4NY9

Crystal Structure Of the Human PXR-LBD In Complex With N-{(2R)-1-[(4S)-4-(4-chlorophenyl)-4-hydroxy-3,3-dimethylpiperidin-1-yl]-3-methyl-1-oxobutan-2-yl}-3-hydroxy-3-methylbutanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of the CCR1 antagonist, BMS-817399, for the treatment of rheumatoid arthritis.

Santella, J.B.Gardner, D.S.Duncia, J.V.Wu, H.Dhar, M.Cavallaro, C.Tebben, A.J.Carter, P.H.Barrish, J.C.Yarde, M.Briceno, S.W.Cvijic, M.E.Grafstrom, R.R.Liu, R.Patel, S.R.Watson, A.J.Yang, G.Rose, A.V.Vickery, R.D.Caceres-Cortes, J.Caporuscio, C.Camac, D.M.Khan, J.A.An, Y.Foster, W.R.Davies, P.Hynes, J.

(2014) J Med Chem 57: 7550-7564

  • DOI: 10.1021/jm5003167
  • Primary Citation of Related Structures:  
    4NY9

  • PubMed Abstract: 
  • High-affinity, functionally potent, urea-based antagonists of CCR1 have been discovered. Modulation of PXR transactivation has revealed the selective and orally bioavailable CCR1 antagonist BMS-817399 (29), which entered clinical trials for the treatment of rheumatoid arthritis ...

    High-affinity, functionally potent, urea-based antagonists of CCR1 have been discovered. Modulation of PXR transactivation has revealed the selective and orally bioavailable CCR1 antagonist BMS-817399 (29), which entered clinical trials for the treatment of rheumatoid arthritis.


    Organizational Affiliation

    Bristol Myers Squibb Company , P.O. Box 4000, Princeton, New Jersey 08543-4000, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor subfamily 1 group I member 2A290Homo sapiensMutation(s): 0 
Gene Names: NR1I2PXR
UniProt & NIH Common Fund Data Resources
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 GroupO75469
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2Q4
Query on 2Q4

Download Ideal Coordinates CCD File 
B [auth A]N-{(2R)-1-[(4S)-4-(4-chlorophenyl)-4-hydroxy-3,3-dimethylpiperidin-1-yl]-3-methyl-1-oxobutan-2-yl}-3-hydroxy-3-methylbutanamide
C23 H35 Cl N2 O4
PTNKPLPRPJERNR-XXBNENTESA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2Q4 BindingDB:  4NY9 EC50: min: 1800, max: 2300 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.232 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.76α = 90
b = 91.76β = 90
c = 85.651γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description