
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0009368 A protein complex comprised of members of the ClpX, ClpC, ClpD, ClpP or ClpR protein families. ClpPs are the proteolytic subunit of active complexes, and ClpA and ClpX form the regulatory subunits. Enzymatically active and inactive complexes can form.
  • GO:0051117 Binding to an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
  • 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.

28 records
Show feature table
Start End DB Term Name
1 175 Gene3D G3DSA:3.90.226.10 -
2 174 PANTHER PTHR10381 ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
2 174 InterPro IPR023562 Clp protease proteolytic subunit /Translocation-enhancing protein TepA
2 170 CDD cd07017 S14_ClpP_2
2 170 InterPro IPR001907 ATP-dependent Clp protease proteolytic subunit
19 34 PRINTS PR00127 Clp protease catalytic subunit P signature
19 34 InterPro IPR001907 ATP-dependent Clp protease proteolytic subunit
40 60 PRINTS PR00127 Clp protease catalytic subunit P signature
40 60 InterPro IPR001907 ATP-dependent Clp protease proteolytic subunit
71 88 PRINTS PR00127 Clp protease catalytic subunit P signature
71 88 InterPro IPR001907 ATP-dependent Clp protease proteolytic subunit
149 168 PRINTS PR00127 Clp protease catalytic subunit P signature
149 168 InterPro IPR001907 ATP-dependent Clp protease proteolytic subunit
92 111 PRINTS PR00127 Clp protease catalytic subunit P signature
92 111 InterPro IPR001907 ATP-dependent Clp protease proteolytic subunit
1 173 NCBIfam TIGR00493 ATP-dependent Clp endopeptidase proteolytic subunit ClpP
1 173 InterPro IPR001907 ATP-dependent Clp protease proteolytic subunit
71 82 ProSitePatterns PS00381 Endopeptidase Clp serine active site.
71 82 InterPro IPR018215 ClpP, Ser active site
1 174 SUPERFAMILY SSF52096 ClpP/crotonase
1 174 InterPro IPR029045 ClpP/crotonase-like domain superfamily
1 174 Hamap MF_00444 ATP-dependent Clp protease proteolytic subunit [clpP].
1 174 InterPro IPR001907 ATP-dependent Clp protease proteolytic subunit
93 106 ProSitePatterns PS00382 Endopeptidase Clp histidine active site.
93 106 InterPro IPR033135 ClpP, histidine active site
1 175 FunFam G3DSA:3.90.226.10:FF:000001 ATP-dependent Clp protease proteolytic subunit
1 173 Pfam PF00574 Clp protease
1 173 InterPro IPR023562 Clp protease proteolytic subunit /Translocation-enhancing protein TepA

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 · FPocket

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

Site 1 FPocket #1
0.576
Likely same site as P2Rank 2 2.9 Å 9 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #3
0.216
Likely same site as P2Rank 1 3.3 Å 7 shared residues 64% of smaller site
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Surrounding area
Site 3 FPocket #7
0.209
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.103
Likely same site as FPocket 3 3.3 Å 7 shared residues 64% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.064
Likely same site as FPocket 1 2.9 Å 9 shared residues 100% of smaller site
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Surrounding area
Residue sets
UniProt: Active site:123-123
UniProt: Active site:98-98
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_A0A0H3GKH6
AlphaFold DB full sequence Viewing
ColabFold KP13_32154
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.

155 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 105 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CMQ PDB via homolog 428.5 Da · LogP 3.14 · TPSA 107.9 Open detail RCSB PDB
E4U PDB via homolog Detail RCSB PDB
FN3 PDB via homolog Detail RCSB PDB
KHS PDB via homolog Detail RCSB PDB
NWT 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
CMQ RCSB PDB P0A6G7 428.5 Da LogP 3.14 TPSA 107.9 ✓ Ro5 ✓ Clean CC(C)C[C@@H](C(=O)N[C@@H](Cc1ccc(cc1)O)[C@H](C)…
E4U RCSB PDB Q2YSF8 490.2 Da LogP 3.36 TPSA 114.5 ✓ Ro5 ✓ Clean B([C@H](CC(C)C)NC(=O)[C@H](Cc1c[nH]c2c1cccc2)NC…
FN3 RCSB PDB Q2YSF8 384.2 Da LogP 0.36 TPSA 124.4 ✓ Ro5 ✓ Clean B([C@@H](CC(C)C)NC(=O)[C@H](Cc1ccccc1)NC(=O)c2c…
KHS RCSB PDB P0A6G7 466.9 Da LogP 4.21 TPSA 76.1 ✓ Ro5 ✓ Clean CC(C)(C(=O)NCCSc1ccccc1Cl)S(=O)(=O)c2ccc(cn2)C(…
NWT RCSB PDB Q2G036 770.9 Da LogP 1.89 TPSA 174.5 1 viol. ✓ Clean CCCC/C=C/C(=O)N[C@@H](Cc1cc(cc(c1)F)F)C(=O)N[C@…

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.