7WID

Crystal structure of Staphylococcus aureus ClpP in complex with ZG180


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Anti-infective therapy using species-specific activators of Staphylococcus aureus ClpP.

Wei, B.Zhang, T.Wang, P.Pan, Y.Li, J.Chen, W.Zhang, M.Ji, Q.Wu, W.Lan, L.Gan, J.Yang, C.G.

(2022) Nat Commun 13: 6909-6909

  • DOI: https://doi.org/10.1038/s41467-022-34753-0
  • Primary Citation of Related Structures:  
    7WGS, 7WH5, 7WID, 7XBZ

  • PubMed Abstract: 

    The emergence of methicillin-resistant Staphylococcus aureus isolates highlights the urgent need to develop more antibiotics. ClpP is a highly conserved protease regulated by ATPases in bacteria and in mitochondria. Aberrant activation of  bacterial ClpP is an alternative method of discovering antibiotics, while it remains difficult to develop selective  Staphylococcus aureus ClpP activators that can avoid disturbing Homo sapiens ClpP functions. Here, we use a structure-based design to identify (R)- and (S)-ZG197 as highly selective Staphylococcus aureus ClpP activators. The key structural elements in Homo sapiens ClpP, particularly W146 and its joint action with the C-terminal motif, significantly contribute to the discrimination of the activators. Our selective activators display wide antibiotic properties towards an array of multidrug-resistant staphylococcal strains in vitro, and demonstrate promising antibiotic efficacy in zebrafish and murine skin infection models. Our findings indicate that the species-specific activators of Staphylococcus aureus ClpP are exciting therapeutic agents to treat staphylococcal infections.


  • Organizational Affiliation

    School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, 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
A, B, C, D, E, F, G, H, I, J, K, L, M, N
195Staphylococcus aureusMutation(s): 0 
Gene Names: ClpP
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
9DF (Subject of Investigation/LOI)
Query on 9DF

Download Ideal Coordinates CCD File 
AA [auth E]
CB [auth N]
DA [auth F]
GA [auth G]
JA [auth H]
AA [auth E],
CB [auth N],
DA [auth F],
GA [auth G],
JA [auth H],
MA [auth I],
O [auth A],
QA [auth J],
R [auth B],
TA [auth K],
V [auth C],
WA [auth L],
Y [auth D],
ZA [auth M]
(6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
C27 H33 F3 N4 O3
KQOUYKFBWWUWOZ-ANJVHQHFSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
BB [auth M]
CA [auth E]
EB [auth N]
FA [auth F]
IA [auth G]
BB [auth M],
CA [auth E],
EB [auth N],
FA [auth F],
IA [auth G],
LA [auth H],
OA [auth I],
PA [auth I],
Q [auth A],
SA [auth J],
T [auth B],
U [auth B],
VA [auth K],
X [auth C],
YA [auth L],
Z [auth D]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth M]
BA [auth E]
DB [auth N]
EA [auth F]
HA [auth G]
AB [auth M],
BA [auth E],
DB [auth N],
EA [auth F],
HA [auth G],
KA [auth H],
NA [auth I],
P [auth A],
RA [auth J],
S [auth B],
UA [auth K],
W [auth C],
XA [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.178α = 90
b = 126.385β = 94.09
c = 145.449γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data 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)China21725801
National Natural Science Foundation of China (NSFC)China22107109

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description