6BNS | pdb_00006bns

STRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN BOUND TETHERED WITH SRC co-activator peptide and Compound 25a AKA BICYCLIC HEXAFLUOROISOPROPYL 2 ALCOHOL SULFONAMIDES

• PDB DOI: https://doi.org/10.2210/pdb6BNS/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-11-17 Released: 2017-12-20 
• Deposition Author(s): DHAR, T.G., GONG, H., WEINSTEIN, D.S., LU, Z., DUAN, J.J.W., STACHURA, S., HAQUE, L., KARMAKAR, A., HEMAGIRI, H., RAUT, D.K., GUPTA, A.K., KHAN, J.A., SACK, J.S., CAMAC, D.M., PUDZIANOWSKI, A.A., WU, D.R., YARDE, M., SHEN, D.R., BOROWSKI, V., XIE, J.H., SUN, H., ARIENZO, C.D., DABROS, M., GALELLA, M.A., WANG, F., WEIGELT, C.A., ZHAO, Q., FOSTER, W., SOMERVILLE, J.E., SALTER-CID, L.M., BARRISH, J.C., CARTER, P.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 
  0.246 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Identification of bicyclic hexafluoroisopropyl alcohol sulfonamides as retinoic acid receptor-related orphan receptor gamma (ROR gamma /RORc) inverse agonists. Employing structure-based drug design to improve pregnane X receptor (PXR) selectivity.

Gong, H., Weinstein, D.S., Lu, Z., Duan, J.J., Stachura, S., Haque, L., Karmakar, A., Hemagiri, H., Raut, D.K., Gupta, A.K., Khan, J., Camac, D., Sack, J.S., Pudzianowski, A., Wu, D.R., Yarde, M., Shen, D.R., Borowski, V., Xie, J.H., Sun, H., D'Arienzo, C., Dabros, M., Galella, M.A., Wang, F., Weigelt, C.A., Zhao, Q., Foster, W., Somerville, J.E., Salter-Cid, L.M., Barrish, J.C., Carter, P.H., Dhar, T.G.M.

(2018) Bioorg Med Chem Lett 28: 85-93

• PubMed: 29233651 
• DOI: https://doi.org/10.1016/j.bmcl.2017.12.006
• Primary Citation Related Structures: 
  6BN6, 6BNS


• PubMed Abstract: 
  

  We disclose the optimization of a high throughput screening hit to yield benzothiazine and tetrahydroquinoline sulfonamides as potent RORγt inverse agonists. However, a majority of these compounds showed potent activity against pregnane X receptor (PXR) and modest activity against liver X receptor α (LXRα). Structure-based drug design (SBDD) led to the identification of benzothiazine and tetrahydroquinoline sulfonamide analogs which completely dialed out LXRα activity and were less potent at PXR. Pharmacodynamic (PD) data for compound 35 in an IL-23 induced IL-17 mouse model is discussed along with the implications of a high Y _max in the PXR assay for long term preclinical pharmacokinetic (PK) studies.

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Organizational Affiliation: 
• Bristol-Myers Squibb, Research and Development, Princeton, NJ 08543-4000, United States.
Bristol-Myers Squibb-Biocon Research Center, Bangalore, India.
Bristol-Myers Squibb, Research and Development, Princeton, NJ 08543-4000, United States. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 81 kDa 
• Atom Count: 4,583 
• Modeled Residue Count: 569 
• Deposited Residue Count: 702 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1 Chimera	A, B	351	Homo sapiens	Mutation(s): 0  Gene Names: NR1I2, PXR, NCOA1, BHLHE74, SRC1 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
UniProt Groups	Q15788O75469

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XGH	C [auth A], D [auth B]	2-[(2S)-4-[(4-fluorophenyl)sulfonyl]-7-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)-3,4-dihydro-2H-1,4-benzothiazin-2-yl]-N-(2-hydroxy-2-methylpropyl)acetamide C23 H23 F7 N2 O5 S2 XUCORPNQMQOUMD-HNNXBMFYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XGH	BindingDB:  6BNS	EC50: 144 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free:  0.246 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.37	α = 90
b = 89.234	β = 90
c = 105.902	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): DHAR, T.G., GONG, H., WEINSTEIN, D.S., LU, Z., DUAN, J.J.W., STACHURA, S., HAQUE, L., KARMAKAR, A., HEMAGIRI, H., RAUT, D.K., GUPTA, A.K., KHAN, J.A., SACK, J.S., CAMAC, D.M., PUDZIANOWSKI, A.A., WU, D.R., YARDE, M., SHEN, D.R., BOROWSKI, V., XIE, J.H., SUN, H., ARIENZO, C.D., DABROS, M., GALELLA, M.A., WANG, F., WEIGELT, C.A., ZHAO, Q., FOSTER, W., SOMERVILLE, J.E., SALTER-CID, L.M., BARRISH, J.C., CARTER, P.H.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2017-12-27
  Changes: Database references
• Version 1.2: 2018-01-03
  Changes: Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references