4NY9 | pdb_00004ny9

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

• PDB DOI: https://doi.org/10.2210/pdb4NY9/pdb

• Classification: TRANSCRIPTION/TRANSCRIPTION inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-12-10 Released: 2014-08-27 
• Deposition Author(s): Khan, J.A., Camac, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.298 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

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

• PubMed: 25101488 
• DOI: https://doi.org/10.1021/jm5003167
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.98 kDa 
• Atom Count: 2,178 
• Modeled Residue Count: 260 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 1 group I member 2	A	290	Homo sapiens	Mutation(s): 0  Gene Names: NR1I2, PXR
UniProt & NIH Common Fund Data Resources
Find proteins for O75469 (Homo sapiens) Explore O75469  Go to UniProtKB:  O75469
PHAROS:  O75469 GTEx:  ENSG00000144852

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2Q4	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
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.76	α = 90
b = 91.76	β = 90
c = 85.651	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-27 
Deposition Author(s): Khan, J.A., Camac, D.M.

Revision History  

• 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
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations