Protein profile

KP13_32154

ATP-dependent Clp protease proteolytic subunit ClpP

Genome: KpKP13

Gene: AHE46016.1 clpP Structure source: AlphaFold + ColabFold UniProt A0A0H3GKH6
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Amino acids 175
Annotations 8
Features 28
PDB binders 5
Druggability 0.576

Overview

Basic information about this protein and its source genome.

Accession
KP13_32154
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46016.1 clpP
Status
annotated
Amino acids
175
Structure source
AlphaFold + ColabFold
EC
3.4.21.92
GO
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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
55.975
Human E-value
3.74e-64
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
71.023
DEG E-value
4.9699999999999995e-95
Localization
Cytoplasmic
ColabFold pLDDT
97.51

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its 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
Normalized 0.875

Sequence

Primary amino-acid sequence viewer.

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GKH6
AlphaFold — — full sequence — Viewing
ColabFold KP13_32154
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.576
3 0.216
7 0.209

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 2.29 0.058
2 1.7 0.029

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

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
2FZS
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
6L3X
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
6L40
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
6NB1
P0A6G7 466.9 Da LogP 4.21 TPSA 76.1 ✓ Ro5 ✓ Clean CC(C)(C(=O)NCCSc1ccccc1Cl)S(=O)(=O)c2ccc(cn2)C(…
NWT
6TTZ
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.