8I71

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 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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))
Go to UniProtKB:  P03147
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 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • 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