8UVL | pdb_00008uvl

Crystal structure of selective IRE1a inhibitor 29 at the enzyme active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.251 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.181 (Depositor) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8UVL

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of Potent, Selective, and Orally Available IRE1 alpha Inhibitors Demonstrating Comparable PD Modulation to IRE1 Knockdown in a Multiple Myeloma Model.

Braun, M.G.Ashkenazi, A.Beveridge, R.E.Castanedo, G.Wallweber, H.A.Beresini, M.H.Clark, K.R.De Bruyn, T.Fu, L.Gibbons, P.Jiang, F.Kaufman, S.Kan, D.Kiefer, J.R.Leclerc, J.P.Lemire, A.Ly, C.Segal, E.Sims, J.Wang, W.Wei, W.Zhao, L.Schwarz, J.B.Rudolph, J.

(2024) J Med Chem 67: 8708-8729

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02425
  • Primary Citation Related Structures: 
    8UVL

  • PubMed Abstract: 

    The lack of selective and safe in vivo IRE1α tool molecules has limited the evaluation of IRE1α as a viable target to treat multiple myeloma. Focus on improving the physicochemical properties of a literature compound by decreasing lipophilicity, molecular weight, and basicity allowed the discovery of a novel series with a favorable in vitro safety profile and good oral exposure. These efforts culminated in the identification of a potent and selective in vivo tool compound, G-5758 , that was well tolerated following multiday oral administration of doses up to 500 mg/kg. G-5758 demonstrated comparable pharmacodynamic effects to induced IRE1 knockdown as measured by XBP1s levels in a multiple myeloma model (KMS-11).


  • Organizational Affiliation
    • Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States.

Macromolecule Content 

  • Total Structure Weight: 52.46 kDa 
  • Atom Count: 3,356 
  • Modeled Residue Count: 403 
  • Deposited Residue Count: 448 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase/endoribonuclease IRE1448Homo sapiensMutation(s): 0 
Gene Names: ERN1IRE1
EC: 2.7.11.1 (PDB Primary Data), 3.1.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O75460 (Homo sapiens)
Explore O75460 
Go to UniProtKB:  O75460
PHAROS:  O75460
GTEx:  ENSG00000178607 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75460
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XOE
(Subject of Investigation/LOI)

Query on XOE



Download:Ideal Coordinates CCD File
J [auth A]1-phenyl-N-(2,3,6-trifluoro-4-{[(3M)-3-(2-{[(3R,5R)-5-fluoropiperidin-3-yl]amino}pyrimidin-4-yl)pyridin-2-yl]oxy}phenyl)methanesulfonamide
C27 H24 F4 N6 O3 S
RBOAUACOQMQNBF-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.251 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.181 (Depositor) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.89α = 90
b = 166.834β = 90
c = 102.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

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: 2024-05-29
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Database references