5GMZ

Hepatitis B virus core protein Y132A mutant in complex with 4-methyl heteroaryldihydropyrimidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Design and Synthesis of Orally Bioavailable 4-Methyl Heteroaryldihydropyrimidine Based Hepatitis B Virus (HBV) Capsid Inhibitors

Qiu, Z.Lin, X.Zhou, M.Liu, Y.Zhu, W.Chen, W.Zhang, W.Guo, L.Liu, H.Wu, G.Huang, M.Jiang, M.Xu, Z.Zhou, Z.Qin, N.Ren, S.Qiu, H.Zhong, S.Zhang, Y.Zhang, Y.Wu, X.Shi, L.Shen, F.Mao, Y.Zhou, X.Yang, W.Wu, J.Z.Yang, G.Mayweg, A.V.Shen, H.C.Tang, G.

(2016) J Med Chem 59: 7651-7666

  • DOI: 10.1021/acs.jmedchem.6b00879
  • Primary Citation of Related Structures:  
    5GMZ

  • PubMed Abstract: 
  • Targeting the capsid protein of hepatitis B virus (HBV) and thus interrupting normal capsid formation have been an attractive approach to block the replication of HBV viruses. We carried out multidimensional structural optimizations based on the hete ...

    Targeting the capsid protein of hepatitis B virus (HBV) and thus interrupting normal capsid formation have been an attractive approach to block the replication of HBV viruses. We carried out multidimensional structural optimizations based on the heteroaryldihydropyrimidine (HAP) analogue Bay41-4109 (1) and identified a novel series of HBV capsid inhibitors that demonstrated promising cellular selectivity indexes, metabolic stabilities, and in vitro safety profiles. Herein we disclose the design, synthesis, structure-activity relationship (SAR), cocrystal structure in complex with HBV capsid proteins and in vivo pharmacological study of the 4-methyl HAP analogues. In particular, the (2S,4S)-4,4-difluoroproline substituted analogue 34a demonstrated high oral bioavailability and liver exposure and achieved over 2 log viral load reduction in a hydrodynamic injected (HDI) HBV mouse model.


    Organizational Affiliation

    Roche Innovation Center Shanghai, ‡Medicinal Chemistry, §Chemical Biology, ∥Pharmaceutical Sciences, and ⊥Discovery Virology, Roche Pharma Research and Early Development , 720 Cailun Road, Shanghai, 201203 China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Core proteinABCDEF155Hepatitis B virusMutation(s): 1 
Gene Names: C
Find proteins for P03147 (Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979))
Explore P03147 
Go to UniProtKB:  P03147
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6XU
Query on 6XU

Download Ideal Coordinates CCD File 
A, B, C, D, E, F
(2S)-4,4-difluoro-1-[[(4S)-4-(4-fluorophenyl)-5-methoxycarbonyl-4-methyl-2-(1,3-thiazol-2-yl)-1H-pyrimidin-6-yl]methyl]pyrrolidine-2-carboxylic acid
C22 H21 F3 N4 O4 S
ZUNJWALIUFZGCH-BTYIYWSLSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B, F
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
A, C, D, E
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.017α = 68.1
b = 67.215β = 68.43
c = 87.669γ = 83.07
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-07-18 
  • Released Date: 2016-08-10 
  • Deposition Author(s): Xu, Z.H., Zhou, Z.

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references