4P3H

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

  • Classification: HYDROLASE
  • Organism(s): Human gammaherpesvirus 8
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2014-03-07 Released: 2014-07-23 
  • Deposition Author(s): Gable, J.E.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS), National Institutes of Health/National Center for Research Resources (NIH/NCRR), NCI and the Helen Diller Family Comprehensive Cancer Center, National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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:  
    4P2T, 4P3H

  • 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 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) ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KSHV proteaseA, B193Human gammaherpesvirus 8Mutation(s): 0 
Gene Names: ORF17
UniProt
Find proteins for O36607 (Human herpesvirus 8)
Explore O36607 
Go to UniProtKB:  O36607
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO36607
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
25G
Query on 25G

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B],
H [auth B]
N-[2-benzyl-4-(1H-tetrazol-5-yl)phenyl]-6-(cyclohexylmethyl)pyridine-2-carboxamide
C27 H28 N6 O
DXIJKKFLXBIMCT-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
25G Binding MOAD:  4P3H IC50: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.12α = 90
b = 95.892β = 90
c = 119.342γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2014-07-23 
  • Deposition Author(s): Gable, J.E.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI090592
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP50-GM08250
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM008284
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United StatesUL1 TR000004
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesUL1 RR024131
NCI and the Helen Diller Family Comprehensive Cancer CenterUnited StatesP30 CA 82103-13
National Science Foundation (NSF, United States)United StatesGRFP1144247

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence