9IRM | pdb_00009irm

Structure of ClpP from Staphylococcus aureus in complex with ZG283


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 
    0.226 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9IRM

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structure-guided development of selective caseinolytic protease P agonists as antistaphylococcal agents.

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

(2024) Cell Rep Med 5: 101837-101837

  • DOI: https://doi.org/10.1016/j.xcrm.2024.101837
  • Primary Citation Related Structures: 
    9IRM, 9IRP

  • PubMed Abstract: 

    Methicillin-resistant Staphylococcus aureus is a ubiquitous pathogen, posing a serious threat to human health worldwide. Thus, there is a high demand for antibiotics with distinct targets. Caseinolytic protease P (ClpP) is a promising target for combating staphylococcal infections; however, selectively activating S. aureus ClpP (SaClpP) rather than Homo sapiens ClpP (HsClpP) remains challenging. Herein, we rationally design and identify ZG297 by structure-based strategy. It binds and activates SaClpP instead of HsClpP. This is due to differentiated ligand binding attributed to crossed "tyrosine/histidine" amino acid pairs. ZG297 substantially inhibits the growth of a broad panel of S. aureus strains in vitro, outperforming the selective (R)-ZG197 agonist. ZG297 also functions as a potent antibiotic against multidrug-resistant S. aureus infections in Galleria mellonella larvae, zebrafish, murine skin, and thigh infection models. Collectively, we demonstrate that ZG297 is a safer and more potent antistaphylococcal agent than acyldepsipeptide 4 and (R)-ZG197.


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

Macromolecule Content 

  • Total Structure Weight: 311.36 kDa 
  • Atom Count: 21,681 
  • Modeled Residue Count: 2,579 
  • Deposited Residue Count: 2,730 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
195Staphylococcus aureusMutation(s): 0 
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WBW
(Subject of Investigation/LOI)

Query on WBW



Download:Ideal Coordinates CCD File
BA [auth G]
DA [auth H]
FA [auth I]
IA [auth J]
KA [auth K]
BA [auth G],
DA [auth H],
FA [auth I],
IA [auth J],
KA [auth K],
MA [auth L],
O [auth A],
OA [auth M],
Q [auth B],
QA [auth N],
T [auth C],
V [auth D],
X [auth E],
Y [auth E]
(6S,9aS)-8-(anthracen-9-ylmethyl)-6-[(2S)-butan-2-yl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
C31 H35 F3 N4 O3
IPOJNTALVGAOOT-GFNGZDJJSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
AA [auth F]
CA [auth G]
EA [auth H]
GA [auth I]
HA [auth I]
AA [auth F],
CA [auth G],
EA [auth H],
GA [auth I],
HA [auth I],
JA [auth J],
LA [auth K],
NA [auth L],
P [auth A],
PA [auth M],
R [auth B],
RA [auth N],
S [auth B],
U [auth C],
W [auth D],
Z [auth E]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free:  0.226 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.41α = 90
b = 127.08β = 95.38
c = 146.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2024-10-23
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Database references