6N80

S. aureus ClpP bound to anti-4a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.9b00878

  • 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 aminob ...

    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 virtural 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E, F, G, I, K, L, M, N, S, T
203Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: clpP
EC: 3.4.21.92
Find proteins for Q2G036 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G036
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JT7
Query on JT7

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, I, K, L, M, N, S, T
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 94.332α = 90.00
b = 126.115β = 93.80
c = 145.461γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01 AI110578

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-24
    Type: Data collection, Database references