4GAE

Crystal structure of plasmodium dxr in complex with a pyridine-containing inhibitor

Structural Biology Knowledgebase: 4GAE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.230

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GAE

Classification: ISOMERASE / ISOMERASE INHIBITOR

Total Structure Weight: 100226.00

Macromolecule Entities
Molecule Chains Length Organism Details
1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast A, B 426 Plasmodium falciparum EC#: 1.1.1.267 IUBMB
Mutation: L247I
Gene Name(s): DXR

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NDP
Query on NDP

A, B NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FOB
Query on FOB

A, B [(1R)-3-[acetyl(hydroxy)amino]-1-(pyridin- 4-yl)propyl]phosphonic acid
C10 H15 N2 O5 P
AMWIPWYKSYZXGB-SNVBAGLBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FOQ
Query on FOQ

A, B [(1S)-3-[acetyl(hydroxy)amino]-1-(pyridin- 4-yl)propyl]phosphonic acid
C10 H15 N2 O5 P
AMWIPWYKSYZXGB-JTQLQIEISA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
FOB N/A in BindingDB
Ki: 13 nM  BindingMOAD
N/A in PDBbind
FOQ N/A in BindingDB
Ki: 13 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.230
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 51.36 α = 90.00
b = 77.28 β = 91.50
c = 109.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-25
  • Released Date: 2013-02-06
  • Deposition author(s): Diao, J., Xue, J., Cai, G., Deng, L., Song, Y.

Revision History

  • 2013-07-10
    Type: Citation | Details: Citation update