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⇱ RCSB PDB - 7BW1: Crystal structure of Steroid 5-alpha-reductase 2 in complex with Finasteride


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Structures from the PDB archive
1,062,058
Computed Structure Models (CSM)

 7BW1 | pdb_00007bw1

Crystal structure of Steroid 5-alpha-reductase 2 in complex with Finasteride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.265 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

wwPDB Validation3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structure of human steroid 5 alpha-reductase 2 with anti-androgen drug finasteride.

Xiao, Q.Wang, L.Supekar, S.Shen, T.Liu, H.Ye, F.Huang, J.Fan, H.Wei, Z.Zhang, C.

(2020) Res Sq 

  • DOI: https://doi.org/10.21203/rs.3.rs-40159/v1
  • Primary Citation Related Structures: 
    7BW1

  • PubMed Abstract: 

    Human steroid 5α-reductase 2 (SRD5α2) as a critical integral membrane enzyme in steroid metabolism catalyzes testosterone to dihydrotestosterone. Mutations on its gene have been linked to 5α-reductase deficiency and prostate cancer. Finasteride and dutasteride as SRD5α2 inhibitors are widely used anti-androgen drugs for benign prostate hyperplasia, which have recently been indicated in the treatment of COVID-19. The molecular mechanisms underlying enzyme catalysis and inhibition remained elusive for SRD5α2 and other eukaryotic integral membrane steroid reductases due to a lack of structural information. Here, we report a crystal structure of human SRD5α2 at 2.8 Å revealing a unique 7-TM structural topology and an intermediate adduct of finasteride and NADPH as NADP-dihydrofinasteride in a largely enclosed binding cavity inside the membrane. Structural analysis together with computational and mutagenesis studies reveals molecular mechanisms for the 5α-reduction of testosterone and the finasteride inhibition involving residues E57 and Y91. Molecular dynamics simulation results indicate high conformational dynamics of the cytosolic region regulating the NADPH/NADP + exchange. Mapping disease-causing mutations of SRD5α2 to our structure suggests molecular mechanisms for their pathological effects. Our results offer critical structural insights into the function of integral membrane steroid reductases and will facilitate drug development.


  • Organizational Affiliation
    • Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
    • Faculty of Health Sciences, University of Macau, Macau SAR 999078, China.
    • Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA15261, USA.
    • Bioinformatics Institute (BII), Agency for Science, Technology and Research (ASTAR), Singapore 138671, Singapore.
    • Tencent AI Lab, Shenzhen, Guangdong 518000, China.

Macromolecule Content 

  • Total Structure Weight: 30.36 kDa 
  • Atom Count: 2,036 
  • Modeled Residue Count: 245 
  • Deposited Residue Count: 258 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-oxo-5-alpha-steroid 4-dehydrogenase 2258Homo sapiensMutation(s): 0 
Gene Names: SRD5A2
EC: 1.3.1.22
Membrane Entity: Yes 
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UniProt & NIH Common Fund Data Resources
Find proteins for P31213 (Homo sapiens)
Explore P31213 
Go to UniProtKB:  P31213
PHAROS:  P31213
GTEx:  ENSG00000277893 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31213
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDX
(Subject of Investigation/LOI)

Query on NDX



Download:Ideal Coordinates CCD File
C [auth A][[(2~{R},3~{S},4~{R},5~{R})-5-[4-[(1~{S},3~{a}~{S},3~{b}~{S},5~{a}~{R},8~{S},9~{a}~{R},9~{b}~{S},11~{a}~{S})-1-(~{tert}-butylcarbamoyl)-9~{a},11~{a}-dimethyl-7-oxidanylidene-1,2,3,3~{a},3~{b},4,5,5~{a},6,8,9,9~{b},10,11-tetradecahydroindeno[5,4-f]quinolin-8-yl]-3-aminocarbonyl-4~{H}-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate
C44 H66 N9 O19 P3
SBPCUEDRMWGINQ-DAPYLVMHSA-N
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OLC

Query on OLC



Download:Ideal Coordinates CCD File
B [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
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SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.265 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.449α = 90
b = 107.449β = 90
c = 103.372γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770791
National Natural Science Foundation of China (NSFC)China31971131

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.