5T2P

Hepatitis B virus core protein Y132A mutant in complex with sulfamoylbenzamide (SBA_R01)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Heteroaryldihydropyrimidine (HAP) and Sulfamoylbenzamide (SBA) Inhibit Hepatitis B Virus Replication by Different Molecular Mechanisms.

Zhou, Z.Hu, T.Zhou, X.Wildum, S.Garcia-Alcalde, F.Xu, Z.Wu, D.Mao, Y.Tian, X.Zhou, Y.Shen, F.Zhang, Z.Tang, G.Najera, I.Yang, G.Shen, H.C.Young, J.A.Qin, N.

(2017) Sci Rep 7: 42374-42374

  • DOI: 10.1038/srep42374
  • Primary Citation of Related Structures:  
    5T2P, 5WRE, 5WTW

  • PubMed Abstract: 
  • Heteroaryldihydropyrimidine (HAP) and sulfamoylbenzamide (SBA) are promising non-nucleos(t)ide HBV replication inhibitors. HAPs are known to promote core protein mis-assembly, but the molecular mechanism of abnormal assembly is still elusive. Likewise, the assembly status of core protein induced by SBA remains unknown ...

    Heteroaryldihydropyrimidine (HAP) and sulfamoylbenzamide (SBA) are promising non-nucleos(t)ide HBV replication inhibitors. HAPs are known to promote core protein mis-assembly, but the molecular mechanism of abnormal assembly is still elusive. Likewise, the assembly status of core protein induced by SBA remains unknown. Here we show that SBA, unlike HAP, does not promote core protein mis-assembly. Interestingly, two reference compounds HAP_R01 and SBA_R01 bind to the same pocket at the dimer-dimer interface in the crystal structures of core protein Y132A hexamer. The striking difference lies in a unique hydrophobic subpocket that is occupied by the thiazole group of HAP_R01, but is unperturbed by SBA_R01. Photoaffinity labeling confirms the HAP_R01 binding pose at the dimer-dimer interface on capsid and suggests a new mechanism of HAP-induced mis-assembly. Based on the common features in crystal structures we predict that T33 mutations generate similar susceptibility changes to both compounds. In contrast, mutations at positions in close contact with HAP-specific groups (P25A, P25S, or V124F) only reduce susceptibility to HAP_R01, but not to SBA_R01. Thus, HAP and SBA are likely to have distinctive resistance profiles. Notably, P25S and V124F substitutions exist in low-abundance quasispecies in treatment-naïve patients, suggesting potential clinical relevance.


    Organizational Affiliation

    Roche Pharma Research and Early Development, Chemical Biology, Roche Innovation Center Shanghai, Shanghai, 201203, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Core protein
A, B, C, D, E, F
A, B, C, D, E, F
155Hepatitis B virusMutation(s): 1 
Gene Names: C
UniProt
Find proteins for L7R9I1 (Hepatitis B virus)
Explore L7R9I1 
Go to UniProtKB:  L7R9I1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL7R9I1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K89
Query on K89

Download Ideal Coordinates CCD File 
DA [auth F],
G [auth A],
J [auth B],
N [auth C],
T [auth D],
DA [auth F],
G [auth A],
J [auth B],
N [auth C],
T [auth D],
Z [auth E]
4-fluoranyl-3-(4-oxidanylpiperidin-1-yl)sulfonyl-~{N}-[3,4,5-tris(fluoranyl)phenyl]benzamide
C18 H16 F4 N2 O4 S
KKMFSVNFPUPGCA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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

Download Ideal Coordinates CCD File 
K [auth B],
O [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
BA [auth E],
CA [auth E],
FA [auth F],
H [auth A],
I [auth A],
BA [auth E],
CA [auth E],
FA [auth F],
H [auth A],
I [auth A],
L [auth B],
Q [auth C],
R [auth C],
S [auth C],
W [auth D]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth E],
EA [auth F],
P [auth C],
U [auth D],
V [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
K89 Binding MOAD:  5T2P IC50: 1900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.927α = 68.49
b = 68.048β = 69.99
c = 85.703γ = 83.49
Software Package:
Software NamePurpose
DENZOdata collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2016-08-24 
  • Released Date: 2017-02-22 
  • Deposition Author(s): Zhou, Z., Xu, Z.H.

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references