3R0I

IspC in complex with an N-methyl-substituted hydroxamic acid

• PDB DOI: https://doi.org/10.2210/pdb3R0I/pdb

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


• Deposited: 2011-03-08 Released: 2011-09-07 
• Deposition Author(s): Behrendt, C.T., Kunfermann, A., Illarionova, V., Matheeussen, A., Pein, M.K., Graewert, T., Bacher, A., Eisenreich, W., Illarionov, B., Fischer, M., Maes, L., Groll, M., Kurz, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.217 
• R-Value Work: 0.163 
• R-Value Observed: 0.166 

Literature

Reverse Fosmidomycin Derivatives against the Antimalarial Drug Target IspC (Dxr).

Behrendt, C.T., Kunfermann, A., Illarionova, V., Matheeussen, A., Pein, M.K., Grawert, T., Kaiser, J., Bacher, A., Eisenreich, W., Illarionov, B., Fischer, M., Maes, L., Groll, M., Kurz, T.

(2011) J Med Chem 54: 6796-6802

• PubMed: 21866890 
• DOI: https://doi.org/10.1021/jm200694q
• Primary Citation of Related Structures:  
  3R0I


• PubMed Abstract: 
  

  Reverse hydroxamate-based inhibitors of IspC, a key enzyme of the non-mevalonate pathway of isoprenoid biosynthesis and a validated antimalarial target, were synthesized and biologically evaluated. The binding mode of one derivative in complex with EcIspC and a divalent metal ion was clarified by X-ray analysis. Pilot experiments have demonstrated in vivo potential.

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Organizational Affiliation: 

Institut für Pharmazeutische und Medizinische Chemie, Heinrich Heine Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 90.4 kDa 
• Atom Count: 6,778 
• Modelled Residue Count: 786 
• Deposited Residue Count: 820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-deoxy-D-xylulose 5-phosphate reductoisomerase	A, B	410	Escherichia coli K-12	Mutation(s): 0  Gene Names: dxr, ispC, yaeM, b0173, JW0168 EC: 1.1.1.267
UniProt
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
C0K	D [auth A], F [auth B]	{(1S)-1-(3,4-difluorophenyl)-4-[hydroxy(methyl)amino]-4-oxobutyl}phosphonic acid C11 H14 F2 N O5 P IZWIBRNXHRUNKD-JTQLQIEISA-N
MN	C [auth A], E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
C0K	Binding MOAD:  3R0I	IC50: 120 (nM) from 1 assay(s)
	PDBBind:  3R0I	IC50: 120 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.217 
• R-Value Work: 0.163 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.254	α = 90
b = 54.584	β = 93.17
c = 107.798	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Behrendt, C.T., Kunfermann, A., Illarionova, V., Matheeussen, A., Pein, M.K., Graewert, T., Bacher, A., Eisenreich, W., Illarionov, B., Fischer, M., Maes, L., Groll, M., Kurz, T.

Revision History  

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2011-10-19
  Changes: Database references
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description