3PDJ

Crystal Structure of Human 11-beta-Hydroxysteroid Dehydrogenase 1 (11b-HSD1) in Complex with 4,4-Disubstituted Cyclohexylbenzamide Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3PDJ/pdb

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


• Deposited: 2010-10-22 Released: 2011-10-05 
• 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: 0.241 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Literature

Synthesis and Optimization of Novel 4,4-Disubstituted Cyclohexylbenzamide Derivatives as Potent 11beta-HSD1 Inhibitors

Sun, D., Wang, Z., Caille, S., DeGraffenreid, M., Gonzalez-Lopez de Turiso, F., Hungate, R., Jaen, J.C., Jiang, B., Julian, L.D., Kelly, R., McMinn, D.L., Kaizerman, J., Rew, Y., Sudom, A., Tu, H., Ursu, S., Walker, N., Willcockson, M., Yan, X., Ye, Q., Powers, J.P.

(2011) Bioorg Med Chem Lett 21: 405-410

• PubMed: 21093258 
• DOI: https://doi.org/10.1016/j.bmcl.2010.10.129
• Primary Citation of Related Structures:  
  3PDJ


• PubMed Abstract: 
  

  The synthesis and SAR of a series of 4,4-disubstituted cyclohexylbenzamide inhibitors of 11β-HSD1 are described. Optimization rapidly led to potent, highly selective, and orally bioavailable inhibitors demonstrating efficacy in both rat and non-human primate ex vivo pharmacodynamic models.

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Organizational Affiliation: 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.71 kDa 
• Atom Count: 4,549 
• Modelled Residue Count: 544 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corticosteroid 11-beta-dehydrogenase isozyme 1	A, B	273	Homo sapiens	Mutation(s): 1  Gene Names: HSD11, HSD11B1, 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	D [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
3PJ	C [auth A], E [auth B]	N-[trans-4-(3-amino-3-oxopropyl)-4-phenylcyclohexyl]-N-cyclopropyl-4-[(1S)-2,2,2-trifluoro-1-hydroxy-1-methylethyl]benzamide C28 H33 F3 N2 O3 GGXWRFSOCBTDDI-YGPDHOBYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3PJ	BindingDB:  3PDJ	IC50: min: 0.8, max: 37 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.241 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.044	α = 90
b = 107.044	β = 90
c = 132.918	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-05 
Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

Revision History  

• Version 1.0: 2011-10-05
  Type: Initial release
  
• Version 1.1: 2024-02-21
  Changes: Data collection, Database references, Derived calculations