4N4W

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b(562),Smoothened homolog475Shigella flexneri 5 str. 8401Homo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: cybCSFV_4255SMOSMOH
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q0SXH8 (Shigella flexneri serotype 5b (strain 8401))
Explore Q0SXH8 
Go to UniProtKB:  Q0SXH8
Find proteins for Q99835 (Homo sapiens)
Explore Q99835 
Go to UniProtKB:  Q99835
PHAROS:  Q99835
GTEx:  ENSG00000128602 
Entity Groups  
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:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SNT
Query on SNT

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: C 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

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

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