3RIE

The structure of Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N-(3-aminopropyl)-trans-cyclohexane-1,4-diamine

PDB DOI: https://doi.org/10.2210/pdb3RIE/pdb

Classification: transferase/transferase inhibitor
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-04-13 Released: 2012-04-25
Deposition Author(s): Williams, M., Sprenger, J., Persson, L., Louw, A.I., Birkholtz, L., Al-Karadaghi, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Work: 0.178
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

A novel inhibitor of Plasmodium falciparum spermidine synthase: a twist in the tail.

Burger, P.B., Williams, M., Sprenger, J., Reeksting, S.B., Botha, M., Muller, I.B., Joubert, F., Birkholtz, L.M., Louw, A.I.

(2015) Malar J 14: 54-54

PubMed: 25651815 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s12936-015-0572-z
Primary Citation of Related Structures:
3RIE

PubMed Abstract:
Plasmodium falciparum is the most pathogenic of the human malaria parasite species and a major cause of death in Africa. It's resistance to most of the current drugs accentuates the pressing need for new chemotherapies. Polyamine metabolism of the parasite is distinct from the human pathway making it an attractive target for chemotherapeutic development. Plasmodium falciparum spermidine synthase (PfSpdS) catalyzes the synthesis of spermidine and spermine. It is a major polyamine flux-determining enzyme and spermidine is a prerequisite for the post-translational activation of P. falciparum eukaryotic translation initiation factor 5A (elF5A). The most potent inhibitors of eukaryotic SpdS's are not specific for PfSpdS.

Organizational Affiliation

Department of Biochemistry, UP Centre for Sustainable Malaria Control, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa. pieter.burger@gmail.com.

Macromolecule Content

Total Structure Weight: 98.6 kDa
Atom Count: 7,493
Modelled Residue Count: 841
Deposited Residue Count: 849
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine synthase	A, B, C	283	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PF11_0301 EC: 2.5.1.16
UniProt
Find proteins for Q8II73 (Plasmodium falciparum (isolate 3D7)) Explore Q8II73 Go to UniProtKB: Q8II73
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8II73
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MTA Query on MTA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain K [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth C]	D [auth A], G [auth B], K [auth C]	5'-DEOXY-5'-METHYLTHIOADENOSINE C₁₁ H₁₅ N₅ O₃ S WUUGFSXJNOTRMR-IOSLPCCCSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain K [auth C]
1PG Query on 1PG Download Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C]	J [auth C]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C₁₁ H₂₄ O₆ SLNYBUIEAMRFSZ-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
JFQ Query on JFQ Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth C] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain H [auth B]	E [auth A], H [auth B], L [auth C]	trans-N-(3-aminopropyl)cyclohexane-1,4-diamine C₉ H₂₁ N₃ QIMPCSMJRMPRJC-KYZUINATSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C]	F [auth A], I [auth B], M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
MTA	BindingDB: 3RIE	IC50: 1.59e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.8	α = 90
b = 134.59	β = 94.55
c = 48.46	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-04-25
Type: Initial release
Version 1.1: 2015-02-25
Changes: Database references
Version 1.2: 2018-03-07
Changes: Advisory, Data collection
Version 1.3: 2019-07-17
Changes: Data collection, Refinement description
Version 1.4: 2019-09-04
Changes: Advisory, Data collection
Version 1.5: 2023-09-13
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description