8SVR

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 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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 Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Find proteins for O75469 (Homo sapiens)
Explore O75469 
Go to UniProtKB:  O75469
PHAROS:  O75469
GTEx:  ENSG00000144852 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ15788O75469
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WT1 (Subject of Investigation/LOI)
Query on WT1

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
(1P)-N-(5-tert-butyl-2-{[(3S)-hexan-3-yl]oxy}phenyl)-5-methyl-1-(2,4,5-trimethoxyphenyl)-1H-1,2,3-triazole-4-carboxamide
C29 H40 N4 O5
YFTNXUROGXJXND-FQEVSTJZSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • 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

View Full Validation Report



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