8SVR | pdb_00008svr

Crystal structure of pregnane X receptor ligand binding domain in complex with SJPYT-326


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 
    0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Chemical manipulation of an activation/inhibition switch in the nuclear receptor PXR.

Garcia-Maldonado, E.Huber, A.D.Chai, S.C.Nithianantham, S.Li, Y.Wu, J.Poudel, S.Miller, D.J.Seetharaman, J.Chen, T.

(2024) Nat Commun 15: 4054-4054

  • DOI: https://doi.org/10.1038/s41467-024-48472-1
  • Primary Citation Related Structures: 
    8SVN, 8SVO, 8SVP, 8SVQ, 8SVR, 8SVS, 8SVT, 8SVU, 8SVX

  • PubMed Abstract: 

    Nuclear receptors are ligand-activated transcription factors that can often be useful drug targets. Unfortunately, ligand promiscuity leads to two-thirds of receptors remaining clinically untargeted. PXR is a nuclear receptor that can be activated by diverse compounds to elevate metabolism, negatively impacting drug efficacy and safety. This presents a barrier to drug development because compounds designed to target other proteins must avoid PXR activation while retaining potency for the desired target. This problem could be avoided by using PXR antagonists, but these compounds are rare, and their molecular mechanisms remain unknown. Here, we report structurally related PXR-selective agonists and antagonists and their corresponding co-crystal structures to describe mechanisms of antagonism and selectivity. Structural and computational approaches show that antagonists induce PXR conformational changes incompatible with transcriptional coactivator recruitment. These results guide the design of compounds with predictable agonist/antagonist activities and bolster efforts to generate antagonists to prevent PXR activation interfering with other drugs.


  • Organizational Affiliation
    • Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.

Macromolecule Content 

  • Total Structure Weight: 80.92 kDa 
  • Atom Count: 4,519 
  • Modeled Residue Count: 560 
  • Deposited Residue Count: 702 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pregnane X receptor ligand binding domain fused to SRC-1 coactivator peptide
A, B
351Homo sapiensMutation(s): 0 
Gene Names: NR1I2PXRNCOA1BHLHE74SRC1
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for O75469 (Homo sapiens)
Explore O75469 
Go to UniProtKB:  O75469
PHAROS:  O75469
GTEx:  ENSG00000144852 
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ15788O75469
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
WT1 BindingDB:  8SVR IC50: min: 7.8, max: 45 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free:  0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.075α = 90
b = 88.498β = 90
c = 105.381γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118041

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references