6PC9

Crystal Structure of EcDsbA in a complex with purified methylpiperazinone 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 (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


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
O7P (Subject of Investigation/LOI)
Query on O7P

Download Ideal Coordinates CCD File 
C [auth A]2-methyl-4-{4-[2-(4-methyl-3-oxopiperazin-1-yl)-2-oxoethyl]phenoxy}benzonitrile
C21 H21 N3 O3
WFOOODRZHBDNTB-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
D [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
O7P Binding MOAD:  6PC9 Kd: 4.80e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.534α = 90
b = 76.711β = 90
c = 86.205γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-06-24
    Changes: Database references
  • Version 1.2: 2020-07-22
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description