6C6N

Human squalene epoxidase (SQLE, squalene monooxygenase) structure with FAD and Cmpd-4"


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure and inhibition mechanism of the catalytic domain of human squalene epoxidase.

Padyana, A.K.Gross, S.Jin, L.Cianchetta, G.Narayanaswamy, R.Wang, F.Wang, R.Fang, C.Lv, X.Biller, S.A.Dang, L.Mahoney, C.E.Nagaraja, N.Pirman, D.Sui, Z.Popovici-Muller, J.Smolen, G.A.

(2019) Nat Commun 10: 97-97

  • DOI: https://doi.org/10.1038/s41467-018-07928-x
  • Primary Citation of Related Structures:  
    6C6N, 6C6P, 6C6R

  • PubMed Abstract: 

    Squalene epoxidase (SQLE), also known as squalene monooxygenase, catalyzes the stereospecific conversion of squalene to 2,3(S)-oxidosqualene, a key step in cholesterol biosynthesis. SQLE inhibition is targeted for the treatment of hypercholesteremia, cancer, and fungal infections. However, lack of structure-function understanding has hindered further progression of its inhibitors. We have determined the first three-dimensional high-resolution crystal structures of human SQLE catalytic domain with small molecule inhibitors (2.3 Å and 2.5 Å). Comparison with its unliganded state (3.0 Å) reveals conformational rearrangements upon inhibitor binding, thus allowing deeper interpretation of known structure-activity relationships. We use the human SQLE structure to further understand the specificity of terbinafine, an approved agent targeting fungal SQLE, and to provide the structural insights into terbinafine-resistant mutants encountered in the clinic. Collectively, these findings elucidate the structural basis for the specificity of the epoxidation reaction catalyzed by SQLE and enable further rational development of next-generation inhibitors.


  • Organizational Affiliation

    Agios Pharmaceuticals, 88 Sidney Street, Cambridge, MA, 02139, USA. anil.padyana@agios.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Squalene monooxygenase
A, B
458Homo sapiensMutation(s): 0 
Gene Names: SQLEERG1
EC: 1.14.14.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q14534 (Homo sapiens)
Explore Q14534 
Go to UniProtKB:  Q14534
PHAROS:  Q14534
GTEx:  ENSG00000104549 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14534
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
M [auth A],
S [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
CPS
Query on CPS

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
P [auth B],
Q [auth B]
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
EKV
Query on EKV

Download Ideal Coordinates CCD File 
L [auth A],
R [auth B]
N-[(3-{[dimethyl(2-methylphenyl)silyl]methoxy}phenyl)methyl]-N-ethyl-6-methoxy-6-methylhepta-2,4-diyn-1-amine
C28 H37 N O2 Si
QOHZDEJDJNDBJB-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
N [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
EKV BindingDB:  6C6N IC50: 70 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.96α = 90
b = 126.96β = 90
c = 166.12γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references