3MBM

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytosine and FoL fragment 717, imidazo[2,1-b][1,3]thiazol-6-ylmethanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.

Begley, D.W.Hartley, R.C.Davies, D.R.Edwards, T.E.Leonard, J.T.Abendroth, J.Burris, C.A.Bhandari, J.Myler, P.J.Staker, B.L.Stewart, L.J.

(2011) J Struct Funct Genomics 12: 63-76

  • DOI: 10.1007/s10969-011-9102-6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening ...

    As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification of several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.


    Related Citations: 
    • Combining functional and structural genomics to sample the essential Burkholderia structome.
      Baugh, L.,Gallagher, L.A.,Patrapuvich, R.,Clifton, M.C.,Gardberg, A.S.,Edwards, T.E.,Armour, B.,Begley, D.W.,Dieterich, S.H.,Dranow, D.M.,Abendroth, J.,Fairman, J.W.,Fox, D.,Staker, B.L.,Phan, I.,Gillespie, A.,Choi, R.,Nakazawa-Hewitt, S.,Nguyen, M.T.,Napuli, A.,Barrett, L.,Buchko, G.W.,Stacy, R.,Myler, P.J.,Stewart, L.J.,Manoil, C.,Van Voorhis, W.C.
      (2013) Plos One 8: e53851


    Organizational Affiliation

    Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA. dbegley@embios.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
A, B, C
183Burkholderia pseudomallei (strain 1710b)Mutation(s): 0 
Gene Names: ispF
EC: 4.6.1.12
Find proteins for Q3JRA0 (Burkholderia pseudomallei (strain 1710b))
Go to UniProtKB:  Q3JRA0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CYT
Query on CYT

Download SDF File 
Download CCD File 
A, B, C
6-AMINOPYRIMIDIN-2(1H)-ONE
CYTOSINE
C4 H5 N3 O
OPTASPLRGRRNAP-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
717
Query on 717

Download SDF File 
Download CCD File 
A, B, C
imidazo[2,1-b][1,3]thiazol-6-ylmethanol
C6 H6 N2 O S
GBUTVPCKMACQMG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
717Kd: 135000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 117.543α = 90.00
b = 67.569β = 96.12
c = 60.030γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
StructureStudiodata collection
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Database references, Version format compliance
  • Version 1.2: 2013-10-30
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description