6B7E

Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with (R)-4-(5-(difluoromethyl)-1H-imidazol-1-yl)-3,3-dimethylisochroman-1-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.104 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High-Confidence Protein-Ligand Complex Modeling by NMR-Guided Docking Enables Early Hit Optimization.

Proudfoot, A.Bussiere, D.E.Lingel, A.

(2017) J. Am. Chem. Soc. 139: 17824-17833

  • DOI: 10.1021/jacs.7b07171
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structure-based drug design is an integral part of modern day drug discovery and requires detailed structural characterization of protein-ligand interactions, which is most commonly performed by X-ray crystallography. However, the success rate of gen ...

    Structure-based drug design is an integral part of modern day drug discovery and requires detailed structural characterization of protein-ligand interactions, which is most commonly performed by X-ray crystallography. However, the success rate of generating these costructures is often variable, in particular when working with dynamic proteins or weakly binding ligands. As a result, structural information is not routinely obtained in these scenarios, and ligand optimization is challenging or not pursued at all, representing a substantial limitation in chemical scaffolds and diversity. To overcome this impediment, we have developed a robust NMR restraint guided docking protocol to generate high-quality models of protein-ligand complexes. By combining the use of highly methyl-labeled protein with experimentally determined intermolecular distances, a comprehensive set of protein-ligand distances is generated which then drives the docking process and enables the determination of the correct ligand conformation in the bound state. For the first time, the utility and performance of such a method is fully demonstrated by employing the generated models for the successful, prospective optimization of crystallographically intractable fragment hits into more potent binders.


    Organizational Affiliation

    Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphopantetheine adenylyltransferase
A, B
167Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: coaD (kdtB, yicA)
EC: 2.7.7.3
Find proteins for P0A6I6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6I6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CWA
Query on CWA

Download SDF File 
Download CCD File 
B
(4R)-4-[5-(difluoromethyl)-1H-imidazol-1-yl]-3,3-dimethyl-3,4-dihydro-1H-2-benzopyran-1-one
C15 H14 F2 N2 O2
LAMQMSRGFJHTEW-GFCCVEGCSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CWAIC50: 320600 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.104 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.171 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 135.480α = 90.00
b = 135.480β = 90.00
c = 135.480γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
Cootmodel building
PDB_EXTRACTdata extraction
xia2data reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release