8I71 | pdb_00008i71

Hepatitis B virus core protein Y132A mutant in complex with Linvencorvir (RG7907), a Hepatitis B Virus (HBV) Core Protein Allosteric Modulator (CpAM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.193 (Depositor), 0.154 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8I71

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of Linvencorvir (RG7907), a Hepatitis B Virus Core Protein Allosteric Modulator, for the Treatment of Chronic HBV Infection.

Zhang, W.Guo, L.Liu, H.Wu, G.Shi, H.Zhou, M.Zhang, Z.Kou, B.Hu, T.Zhou, Z.Xu, Z.Zhou, X.Zhou, Y.Tian, X.Yang, G.Young, J.A.T.Qiu, H.Ottaviani, G.Xie, J.Mayweg, A.V.Shen, H.C.Zhu, W.

(2023) J Med Chem 66: 4253-4270

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00173
  • Primary Citation Related Structures: 
    8I71

  • PubMed Abstract: 

    Described herein is the first-time disclosure of Linvencorvir (RG7907), a clinical compound and a hepatitis B virus (HBV) core protein allosteric modulator, for the treatment of chronic HBV infection. Built upon the core structure of hetero aryl dihydropyrimidine, RG7907 was rationally designed by combining all the drug-like features of low CYP3A4 induction, potent anti-HBV activity, high metabolic stability, low hERG liability, and favorable animal pharmacokinetic (PK) profiles. In particular, the chemistry strategy to mitigate CYP3A4 induction through introducing a large, rigid, and polar substituent at the position that has less interaction with the therapeutic biological target (HBV core proteins herein) is of general interest to the medicinal chemistry community. RG7907 demonstrated favorable animal PK, pharmacodynamics, and safety profiles with sufficient safety margins supporting its clinical development in healthy volunteers and HBV-infected patients.


  • Organizational Affiliation
    • China Innovation Center of Roche, Medicinal Chemistry, Building 5, 371 Lishizhen Road, Shanghai 201203, China.

Macromolecule Content 

  • Total Structure Weight: 109.68 kDa 
  • Atom Count: 8,328 
  • Modeled Residue Count: 905 
  • Deposited Residue Count: 930 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein
A, B, C, D, E
A, B, C, D, E, F
155Hepatitis B virus subtype adywMutation(s): 1 
UniProt
Find proteins for P03147 (Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979))
Explore P03147 
Go to UniProtKB:  P03147
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03147
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OTI
(Subject of Investigation/LOI)

Query on OTI



Download:Ideal Coordinates CCD File
BA [auth E]
EA [auth F]
L [auth A]
Q [auth B]
V [auth C]
BA [auth E],
EA [auth F],
L [auth A],
Q [auth B],
V [auth C],
Z [auth D]
3-[(8~{a}~{S})-7-[[5-ethoxycarbonyl-4-(3-fluoranyl-2-methyl-phenyl)-2-(1,3-thiazol-2-yl)-1,4-dihydropyrimidin-6-yl]methyl]-3-oxidanylidene-5,6,8,8~{a}-tetrahydro-1~{H}-imidazo[1,5-a]pyrazin-2-yl]-2,2-dimethyl-propanoic acid
C29 H35 F N6 O5 S
YLJBFYZGSKMBEZ-XNUZUHMRSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
O [auth B],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
M [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
IPA

Query on IPA



Download:Ideal Coordinates CCD File
CA [auth F]
DA [auth F]
H [auth A]
I [auth A]
N [auth B]
CA [auth F],
DA [auth F],
H [auth A],
I [auth A],
N [auth B],
S [auth C],
T [auth C],
U [auth C],
Y [auth D]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth E],
G [auth A],
R [auth C],
W [auth D],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.193 (Depositor), 0.154 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.392α = 68.6
b = 67.565β = 69.81
c = 86.246γ = 83.87
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary