3FCO

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

• PDB DOI: https://doi.org/10.2210/pdb3FCO/pdb

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


• Deposited: 2008-11-21 Released: 2009-12-01 
• Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.254 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 

Literature

Optimization of novel di-substituted cyclohexylbenzamide derivatives as potent 11 beta-HSD1 inhibitors.

McMinn, D.L., Rew, Y., Sudom, A., Caille, S., Degraffenreid, M., He, X., Hungate, R., Jiang, B., Jaen, J., Julian, L.D., Kaizerman, J., Novak, P., Sun, D., Tu, H., Ursu, S., Walker, N.P., Yan, X., Ye, Q., Wang, Z., Powers, J.P.

(2009) Bioorg Med Chem Lett 19: 1446-1450

• PubMed: 19185488 
• DOI: https://doi.org/10.1016/j.bmcl.2009.01.026
• Primary Citation of Related Structures:  
  3FCO


• PubMed Abstract: 
  

  Novel 4,4-disubstituted cyclohexylbenzamide inhibitors of 11beta-HSD1 were optimized to account for liabilities relating to in vitro pharmacokinetics, cytotoxicity and protein-related shifts in potency. A representative compound showing favorable in vivo pharmacokinetics was found to be an efficacious inhibitor of 11beta-HSD1 in a rat pharmacodynamic model (ED(50)=10mg/kg).

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Organizational Affiliation: 

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

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: 65.98 kDa 
• Atom Count: 4,328 
• Modelled Residue Count: 533 
• 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
IIG	D [auth A], F [auth B]	N-cyclopropyl-N-(cis-4-cyclopropyl-4-hydroxycyclohexyl)-4-[(1S)-2,2,2-trifluoro-1-hydroxy-1-methylethyl]benzamide C22 H28 F3 N O3 SWXZIRVTPISJMP-SESVDKBCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IIG	BindingDB:  3FCO	IC50: min: 14, max: 121 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.254 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.185	α = 90
b = 109.185	β = 90
c = 135.869	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

Revision History  

• Version 1.0: 2009-12-01
  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: 2023-12-27
  Changes: Data collection