1HDC

MECHANISM OF INHIBITION OF 3ALPHA,20BETA-HYDROXYSTEROID DEHYDROGENASE BY A LICORICE-DERIVED STEROIDAL INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb1HDC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces exfoliatus
• Mutation(s): No 


• Deposited: 1994-10-21 Released: 1995-02-07 
• Deposition Author(s): Ghosh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.194 

Literature

Mechanism of inhibition of 3 alpha, 20 beta-hydroxysteroid dehydrogenase by a licorice-derived steroidal inhibitor.

Ghosh, D., Erman, M., Wawrzak, Z., Duax, W.L., Pangborn, W.

(1994) Structure 2: 973-980

• PubMed: 7866748 
• DOI: https://doi.org/10.1016/s0969-2126(94)00099-9
• Primary Citation of Related Structures:  
  1HDC


• PubMed Abstract: 
  

  Bacterial 3 alpha, 20 beta-hydroxysteroid dehydrogenase (3 alpha, 20 beta-HSD) reversibly oxidizes the 3 alpha and 20 beta hydroxyl groups of androstanes and pregnanes and uses nicotinamide adenine dinucleotide as a cofactor. 3 alpha, 20 beta-HSD belongs to a family of short-chain dehydrogenases that has a highly conserved Tyr-X-X-X-Lys sequence. The family includes mammalian enzymes involved in hypertension, digestion, fertility and spermatogenesis. Several members of the enzyme family, including 3 alpha, 20 beta-HSD, are competitively inhibited by glycyrrhizic acid, a steroidal compound found in licorice, and its derivative, carbenoxolone, an anti-inflammatory glucocorticoid.

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Organizational Affiliation: 

Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203-1196.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 107.85 kDa 
• Atom Count: 7,558 
• Modelled Residue Count: 1,012 
• Deposited Residue Count: 1,016 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE	A, B, C, D	254	Streptomyces exfoliatus	Mutation(s): 0  EC: 1.1.1.53
UniProt
Find proteins for P19992 (Streptomyces exfoliatus) Explore P19992  Go to UniProtKB:  P19992

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CBO	E [auth A], F [auth B], G [auth C], H [auth D]	CARBENOXOLONE C34 H50 O7 OBZHEBDUNPOCJG-WBXJDKIVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CBO	Binding MOAD:  1HDC	Ki: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.194 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.05	α = 101.78
b = 60.04	β = 104.41
c = 59.84	γ = 96.31

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-02-07 
Deposition Author(s): Ghosh, D.

Revision History  

• Version 1.0: 1995-02-07
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations