Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 28265.92 
• Atom Count: 1845 
• Residue Count: 238 
• Unique protein chains: 1

2BLB

X-ray crystal structure of Plasmodium vivax dihydrofolate reductase in complex with pyrimethamine and its derivative

• DOI: 10.2210/pdb2BLB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Plasmodium vivax
• Expression System: Escherichia coli


• Deposited: 2005-03-03 Released: 2005-09-07 
• Deposition Author(s): Kongsaeree, P., Khongsuk, P., Leartsakulpanich, U., Chitnumsub, P., Tarnchompoo, B., Walkinshaw, M.D., Yuthavong, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.300 
• R-Value Work: 0.192 

Literature

Crystal Structure of Dihydrofolate Reductase from Plasmodium Vivax: Pyrimethamine Displacement Linked with Mutation-Induced Resistance.

Kongsaeree, P., Khongsuk, P., Leartsakulpanich, U., Chitnumsub, P., Tarnchompoo, B., Walkinshaw, M.D., Yuthavong, Y.

(2005) Proc.Natl.Acad.Sci.USA 102: 13046

• PubMed: 16135570 
• DOI: 10.1073/pnas.0501747102
• Primary Citation of Related Structures:  
  2BLC, 2BLA, 2BL9


• PubMed Abstract: 
  

Pyrimethamine (Pyr) targets dihydrofolate reductase of Plasmodium vivax (PvDHFR) as well as other malarial parasites, but its use as antimalarial is hampered by the widespread high resistance. Comparison of the crystal structures of PvDHFR from wild-type and the Pyr-resistant (SP21, Ser-58 --> Arg + Ser-117 --> Asn) strain as complexes with NADPH and Pyr or its analog lacking p-Cl (Pyr20) clearly shows that the steric conflict arising from the side chain of Asn-117 in the mutant enzyme, accompanied by the loss of binding to Ser-120, is mainly responsible for the reduction in binding of Pyr. Pyr20 still effectively inhibits both the wild-type and SP21 proteins, and the x-ray structures of these complexes show how Pyr20 fits into both active sites without steric strain. These structural insights suggest a general approach for developing new generations of antimalarial DHFR inhibitors that, by only occupying substrate space of the active site, would retain binding affinity with the mutant enzymes.

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Organizational Affiliation: 

Department of Chemistry and Center for Protein Structure and Function, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE	A	238	Plasmodium vivax	Mutation(s): 0
Find proteins for O02604 (Plasmodium vivax) Go to UniProtKB:  O02604

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CP7	A	6-ETHYL-5-PHENYLPYRIMIDINE-2,4-DIAMINE C12 H14 N4 XREDUPOVEQDQQS-UHFFFAOYSA-N
NDP	A	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
MES	A	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
CP7	Ki: 0 - 0.1 nM (98) BINDINGDB
CP7	IC50: 1520 - 1820 nM (98) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.300 
• R-Value Work: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 130.480	α = 90.00
b = 55.570	β = 106.76
c = 45.270	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
CNS	refinement
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-03-03 
• Released Date: 2005-09-07 
• Deposition Author(s): Kongsaeree, P., Khongsuk, P., Leartsakulpanich, U., Chitnumsub, P., Tarnchompoo, B., Walkinshaw, M.D., Yuthavong, Y.

Revision History 

• Version 1.0: 2005-09-07
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-06-28
  Type: Data collection