Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 93.43 kDa 
• Atom Count: 6598 
• Modelled Residue Count: 798 
• Deposited Residue Count: 840 
• Unique protein chains: 1

3ANN

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with quinolin-2-ylmethylphosphonic acid

• DOI: 10.2210/pdb3ANN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-03 Released: 2011-02-23 
• Deposition Author(s): Endo, K., Kato, M., Deng, L., Song, Y., Yajima, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Structures of 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase/Lipophilic Phosphonate Complexes

Deng, L., Endo, K., Kato, M., Cheng, G., Yajima, S., Song, Y.

(2011) ACS Med Chem Lett 2: 165-170

• PubMed: 21379374 
• DOI: 10.1021/ml100243r
• Primary Citation of Related Structures:  
  3ANL, 3ANM, 3ANN


• PubMed Abstract: 
  

Fosmidomycin, a potent inhibitor of 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), has antibacterial and antimalaria activity. Due to its poor pharmacokinetics, more lipophilic DXR inhibitors are needed. However, the hydrophobic binding site(s) in DXR remains elusive. Here, pyridine/quinoline containing phosphonates are identified to be DXR inhibitors with IC(50) values as low as 840 nM. We also report three DXR:inhibitor structures, revealing a novel binding mode. The indole group of Trp211 is found to move ~4.6 Å to open up a mainly hydrophobic pocket, where the pyridine/quinoline rings of the inhibitors are located and have strong π-π stacking/charge-transfer interactions with the indole. Docking studies demonstrate our structures could be used to predict the binding modes of other lipophilic DXR inhibitors. Overall, this work shows an important role of Trp211 in inhibitor recognition and provides a structural basis for future drug design and development.

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Organizational Affiliation: 

Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-deoxy-D-xylulose 5-phosphate reductoisomerase	A, B	420	Escherichia coli K-12	Mutation(s): 0  Gene Names: dxr, ispC, yaeM, b0173, JW0168 EC: 1.1.1.267
Find proteins for P45568 (Escherichia coli (strain K12)) Explore P45568  Go to UniProtKB:  P45568

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], E [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
SYE	D [auth A], F [auth B]	(quinolin-2-ylmethyl)phosphonic acid C10 H10 N O3 P SZCYKKWPKXABPU-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SYE	IC50:  15900   nM  Binding MOAD
SYE	IC50:  15900   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.627	α = 90
b = 59.279	β = 90
c = 87.208	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-09-03 
• Released Date: 2011-02-23 
Deposition Author(s): Endo, K., Kato, M., Deng, L., Song, Y., Yajima, S.

Revision History  

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-10-19
  Changes: Database references