8VKZ

Crystal structure of Glucocorticoid Receptor in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Minimising the payload solvent exposed hydrophobic surface area optimises the antibody-drug conjugate properties.

Hobson, A.D.Zhu, H.Qiu, W.Judge, R.A.Longenecker, K.

(2024) RSC Med Chem 15: 832-838

  • DOI: https://doi.org/10.1039/d3md00540b
  • Primary Citation of Related Structures:  
    8VKZ

  • PubMed Abstract: 

    Glucocorticoid receptor modulators (GRMs) are an established and successful compound class for the treatment of multiple diseases. In addition, they are an area of high interest as payloads for antibody-drug conjugate s(ADCs) in both immunology and oncology. Solving the crystal structure of compound 2, the GRM payload from ABBV-3373 and ABBV-154, in the ligand binding domain of the glucocorticoid receptor (GR) revealed key information to facilitate optimal ADC payload design. All four critical H-bonds between the oxygen functional groups on the hexadecahydro-1 H -cyclopenta[ a ]phenanthrene ring system of the small molecule and protein were shown to be made (carbonyl at C3 to Gln570 and Arg611 and Asn564, carbonyl at C20 to Thr739, hydroxyl at C21 to Asn 564 and Thr739). In addition, an extra H-bond between the linker attachment site on compound 2, the aniline in the biaryl region, was observed. Confirmation of the stereochemistry of the acetal in compound 2 as ( R ) was established. Finally, the importance of minimising the exposed hydrophobic surface area of a payload to reduce the negative impact on the properties of resulting ADCs, like aggregation, was rationalised by comparison of ( R )-acetal compound 2 and ( S )-acetal compound 3.


  • Organizational Affiliation

    AbbVie Bioresearch Center 381 Plantation Street Worcester Massachusetts 01605 USA adrian.hobson@abbvie.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucocorticoid receptor
A, B
252Homo sapiensMutation(s): 3 
Gene Names: NR3C1GRL
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens)
Explore P04150 
Go to UniProtKB:  P04150
PHAROS:  P04150
GTEx:  ENSG00000113580 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04150
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2C [auth D],
D [auth E]
14Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ACE (Subject of Investigation/LOI)
Query on A1ACE

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
(4aR,4bS,5R,6aS,6bS,8R,9aR,10aR,10bR)-8-{4-[(3-aminophenyl)methyl]phenyl}-5-hydroxy-6b-(hydroxyacetyl)-4a,6a-dimethyl-4a,4b,5,6,6a,6b,9a,10,10a,10b,11,12-dodecahydro-2H,8H-naphtho[2',1':4,5]indeno[1,2-d][1,3]dioxol-2-one
C35 H39 N O6
MPEPSOPXQDGEHP-XSZYCUJUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.51α = 90
b = 141.65β = 93.46
c = 47.9γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
XDSdata 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: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Database references