3FRJ

Crystal Structure of 11b-Hydroxysteroid Dehydrogenase-1 (11b-HSD1) in Complex with Piperidyl Benzamide Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3FRJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-01-08 Released: 2009-06-16 
• Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.231 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Discovery and optimization of piperidyl benzamide derivatives as a novel class of 11beta-HSD1 inhibitors.

Rew, Y., McMinn, D.L., Wang, Z., He, X., Hungate, R.W., Jaen, J.C., Sudom, A., Sun, D., Tu, H., Ursu, S., Villemure, E., Walker, N.P., Yan, X., Ye, Q., Powers, J.P.

(2009) Bioorg Med Chem Lett 19: 1797-1801

• PubMed: 19217779 
• DOI: https://doi.org/10.1016/j.bmcl.2009.01.058
• Primary Citation of Related Structures:  
  3FRJ


• PubMed Abstract: 
  

  Discovery and optimization of a piperidyl benzamide series of 11beta-HSD1 inhibitors is described. This series was derived from a cyclohexyl benzamide lead structures to address PXR selectivity, high non-specific protein binding, poor solubility, limited in vivo exposure, and in vitro cytotoxicity issues observed with the cyclohexyl benzamide structures. These efforts led to the discovery of piperidyl benzamide 15 which features improved properties over the cyclohexyl benzamide derivatives.

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Organizational Affiliation: 

Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.61 kDa 
• Atom Count: 4,351 
• Modelled Residue Count: 527 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corticosteroid 11-beta-Dehydrogenase, Isozyme 1	A, B	286	Homo sapiens	Mutation(s): 1  Gene Names: HSD11B1, HSD11, HSD11L 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
A49	D [auth B]	N-{1-[(1-carbamoylcyclopropyl)methyl]piperidin-4-yl}-N-cyclopropyl-4-[(1S)-2,2,2-trifluoro-1-hydroxy-1-methylethyl]benzamide C23 H30 F3 N3 O3 FAVXIEFZKPJZRT-NRFANRHFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A49	BindingDB:  3FRJ	IC50: 14 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.231 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.917	α = 90
b = 104.917	β = 90
c = 134.784	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection