4X2T

X-ray crystal structure of the orally available aminopeptidase inhibitor, Tosedostat, bound to the M17 Leucyl Aminopeptidase from P. falciparum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray crystal structures of an orally available aminopeptidase inhibitor, Tosedostat, bound to anti-malarial drug targets PfA-M1 and PfA-M17.

Drinkwater, N.Bamert, R.S.Sivaraman, K.K.Paiardini, A.McGowan, S.

(2015) Proteins 83: 789-795

  • DOI: 10.1002/prot.24771
  • Primary Citation of Related Structures:  
    4X2T, 4X2U

  • PubMed Abstract: 
  • New anti-malarial treatments are desperately required to face the spread of drug resistant parasites. Inhibition of metalloaminopeptidases, PfA-M1 and PfA-M17, is a validated therapeutic strategy for treatment of Plasmodium falciparum malaria. Here, we describe the crystal structures of PfA-M1 and PfA-M17 bound to chemotherapeutic agent Tosedostat ...

    New anti-malarial treatments are desperately required to face the spread of drug resistant parasites. Inhibition of metalloaminopeptidases, PfA-M1 and PfA-M17, is a validated therapeutic strategy for treatment of Plasmodium falciparum malaria. Here, we describe the crystal structures of PfA-M1 and PfA-M17 bound to chemotherapeutic agent Tosedostat. The inhibitor occupies the enzymes' putative product egress channels in addition to the substrate binding pockets; however, adopts different binding poses when bound to PfA-M1 and PfA-M17. These findings will be valuable for the continued development of selective inhibitors of PfA-M1 and PfA-M17.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, 3800, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
M17 leucyl aminopeptidase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
519Plasmodium falciparum 3D7Mutation(s): 3 
Gene Names: LAPPF14_0439PF3D7_1446200
EC: 3.4.11.1
UniProt
Find proteins for Q8IL11 (Plasmodium falciparum (isolate 3D7))
Explore Q8IL11 
Go to UniProtKB:  Q8IL11
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TOD
Query on TOD

Download Ideal Coordinates CCD File 
AB [auth G] , AC [auth L] , CA [auth C] , IB [auth H] , NB [auth I] , O [auth A] , PA [auth E] , SB [auth J] , 
AB [auth G],  AC [auth L],  CA [auth C],  IB [auth H],  NB [auth I],  O [auth A],  PA [auth E],  SB [auth J],  WA [auth F],  WB [auth K],  X [auth B]
(2S)-({(2R)-2-[(1S)-1-hydroxy-2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}amino)(phenyl)ethanoic acid
C16 H22 N2 O6
FIVIXKOBUJPPEI-AGIUHOORSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
EB [auth G] , FA [auth C] , FB [auth G] , GA [auth C] , KB [auth H] , LA [auth D] , MA [auth D] , T [auth A] , 
EB [auth G],  FA [auth C],  FB [auth G],  GA [auth C],  KB [auth H],  LA [auth D],  MA [auth D],  T [auth A],  TA [auth E],  Z [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CB [auth G] , CC [auth L] , DB [auth G] , DC [auth L] , EA [auth C] , KA [auth D] , PB [auth I] , Q [auth A] , 
CB [auth G],  CC [auth L],  DB [auth G],  DC [auth L],  EA [auth C],  KA [auth D],  PB [auth I],  Q [auth A],  R [auth A],  RA [auth E],  S [auth A],  SA [auth E],  Y [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , GB [auth H] , HA [auth D] , HB [auth H] , IA [auth D] , LB [auth I] , M [auth A] , 
AA [auth C],  BA [auth C],  GB [auth H],  HA [auth D],  HB [auth H],  IA [auth D],  LB [auth I],  M [auth A],  MB [auth I],  N [auth A],  NA [auth E],  OA [auth E],  QB [auth J],  RB [auth J],  UA [auth F],  UB [auth K],  V [auth B],  VA [auth F],  VB [auth K],  W [auth B],  YA [auth G],  YB [auth L],  ZA [auth G],  ZB [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download Ideal Coordinates CCD File 
BB [auth G] , BC [auth L] , DA [auth C] , JA [auth D] , JB [auth H] , OB [auth I] , P [auth A] , QA [auth E] , 
BB [auth G],  BC [auth L],  DA [auth C],  JA [auth D],  JB [auth H],  OB [auth I],  P [auth A],  QA [auth E],  TB [auth J],  U [auth B],  XA [auth F],  XB [auth K]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.715α = 90
b = 176.698β = 90
c = 223.977γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1063786
Australian Research Council (ARC)AustraliaFT100100690

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence