4P2T

Crystal structure of Kaposi's sarcoma-associated herpesvirus (KSHV) protease in complex with a dimer disruptor

  • Classification: HYDROLASE
  • Organism(s): Human herpesvirus 8 type P (isolate GK18)
  • Expression System: Escherichia coli

  • Deposited: 2014-03-04 Released: 2014-07-16 
  • Deposition Author(s): Gable, J.E.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases; National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Center for Advancing Translational Sciences; National Institutes of Health/National Center for Research Resources; NCI and the Helen Diller Family Comprehensive Cancer Center; National Science Foundation (United States) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Broad-spectrum allosteric inhibition of herpesvirus proteases.

Gable, J.E.Lee, G.M.Jaishankar, P.Hearn, B.R.Waddling, C.A.Renslo, A.R.Craik, C.S.

(2014) Biochemistry 53: 4648-4660

  • DOI: 10.1021/bi5003234
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Herpesviruses rely on a homodimeric protease for viral capsid maturation. A small molecule, DD2, previously shown to disrupt dimerization of Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) by trapping an inactive monomeric conformation and ...

    Herpesviruses rely on a homodimeric protease for viral capsid maturation. A small molecule, DD2, previously shown to disrupt dimerization of Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) by trapping an inactive monomeric conformation and two analogues generated through carboxylate bioisosteric replacement (compounds 2 and 3) were shown to inhibit the associated proteases of all three human herpesvirus (HHV) subfamilies (α, β, and γ). Inhibition data reveal that compound 2 has potency comparable to or better than that of DD2 against the tested proteases. Nuclear magnetic resonance spectroscopy and a new application of the kinetic analysis developed by Zhang and Poorman [Zhang, Z. Y., Poorman, R. A., et al. (1991) J. Biol. Chem. 266, 15591-15594] show DD2, compound 2, and compound 3 inhibit HHV proteases by dimer disruption. All three compounds bind the dimer interface of other HHV proteases in a manner analogous to binding of DD2 to KSHV protease. The determination and analysis of cocrystal structures of both analogues with the KSHV Pr monomer verify and elaborate on the mode of binding for this chemical scaffold, explaining a newly observed critical structure-activity relationship. These results reveal a prototypical chemical scaffold for broad-spectrum allosteric inhibition of human herpesvirus proteases and an approach for the identification of small molecules that allosterically regulate protein activity by targeting protein-protein interactions.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158-2280, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
KSHV Protease
A, B
194Human herpesvirus 8 type P (isolate GK18)Mutation(s): 0 
Gene Names: ORF17
Find proteins for Q2HRB6 (Human herpesvirus 8 type P (isolate GK18))
Go to UniProtKB:  Q2HRB6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
24Q
Query on 24Q

Download SDF File 
Download CCD File 
A, B
6-(cyclohexylmethyl)-N-[4-(methylsulfonylcarbamoyl)-2-(phenylmethyl)phenyl]pyridine-2-carboxamide
C28 H31 N3 O4 S
ZNGZJFRXFZQBMG-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
24QIC50: 3700 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.185 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 69.737α = 90.00
b = 95.947β = 90.00
c = 119.245γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-03-04 
  • Released Date: 2014-07-16 
  • Deposition Author(s): Gable, J.E.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01-AI090592
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP50-GM08250
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM008284
National Institutes of Health/National Center for Advancing Translational SciencesUnited StatesUL1 TR000004
National Institutes of Health/National Center for Research ResourcesUnited StatesUL1 RR024131
NCI and the Helen Diller Family Comprehensive Cancer CenterUnited StatesP30 CA 82103-13
National Science Foundation (United States)United StatesGRFP1144247

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary