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: 1.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1007/s10969-011-9102-6
  • Primary Citation of Related Structures:  
    3F0D, 3F0E, 3F0G, 3IEQ, 3IEW, 3IKE, 3IKF, 3JVH, 3K14, 3K2X, 3MBM, 3P0Z, 3P10, 3QHD

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
A, B, C
183Burkholderia pseudomalleiMutation(s): 0 
Gene Names: ispFmecSBPSL2098
EC: 4.6.1.12
UniProt
Find proteins for Q3JRA0 (Burkholderia pseudomallei (strain 1710b))
Explore Q3JRA0 
Go to UniProtKB:  Q3JRA0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3JRA0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
717
Query on 717

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
K [auth C]
imidazo[2,1-b][1,3]thiazol-6-ylmethanol
C6 H6 N2 O S
GBUTVPCKMACQMG-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
G [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
CYT
Query on CYT

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C]
6-AMINOPYRIMIDIN-2(1H)-ONE
C4 H5 N3 O
OPTASPLRGRRNAP-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
L [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
717 BindingDB:  3MBM Kd: 1.35e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.543α = 90
b = 67.569β = 96.12
c = 60.03γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Database references, Version format compliance
  • Version 1.2: 2013-10-30
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description