5PGY

CRYSTAL STRUCTURE OF 11BETA-HSD1 DOUBLE MUTANT (L262R, F278E) COMPLEXED WITH 2-[(5R,7S)-6-HYDROXY-2-PHENYLADAMANTAN-2-YL]-1-(3-HYDROXYAZETIDIN-1-YL)ETHAN-1-ONE (BMS-816336)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 
    0.226 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.187 (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 NAPClick on this verticalbar to view detailsBest fitted 8KGClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Discovery of Clinical Candidate 2-((2S,6S)-2-Phenyl-6-hydroxyadamantan-2-yl)-1-(3'-hydroxyazetidin-1-yl)ethanone [BMS-816336], an Orally Active Novel Selective 11 beta-Hydroxysteroid Dehydrogenase Type 1 Inhibitor.

Ye, X.Y.Chen, S.Y.Wu, S.Yoon, D.S.Wang, H.Hong, Z.O'Connor, S.P.Li, J.Li, J.J.Kennedy, L.J.Walker, S.J.Nayeem, A.Sheriff, S.Camac, D.M.Ramamurthy, V.Morin, P.E.Zebo, R.Taylor, J.R.Morgan, N.N.Ponticiello, R.P.Harrity, T.Apedo, A.Golla, R.Seethala, R.Wang, M.Harper, T.W.Sleczka, B.G.He, B.Kirby, M.Leahy, D.K.Li, J.Hanson, R.L.Guo, Z.Li, Y.X.DiMarco, J.D.Scaringe, R.Maxwell, B.Moulin, F.Barrish, J.C.Gordon, D.A.Robl, J.A.

(2017) J Med Chem 60: 4932-4948

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00211
  • Primary Citation of Related Structures:  
    5PGU, 5PGV, 5PGW, 5PGX, 5PGY, 5PGZ

  • PubMed Abstract: 

    BMS-816336 (6n-2), a hydroxy-substituted adamantyl acetamide, has been identified as a novel, potent inhibitor against human 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) enzyme (IC 50 3.0 nM) with >10000-fold selectivity over human 11β-hydroxysteroid dehydrogenase type 2 (11β-HSD2). 6n-2 exhibits a robust acute pharmacodynamic effect in cynomolgus monkeys (ED 50 0.12 mg/kg) and in DIO mice. It is orally bioavailable (%F ranges from 20 to 72% in preclinical species) and has a predicted pharmacokinetic profile of a high peak to trough ratio and short half-life in humans. This ADME profile met our selection criteria for once daily administration, targeting robust inhibition of 11β-HSD1 enzyme for the first 12 h period after dosing followed by an "inhibition holiday" so that the potential for hypothalamic-pituitary-adrenal (HPA) axis activation might be mitigated. 6n-2 was found to be well-tolerated in phase 1 clinical studies and represents a potential new treatment for type 2 diabetes, metabolic syndrome, and other human diseases modulated by glucocorticoid control.


  • Organizational Affiliation

    Discovery Chemistry, ‡Pharmaceutical Candidate Optimization, §Computer-Assisted Drug Design, ∥Metabolic Diseases Biology, ⊥Lead Evaluation, #Process Chemistry, ∇Chemical Synthesis, ○Discovery Toxicology, Research and Development, Bristol-Myers Squibb , 350 Carter Road, Princeton, New Jersey 08540, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Corticosteroid 11-beta-dehydrogenase isozyme 1A,
B,
C [auth D],
D [auth E]
286Homo sapiensMutation(s): 2 
Gene Names: HSD11B1HSD11HSD11LSDR26C1
EC: 1.1.1.146 (PDB Primary Data), 1.1.1.201 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P28845 (Homo sapiens)
Explore P28845 
Go to UniProtKB:  P28845
PHAROS:  P28845
GTEx:  ENSG00000117594 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28845
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth D],
K [auth E]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
8KG
Query on 8KG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth D],
L [auth E]
2-[(5R,7S)-6-HYDROXY-2-PHENYLADAMANTAN-2-YL]-1-(3-HYDROXYAZETIDIN-1-YL)ETHAN-1-ONE
C21 H27 N O3
OAAZMUGLOXGVNH-TUOVGCFYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
8KG BindingDB:  5PGY IC50: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.5α = 90
b = 92.3β = 90
c = 162.4γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
AMoREphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

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 NAPClick on this verticalbar to view detailsBest fitted 8KGClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2017-11-01 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Structure summary
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references