9K2B | pdb_00009k2b

Structure of ClpP from Staphylococcus aureus in complex with ZY18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1EELClick on this verticalbar to view detailsBest fitted MPDClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Structure-Guided Development of ClpP Agonists with Potent Therapeutic Activities against Staphylococcus aureus Infection.

Zhang, T.Wu, W.Zhao, Y.Ding, Z.Wei, B.Yang, T.Li, J.Wang, P.Lan, L.Gan, J.Yang, C.G.

(2025) J Med Chem 68: 1810-1823

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02562
  • Primary Citation of Related Structures:  
    9K2A, 9K2B, 9K2C, 9K2D, 9K2K

  • PubMed Abstract: 

    Peritonitis caused by Staphylococcus aureus poses a severe threat to patients with end-stage renal failure. Treating multidrug-resistant S. aureus infections requires the use of antibiotics with diverse mechanisms of action. Caseinolytic protease P (ClpP) is a promising antibacterial target; however, selective activation of S. aureus ClpP ( Sa ClpP) over human ClpP ( Hs ClpP) remains challenging. We previously identified ( R )-ZG197 as a selective Sa ClpP agonist, but its potency was suboptimal. Herein, we develop ( R )-ZG197 analogs through a structure-guided approach and examine their structure-activity relationships. Notably, ZY39 demonstrates improved activation of Sa ClpP and superior binding affinity. Interestingly, while ZY39 facilitates the enzymatic hydrolysis of Sa ClpP and Hs ClpP in vitro , it does not target Hs ClpP in cellular environments. Furthermore, ZY39 effectively inhibits the growth of multidrug-resistant S. aureus strains and shows excellent therapeutic efficacy in a murine model of peritonitis. These findings highlight ZY39 as a promising Sa ClpP agonist for combating staphylococcal infections.


  • Organizational Affiliation

    State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E
201Staphylococcus aureus subsp. aureus Mu3Mutation(s): 0 
Gene Names: clpPSAHV_0765
EC: 3.4.21.92
UniProt
Find proteins for Q2G036 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G036 
Go to UniProtKB:  Q2G036
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G036
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EEL (Subject of Investigation/LOI)
Query on A1EEL

Download Ideal Coordinates CCD File 
AA [auth D]
CB [auth M]
DA [auth E]
FB [auth N]
GA [auth F]
(6~{S},9~{a}~{S})-6-[(2~{S})-butan-2-yl]-~{N}-[(2~{S})-2-methylbutyl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-3,6,9,9~{a}-tetrahydro-2~{H}-pyrazino[1,2-a]pyrimidine-1-carboxamide
C28 H38 N4 O3
DSUXNYPFVGTLTM-NLVWIRSPSA-N
MPD (Subject of Investigation/LOI)
Query on MPD

Download Ideal Coordinates CCD File 
BB [auth M]
CA [auth E]
EB [auth N]
FA [auth F]
IA [auth G]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AB [auth M]
BA [auth E]
DB [auth N]
EA [auth F]
HA [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.293α = 90
b = 127.033β = 95.43
c = 145.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1EELClick on this verticalbar to view detailsBest fitted MPDClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22037007
National Natural Science Foundation of China (NSFC)China22107109
National Natural Science Foundation of China (NSFC)China22307029

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release