6PG2 | pdb_00006pg2

Crystal Structure of EcDsbA in a complex with unpurified reaction product H5 (morpholine 8)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.223 (Depositor) 
  • R-Value Work: 
    0.184 (Depositor) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history


Literature

Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiL X ).

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: https://doi.org/10.1021/acs.jmedchem.0c00111
  • Primary Citation of Related Structures:  
    5QKC, 5QKD, 5QKE, 5QKF, 5QKG, 5QKH, 5QKI, 5QKJ, 5QKK, 5QKL, 5QKM, 5QKN, 5QKO, 5QKP, 5QKQ, 5QKR, 5QKS, 5QKT, 5QKU, 5QKV, 5QKW, 5QKX, 5QKY, 5QKZ, 5QL0, 5QL1, 5QL2, 5QL3, 5QL4, 5QL5, 5QL6, 5QL7, 5QL8, 5QL9, 5QLA, 5QLB, 5QLC, 5QLD, 5QLE, 5QLF, 5QLG, 5QLH, 5QLI, 5QLJ, 5QLK, 5QLL, 5QLM, 5QLN, 5QLO, 5QLP

  • 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. 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
    • Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiol:disulfide interchange protein DsbA
A, B
189Escherichia coli K-12Mutation(s): 0 
Gene Names: dsbAdsfppfAb3860JW3832
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12))
Explore P0AEG4 
Go to UniProtKB:  P0AEG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEG4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O6Y (Subject of Investigation/LOI)
Query on O6Y

Download Ideal Coordinates CCD File 
C [auth A]2-methyl-4-{4-[2-(morpholin-4-yl)-2-oxoethyl]phenoxy}benzonitrile
C20 H20 N2 O3
QOJWBEUMAJACBY-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
D [auth B]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
O6Y BindingDB:  6PG2 Kd: 3.65e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.223 (Depositor) 
  • R-Value Work:  0.184 (Depositor) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.674α = 90
b = 63.912β = 125.693
c = 74.455γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaProject Grant APP1099151
Australian Research Council (ARC)AustraliaLIEF LE160100047

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary