Crystal Structure of Human Integral Membrane Stearoyl-CoA Desaturase with Substrate

Experimental Data Snapshot

  • Resolution: 3.25 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

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Crystal structure of human stearoyl-coenzyme A desaturase in complex with substrate.

Wang, H.Klein, M.G.Zou, H.Lane, W.Snell, G.Levin, I.Li, K.Sang, B.C.

(2015) Nat Struct Mol Biol 22: 581-585

  • DOI: https://doi.org/10.1038/nsmb.3049
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Stearoyl-coenzyme A desaturase-1 (SCD1) has an important role in lipid metabolism, and SCD1 inhibitors are potential therapeutic agents for the treatment of metabolic diseases and cancers. Here we report the 3.25-Å crystal structure of human SCD1 in complex with its substrate, stearoyl-coenzyme A, which defines the new SCD1 dimetal catalytic center and reveals the determinants of substrate binding to provide insights into the catalytic mechanism of desaturation of the stearoyl moiety. The structure also provides a mechanism for localization of SCD1 in the endoplasmic reticulum: human SCD1 folds around a tight hydrophobic core formed from four long α-helices that presumably function as an anchor spanning the endoplasmic reticulum membrane. Furthermore, our results provide a framework for the rational design of pharmacological inhibitors targeting the SCD1 enzyme.

  • Organizational Affiliation

    Department of Structural Biology and Core Sciences &Technology, Takeda California, San Diego, California, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-CoA desaturase318Homo sapiensMutation(s): 3 
Gene Names: SCD
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O00767 (Homo sapiens)
Explore O00767 
Go to UniProtKB:  O00767
PHAROS:  O00767
GTEx:  ENSG00000099194 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00767
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.25 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.108α = 90
b = 134.108β = 90
c = 112.561γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Experimental preparation, Source and taxonomy