4QIM

Structure of the human smoothened receptor in complex with ANTA XV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for Smoothened receptor modulation and chemoresistance to anticancer drugs.

Wang, C.Wu, H.Evron, T.Vardy, E.Han, G.W.Huang, X.P.Hufeisen, S.J.Mangano, T.J.Urban, D.J.Katritch, V.Cherezov, V.Caron, M.G.Roth, B.L.Stevens, R.C.

(2014) Nat Commun 5: 4355-4355

  • DOI: 10.1038/ncomms5355
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Smoothened receptor (SMO) mediates signal transduction in the hedgehog pathway, which is implicated in normal development and carcinogenesis. SMO antagonists can suppress the growth of some tumours; however, mutations at SMO have been found to ab ...

    The Smoothened receptor (SMO) mediates signal transduction in the hedgehog pathway, which is implicated in normal development and carcinogenesis. SMO antagonists can suppress the growth of some tumours; however, mutations at SMO have been found to abolish their antitumour effects, a phenomenon known as chemoresistance. Here we report three crystal structures of human SMO bound to the antagonists SANT1 and Anta XV, and the agonist, SAG1.5, at 2.6-2.8 Å resolution. The long and narrow cavity in the transmembrane domain of SMO harbours multiple ligand binding sites, where SANT1 binds at a deeper site as compared with other ligands. Distinct interactions at D473(6.54f) elucidated the structural basis for the differential effects of chemoresistance mutations on SMO antagonists. The agonist SAG1.5 induces a conformational rearrangement of the binding pocket residues, which could contribute to SMO activation. Collectively, these studies reveal the structural basis for the modulation of SMO by small molecules.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Smoothened homolog/Soluble cytochrome b562 chimeric protein
A
468Homo sapiensEscherichia coli
This entity is chimeric
Mutation(s): 3 
Gene Names: SMO (SMOH), cybC
Find proteins for Q99835 (Homo sapiens)
Go to Gene View: SMO
Go to UniProtKB:  Q99835
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
A8T
Query on A8T

Download SDF File 
Download CCD File 
A
2-{6-[4-(4-benzylphthalazin-1-yl)piperazin-1-yl]pyridin-3-yl}propan-2-ol
C27 H29 N5 O
KSWYJUIFHPSZOL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A8TIC50: 2.7 - 35 nM (97) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.830α = 90.00
b = 79.840β = 90.00
c = 170.070γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
BUSTERrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references
  • Version 1.2: 2017-08-02
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-22
    Type: Refinement description