5GMZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.196 
  • R-Value Work: 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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Core protein
A, B, C, D, E, F
155Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979)Mutation(s): 1 
Gene Names: C
Find proteins for P03147 (Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979))
Go to UniProtKB:  P03147
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, C, D, E
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
6XU
Query on 6XU

Download SDF File 
Download 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 66.017α = 68.10
b = 67.215β = 68.43
c = 87.669γ = 83.07
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references