7BW1

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 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

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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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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 
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
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
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • 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

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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