4N4W

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

Structural Biology Knowledgebase: 4N4W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.204

Literature

Macromolecules
Sequence Display for 4N4W

Classification: Membrane Protein Transport Protein

Total Structure Weight: 55388.00

Macromolecule Entities
Molecule Chains Length Organism Details
Chimera protein of smoothened receptor_BRIL and Cytochrome b(562) A 475 Shigella flexneri Homo sapiens Fragment: Chimera of Cytochrome b(562) and Smoothened residues 190-555 of UNP Q99835
Mutation: M7W, H102I, R106L
Gene Name(s): cybC SFV_4255 SMO Gene View SMOH
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: Smoothened (SMO) receptor with bound antagonist, LY2940680


Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SNT
Query on SNT

A (E)-N-(4-benzylpiperazin-1-yl)-1-(3,5-dimethyl- 1-phenyl-1H-pyrazol-4-yl)methanimine
SANT-1 (Synonym)
C23 H27 N5
FOORCIAZMIWALX-JJIBRWJFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OLC
Query on OLC

A (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol (Synonym)
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PG4
Query on PG4

A TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SNT IC50: 4.7 - 25 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.204
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 84.64 α = 90.00
b = 110.88 β = 90.00
c = 145.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-10-08
  • Released Date: 2014-01-22
  • Deposition author(s): Wang, C., Wu, H., Han, G.W., Cherezov, V., Stevens, R.C., GPCR Network (GPCR)

Revision History

  • 2014-07-30
    Type: Citation | Details: Citation update