4HFR | pdb_00004hfr

Human 11beta-Hydroxysteroid Dehydrogenase Type 1 in complex with an orally bioavailable acidic inhibitor AZD4017.

• PDB DOI: https://doi.org/10.2210/pdb4HFR/pdb

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


• Deposited: 2012-10-05 Released: 2012-10-17 
• Deposition Author(s): Ogg, D.J., Gerhardt, S., Hargreaves, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 
  0.227 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Discovery of a Potent, Selective, and Orally Bioavailable Acidic 11 -Hydroxysteroid Dehydrogenase Type 1 (11 -HSD1) Inhibitor: Discovery of 2-[(3S)-1-[5-(Cyclohexylcarbamoyl)-6-propylsulfanylpyridin-2-yl]-3-piperidyl]acetic Acid (AZD4017)

Scott, J.S., Bowker, S.S., Deschoolmeester, J., Gerhardt, S., Hargreaves, D., Kilgour, E., Lloyd, A., Mayers, R.M., McCoull, W., Newcombe, N.J., Ogg, D., Packer, M.J., Rees, A., Revill, J., Schofield, P., Selmi, N., Swales, J.G., Whittamore, P.R.

(2012) J Med Chem 55: 5951-5964

• PubMed: 22691057 
• DOI: https://doi.org/10.1021/jm300592r
• Primary Citation Related Structures: 
  4HFR


• PubMed Abstract: 
  

  Inhibition of 11β-HSD1 is an attractive mechanism for the treatment of obesity and other elements of the metabolic syndrome. We report here the discovery of a nicotinic amide derived carboxylic acid class of inhibitors that has good potency, selectivity, and pharmacokinetic characteristics. Compound 11i (AZD4017) is an effective inhibitor of 11β-HSD1 in human adipocytes and exhibits good druglike properties and as a consequence was selected for clinical development.

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Organizational Affiliation: 
• Cardiovascular and Gastrointestinal Innovative Medicines Unit, AstraZeneca Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. [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: 62.08 kDa 
• Atom Count: 4,053 
• Modeled Residue Count: 508 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corticosteroid 11-beta-dehydrogenase isozyme 1	A, B	272	Homo sapiens	Mutation(s): 5  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
14M	D [auth A], F [auth B]	{(3S)-1-[5-(cyclohexylcarbamoyl)-6-(propylsulfanyl)pyridin-2-yl]piperidin-3-yl}acetic acid C22 H33 N3 O3 S NCDZABJPWMBMIQ-INIZCTEOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
14M	BindingDB:  4HFR	IC50: min: 2, max: 7 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free:  0.227 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.193	α = 90
b = 108.193	β = 90
c = 135.29	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Ogg, D.J., Gerhardt, S., Hargreaves, D.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2014-11-12
  Changes: Structure summary
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description