6N80 | pdb_00006n80

S. aureus ClpP bound to anti-4a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.201 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6N80

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

De Novo Design of Boron-Based Peptidomimetics as Potent Inhibitors of Human ClpP in the Presence of Human ClpX.

Tan, J.Grouleff, J.J.Jitkova, Y.Diaz, D.B.Griffith, E.C.Shao, W.Bogdanchikova, A.F.Poda, G.Schimmer, A.D.Lee, R.E.Yudin, A.K.

(2019) J Med Chem 62: 6377-6390

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00878
  • Primary Citation Related Structures: 
    6N80

  • PubMed Abstract: 

    Boronic acids have attracted the attention of synthetic and medicinal chemists due to boron's ability to modulate enzyme function. Recently, we demonstrated that boron-containing amphoteric building blocks facilitate the discovery of bioactive aminoboronic acids. Herein, we have augmented this capability with a de novo library design and a virtual screening platform modified for covalent ligands. This technique has allowed us to rapidly design and identify a series of α-aminoboronic acids as the first inhibitors of human ClpXP, which is responsible for the degradation of misfolded proteins.


  • Organizational Affiliation
    • Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada.

Macromolecule Content 

  • Total Structure Weight: 322.29 kDa 
  • Atom Count: 21,063 
  • Modeled Residue Count: 2,524 
  • Deposited Residue Count: 2,842 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit203Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: clpPSAOUHSC_00790
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JT7

Query on JT7



Download:Ideal Coordinates CCD File
AA [auth S]
BA [auth T]
O [auth A]
P [auth B]
Q [auth C]
AA [auth S],
BA [auth T],
O [auth A],
P [auth B],
Q [auth C],
R [auth D],
S [auth E],
T [auth F],
U [auth G],
V [auth I],
W [auth K],
X [auth L],
Y [auth M],
Z [auth N]
N-[(1R)-1-borono-3-methylbutyl]-N~2~-(2-chloro-4-methoxybenzene-1-carbonyl)-L-leucinamide
C19 H30 B Cl N2 O5
IUZAVACFOSUDSF-IRXDYDNUSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.201 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.332α = 90
b = 126.115β = 93.8
c = 145.461γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI110578

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary