5QO8

Group deposition of apo datasets for PANDDA analysis - Crystal Structure of apo EcDsbA after initial refinement (apo_dataset_38)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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.C.Scanlon, M.J.

(2020) J Med Chem 63: 6863-6875

  • DOI: 10.1021/acs.jmedchem.0c00111
  • Primary Citation of Related Structures:  
    6PIQ, 6PLI, 5QKH, 5QKG, 5QKJ, 5QKI, 5QKL, 5QKK, 5QKN, 5QKM, 5QKD, 5QKC, 5QKF, 5QKE, 5QLI, 5QLH, 5QLK, 5QLJ, 5QLM, 5QLL, 5QLO, 5QM0, 5QLN, 5QLA, 5QLC, 5QLB, 5QLE, 5QLD, 5QLG, 5QLF, 5QKX, 5QL9, 5QKW, 5QL8, 5QKZ, 5QKY, 5QKP, 5QL1, 5QKO, 5QL0, 5QKR, 5QL3, 5QKQ, 5QL2, 5QKT, 5QL5, 5QKS, 5QL4, 5QKV, 5QL7

  • 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 an analysis using X-ray crystallography of a diverse library of compounds prepared using microscale parallel synthesis ...

    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 an 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

    Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thiol:disulfide interchange proteinA, B189Escherichia coli K-12Mutation(s): 0 
Gene Names: dsbAdsfppfAb3860JW3832
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12))
Explore P0AEG4 
Go to UniProtKB:  P0AEG4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.476α = 90
b = 64.86β = 126.15
c = 74.973γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2020-07-22
    Changes: Database references