4N4W | pdb_00004n4w

Structure of the human smoothened receptor in complex with SANT-1.


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.80 Å
  • R-Value Free:&nbsp
    0.253 (Depositor), 0.270 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.204 (Depositor), 0.220 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.207&nbsp(Depositor)&nbsp

Starting Model: experimental
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Ligand Structure Quality Assessment&nbsp


This is version 2.2 of the entry. See complete&nbsphistory.&nbsp


Literature

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

Wang, C.,&nbspWu, H.,&nbspEvron, T.,&nbspVardy, E.,&nbspHan, G.W.,&nbspHuang, X.P.,&nbspHufeisen, S.J.,&nbspMangano, T.J.,&nbspUrban, D.J.,&nbspKatritch, V.,&nbspCherezov, V.,&nbspCaron, M.G.,&nbspRoth, B.L.,&nbspStevens, R.C.

(2014) Nat Commun&nbsp5: 4355-4355

  • DOI:&nbsphttps://doi.org/10.1038/ncomms5355
  • Primary Citation of Related Structures: &nbsp
    4N4W, 4QIM, 4QIN

  • PubMed Abstract:&nbsp

    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:&nbsp

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b(562),Smoothened homolog475Shigella flexneri 5 str. 8401,&nbspHomo sapiens
This entity is chimeric
Mutation(s): 3&nbsp
Gene Names:&nbspcybC,&nbspSFV_4255,&nbspSMO,&nbspSMOH
Membrane Entity:&nbspYes&nbsp
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspQ0SXH8&nbsp(Shigella flexneri serotype 5b (strain 8401))
Explore&nbspQ0SXH8&nbsp
Go to UniProtKB: &nbspQ0SXH8
Find proteins for&nbspQ99835&nbsp(Homo sapiens)
Explore&nbspQ99835&nbsp
Go to UniProtKB: &nbspQ99835
PHAROS: &nbspQ99835
GTEx: &nbspENSG00000128602&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ99835Q0SXH8
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
4N/A
Glycosylation Resources
GlyTouCan: &nbspG81315DD
GlyCosmos: &nbspG81315DD
GlyGen: &nbspG81315DD
Small Molecules
Ligands&nbsp5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SNT
Query on SNT

Download Ideal Coordinates CCD File&nbsp
C [auth A](E)-N-(4-benzylpiperazin-1-yl)-1-(3,5-dimethyl-1-phenyl-1H-pyrazol-4-yl)methanimine
C23 H27 N5
FOORCIAZMIWALX-JJIBRWJFSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File&nbsp
F [auth A],
G [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File&nbsp
I [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File&nbsp
H [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File&nbsp
D [auth A],
E [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations&nbsp
IDSourceBinding Affinity
SNT BindingDB:&nbsp 4N4W IC50:&nbspmin: 4.7, max: 25&nbsp(nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.80 Å
  • R-Value Free:&nbsp 0.253 (Depositor), 0.270 (DCC)&nbsp
  • R-Value Work:&nbsp 0.204 (Depositor), 0.220 (DCC)&nbsp
  • R-Value Observed:&nbsp0.207&nbsp(Depositor)&nbsp
Space Group:&nbspC 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.64α = 90
b = 110.88β = 90
c = 145.21γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment&nbsp


Entry History&nbsp

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2017-06-07
    Changes: Database references, Structure summary
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary