5TZO

Computationally Designed Fentanyl Binder - Fen49*-Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Computational design of environmental sensors for the potent opioid fentanyl.

Bick, M.J.Greisen, P.J.Morey, K.J.Antunes, M.S.La, D.Sankaran, B.Reymond, L.Johnsson, K.Medford, J.I.Baker, D.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.28909
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues ...

    We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to optimize binding affinity. Co-crystal structures of the highest affinity binder reveal a highly preorganized binding site, and an overall architecture and ligand placement in close agreement with the design model. We use the designs to generate plant sensors for fentanyl by coupling ligand binding to design stability. The method should be generally useful for detecting toxic hydrophobic compounds in the environment.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-1,4-beta-xylanase A
A, B, C
188Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: xynA
EC: 3.2.1.8
Find proteins for P18429 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P18429
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
7V7
Query on 7V7

Download SDF File 
Download CCD File 
A, B, C
N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide
C22 H28 N2 O
PJMPHNIQZUBGLI-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.070α = 90.00
b = 73.250β = 90.00
c = 136.640γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited States5F32CA171572-03
Defense Threat Reduction AgencyUnited StatesHDTRA1-13-1-0054
Life Sciences Discovery FundUnited States9598385

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release