4MGV

Crystal structure of FK506 binding domain of plasmodium VIVAX FKBP35 In complex with inhibitor D5

• PDB DOI: https://doi.org/10.2210/pdb4MGV/pdb

• Classification: ISOMERASE
• Organism(s): Plasmodium vivax Sal-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-29 Released: 2013-12-04 
• Deposition Author(s): Rajan, S., Harikishore, A., Yoon, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.235 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

Adamantyl derivative as a potent inhibitor of Plasmodium FK506 binding protein 35.

Harikishore, A., Leow, M.L., Niang, M., Rajan, S., Pasunooti, K.K., Preiser, P.R., Liu, X., Yoon, H.S.

(2013) ACS Med Chem Lett 4: 1097-1101

• PubMed: 24900611 
• DOI: https://doi.org/10.1021/ml400306r
• Primary Citation of Related Structures:  
  4MGV


• PubMed Abstract: 
  

  FKBP35, FK506 binding protein family member, in Plasmodium species displays a canonical peptidyl-prolyl isomerase (PPIase) activity and is intricately involved in the protein folding process. Inhibition of PfFKBP35 by FK506 or its analogues were shown to interfere with the in vitro growth of Plasmodium falciparum. In this study, we have synthesized adamantyl derivatives, Supradamal (SRA/4a) and its analogues SRA1/4b and SRA2/4c, which demonstrate submicromolar inhibition of Plasmodium falciparum FK506 binding domain 35 (FKBD35) PPIase activity. SRA and its analogues not only inhibit the in vitro growth of Plasmodium falciparum 3D7 strain but also show stage specific activity by inhibiting the trophozoite stage of the parasite. SRA/4a also inhibits the Plasmodium vivax FKBD35 PPIase activity and our crystal structure of PvFKBD35 in complex with the SRA provides structural insights in achieving selective inhibition against Plasmodium FKBPs.

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Organizational Affiliation: 

School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, 637665 Singapore.

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: 14.27 kDa 
• Atom Count: 1,092 
• Modelled Residue Count: 122 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
70 kDa peptidylprolyl isomerase, putative	A	126	Plasmodium vivax Sal-1	Mutation(s): 0  Gene Names: PVX_101260 EC: 5.2.1.8
UniProt
Find proteins for A5K8X6 (Plasmodium vivax (strain Salvador I)) Explore A5K8X6  Go to UniProtKB:  A5K8X6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D5I	B [auth A]	N'-(1-adamantylcarbonyl)pyridine-4-carbohydrazide C17 H21 N3 O2 VXKCGGYPMLXZKG-FBBPANFNSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D5I	PDBBind:  4MGV	IC50: 75 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.235 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.45	α = 90
b = 46.01	β = 117.37
c = 55.1	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-04 
Deposition Author(s): Rajan, S., Harikishore, A., Yoon, H.S.

Revision History  

• Version 1.0: 2013-12-04
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary