4K3N | pdb_00004k3n

Phosphonic Arginine Mimetics as Inhibitors of the M17 Aminopeptidases from Plasmodium falciparum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.240 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Synthesis and Structure-Activity Relationships of Phosphonic Arginine Mimetics as Inhibitors of the M1 and M17 Aminopeptidases from Plasmodium falciparum.

Kannan Sivaraman, K.Paiardini, A.Sienczyk, M.Ruggeri, C.Oellig, C.A.Dalton, J.P.Scammells, P.J.Drag, M.McGowan, S.

(2013) J Med Chem 56: 5213-5217

  • DOI: https://doi.org/10.1021/jm4005972
  • Primary Citation of Related Structures:  
    4K3N, 4K5L, 4K5M, 4K5N, 4K5O, 4K5P

  • PubMed Abstract: 

    The malaria parasite Plasmodium falciparum employs two metallo-aminopeptidases, PfA-M1 and PfA-M17, which are essential for parasite survival. Compounds that inhibit the activity of either enzyme represent leads for the development of new antimalarial drugs. Here we report the synthesis and structure-activity relationships of a small library of phosphonic acid arginine mimetics that probe the S1 pocket of both enzymes and map the necessary interactions that would be important for a dual inhibitor.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, VIC 3800, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
M17 leucyl aminopeptidase
A, B, C, D, E
528Plasmodium falciparum 3D7Mutation(s): 3 
Gene Names: LAPPF14_0439
EC: 3.4.13 (UniProt), 3.4.11.1 (UniProt)
UniProt
Find proteins for Q8IL11 (Plasmodium falciparum (isolate 3D7))
Explore Q8IL11 
Go to UniProtKB:  Q8IL11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IL11
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2PE
Query on 2PE

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
DD [auth J]
HB [auth E]
IC [auth H]
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
1OT
Query on 1OT

Download Ideal Coordinates CCD File 
BB [auth E]
GA [auth C]
GC [auth H]
HD [auth K]
LB [auth F]
{(R)-amino[4-(1H-pyrazol-1-yl)phenyl]methyl}phosphonic acid
C10 H12 N3 O3 P
KEKSMECJAGVZSC-SNVBAGLBSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
AC [auth G]
AD [auth J]
BC [auth G]
BD [auth J]
CC [auth G]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
CB [auth E]
DB [auth E]
HA [auth C]
HC [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AB [auth E]
DA [auth C]
DC [auth H]
ED [auth K]
FA [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
EA [auth C]
EC [auth H]
FD [auth K]
JB [auth F]
LC [auth I]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.716α = 90
b = 177.079β = 90
c = 229.185γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 1OTClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2013-06-12 
  • Deposition Author(s): McGowan, S.

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description