5V5D

Room temperature (280K) crystal structure of Kaposi's sarcoma-associated herpesvirus protease in complex with allosteric inhibitor (compound 250)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.104 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases.

Acker, T.M.Gable, J.E.Bohn, M.F.Jaishankar, P.Thompson, M.C.Fraser, J.S.Renslo, A.R.Craik, C.S.

(2017) J. Am. Chem. Soc. 139: 11650-11653

  • DOI: 10.1021/jacs.7b04030
  • Primary Citation of Related Structures:  5V5E

  • PubMed Abstract: 
  • Targeting of cryptic binding sites represents an attractive but underexplored approach to modulating protein function with small molecules. Using the dimeric protease (Pr) from Kaposi's sarcoma-associated herpesvirus (KSHV) as a model system, we soug ...

    Targeting of cryptic binding sites represents an attractive but underexplored approach to modulating protein function with small molecules. Using the dimeric protease (Pr) from Kaposi's sarcoma-associated herpesvirus (KSHV) as a model system, we sought to dissect a putative allosteric network linking a cryptic site at the dimerization interface to enzyme function. Five cryogenic X-ray structures were solved of the monomeric protease with allosteric inhibitors bound to the dimer interface site. Distinct coordinated movements captured by the allosteric inhibitors were also revealed as alternative states in room-temperature X-ray data and comparative analyses of other dimeric herpesvirus proteases. A two-step mechanism was elucidated through detailed kinetic analyses and suggests an enzyme isomerization model of inhibition. Finally, a representative allosteric inhibitor from this class was shown to be efficacious in a cellular model of viral infectivity. These studies reveal a coordinated dynamic network of atomic communication linking cryptic binding site occupancy and allosteric inactivation of KHSV Pr that can be exploited to target other members of this clinically relevant family of enzymes.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ORF 17
A, B
193Human herpesvirus 8Gene Names: ORF17
Find proteins for O40922 (Human herpesvirus 8)
Go to UniProtKB:  O40922
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8OY
Query on 8OY

Download SDF File 
Download CCD File 
A, B
4-{[6-(cyclohexylmethyl)pyridine-2-carbonyl]amino}-3-(phenylamino)benzoic acid
C26 H27 N3 O3
PIPBPJWDZSBLMQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.104 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.174 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 69.060α = 90.00
b = 94.090β = 90.00
c = 119.680γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01-AI090592
National Institutes of Health/National Institute of General Medical SciencesUnited States1F32GM111012
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited States5F32HL129989-03

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-08-16
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence