5YXL

A ligand M binding to FXR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.223 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NIWClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

A ligand M binding to FXR

Yi, L.Yong, L.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bile acid receptor
A, C
229Homo sapiensMutation(s): 0 
Gene Names: NR1H4BARFXRHRR1RIP14
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens)
Explore Q96RI1 
Go to UniProtKB:  Q96RI1
PHAROS:  Q96RI1
GTEx:  ENSG00000012504 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RI1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Nuclear receptor coactivator 2
B, D
8Homo 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  
UniProt GroupQ15596
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NIW
Query on NIW

Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]
2-methoxyethyl propan-2-yl 2,6-dimethyl-4-(3-nitrophenyl)pyridine-3,5-dicarboxylate
C21 H24 N2 O7
SJJUCKCPGPCJQM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free:  0.223 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.509α = 90
b = 117.341β = 90
c = 151.137γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NIWClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references