3CZR

Crystal Structure of Human 11-beta-Hydroxysteroid Dehydrogenase (HSD1) in Complex with Arylsulfonylpiperazine Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3CZR/pdb

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


• Deposited: 2008-04-29 Released: 2008-06-17 
• Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.247 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Literature

Discovery and Initial SAR of Arylsulfonylpiperazine Inhibitors of 11beta-Hydroxysteroid Dehydrogenase Type 1 (11beta-HSD1)

Sun, D., Wang, Z., Di, Y., Jaen, J.C., Labelle, M., Ma, J., Miao, S., Sudom, A., Tang, L., Tomooka, C.S., Tu, H., Ursu, S., Walker, N., Yan, X., Ye, Q., Powers, J.P.

(2008) Bioorg Med Chem Lett 18: 3513-3516

• PubMed: 18511278 
• DOI: https://doi.org/10.1016/j.bmcl.2008.05.025
• Primary Citation of Related Structures:  
  3CZR


• PubMed Abstract: 
  

  High-throughput screening of a small-molecule compound library resulted in the identification of a series of arylsulfonylpiperazines that are potent and selective inhibitors of human 11beta-Hydroxysteroid Dehydrogenase Type 1 (11beta-HSD1). Optimization of the initial lead resulted in the discovery of compound (R)-45 (11beta-HSD1 IC(50)=3nM).

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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)

Macromolecule Content

• Total Structure Weight: 66.19 kDa 
• Atom Count: 4,390 
• Modelled Residue Count: 528 
• 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 3 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
CPS	F [auth B]	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C32 H58 N2 O7 S UMCMPZBLKLEWAF-BCTGSCMUSA-N
3CZ	D [auth A]	(2R)-1-[(4-tert-butylphenyl)sulfonyl]-2-methyl-4-(4-nitrophenyl)piperazine C21 H27 N3 O4 S SOFGQQQVQZQJFS-MRXNPFEDSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3CZ	BindingDB:  3CZR	IC50: min: 3, max: 57 (nM) from 3 assay(s)
		EC50: 57 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.247 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.216	α = 90
b = 110.216	β = 90
c = 132.991	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-17 
Deposition Author(s): Wang, Z., Sudom, A., Walker, N.P.

Revision History  

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations, Source and taxonomy
• Version 1.3: 2024-02-21
  Changes: Data collection