6WHD

Crystal structure of E.coli DsbA in complex with diaryl ether analogue 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report



Literature

Rapid elaboration of fragments into leads by X-ray crystallographic screening of parallel chemical libraries (REFiLx).

Bentley, M.R.Ilyichova, O.V.Wang, G.Williams, M.L.Sharma, G.Alwan, W.S.Whitehouse, R.L.Mohanty, B.Scammells, P.J.Heras, B.Martin, J.L.Totsika, M.Capuano, B.Doak, B.Scanlon, M.J.

(2020) J Med Chem 

  • DOI: 10.1021/acs.jmedchem.0c00111
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A bottleneck in fragment-based lead development is the lack of systematic approaches to elaborate the initial fragment hits, which usually bind with low affinity to their target. Herein we describe analysis using X-ray crystallography of a diverse li ...

    A bottleneck in fragment-based lead development is the lack of systematic approaches to elaborate the initial fragment hits, which usually bind with low affinity to their target. Herein we describe analysis using X-ray crystallography of a diverse library of compounds prepared using microscale parallel synthesis. This approach yielded an 8-fold increase in affinity and detailed structural information for the resulting complex, providing an efficient and broadly applicable approach to early fragment development.


    Organizational Affiliation

    Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiol:disulfide interchange protein DsbA
A, B
189Escherichia coli K-12Mutation(s): 0 
Gene Names: dsbAdsfppfAb3860JW3832
Find proteins for P0AEG4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEG4
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KFS
Query on KFS

Download CCD File 
A, B
[4-(4-cyano-3-methylphenoxy)phenyl]acetic acid
C16 H13 N O3
VDBBDYPELPDNGF-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download CCD File 
B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.77α = 90
b = 64.5β = 125.89
c = 74.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-04-08 
  • Released Date: 2020-06-24 
  • Deposition Author(s): Wang, G., Heras, B.

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT1099151

Revision History 

  • Version 1.0: 2020-06-24
    Type: Initial release