3T8W

A bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases

Harbut, M.B.Velmourougane, G.Dalal, S.Reiss, G.Whisstock, J.C.Onder, O.Brisson, D.McGowan, S.Klemba, M.Greenbaum, D.C.

(2011) Proc Natl Acad Sci U S A 108: E526-E534

  • DOI: https://doi.org/10.1073/pnas.1105601108
  • Primary Citation of Related Structures:  
    3T8V, 3T8W

  • PubMed Abstract: 

    Malaria causes worldwide morbidity and mortality, and while chemotherapy remains an excellent means of malaria control, drug-resistant parasites necessitate the discovery of new antimalarials. Peptidases are a promising class of drug targets and perform several important roles during the Plasmodium falciparum erythrocytic life cycle. Herein, we report a multidisciplinary effort combining activity-based protein profiling, biochemical, and peptidomic approaches to functionally analyze two genetically essential P. falciparum metallo-aminopeptidases (MAPs), PfA-M1 and Pf-LAP. Through the synthesis of a suite of activity-based probes (ABPs) based on the general MAP inhibitor scaffold, bestatin, we generated specific ABPs for these two enzymes. Specific inhibition of PfA-M1 caused swelling of the parasite digestive vacuole and prevented proteolysis of hemoglobin (Hb)-derived oligopeptides, likely starving the parasite resulting in death. In contrast, inhibition of Pf-LAP was lethal to parasites early in the life cycle, prior to the onset of Hb degradation suggesting that Pf-LAP has an essential role outside of Hb digestion.


  • Organizational Affiliation

    Department of Pharmacology, University of Pennsylvania, 433 South University Avenue, 304G Lynch Laboratories, Philadelphia, PA 19104-6018, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
M17 leucyl aminopeptidase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
528Plasmodium falciparum 3D7Mutation(s): 3 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGZ
Query on DGZ

Download Ideal Coordinates CCD File 
AC [auth H]
CA [auth C]
FD [auth K]
HB [auth F]
IC [auth I]
AC [auth H],
CA [auth C],
FD [auth K],
HB [auth F],
IC [auth I],
NA [auth D],
OB [auth G],
OD [auth L],
P [auth A],
UC [auth J],
X [auth B],
XA [auth E]
N-((2R,3S,6S,18S,21S)-2-amino-18-(4-benzoylbenzyl)-21-carbamoyl-3-hydroxy-6-(naphthalen-2-ylmethyl)-4,7,16,19-tetraoxo-1-phenyl-11,14-dioxa-5,8,17,20-tetraazapentacosan-25-yl)hex-5-ynamide
C57 H67 N7 O10
DTRONJOHRJXFLK-VGMISYGZSA-N
2PE
Query on 2PE

Download Ideal Coordinates CCD File 
EC [auth H],
Y [auth B]
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
AD [auth J]
BB [auth E]
BD [auth J]
CB [auth E]
DB [auth E]
AD [auth J],
BB [auth E],
BD [auth J],
CB [auth E],
DB [auth E],
HD [auth K],
IA [auth C],
IB [auth F],
ID [auth K],
JA [auth C],
JB [auth F],
JD [auth K],
KB [auth F],
KD [auth K],
OC [auth I],
PC [auth I],
QA [auth D],
QC [auth I],
QD [auth L],
RA [auth D],
RD [auth L],
S [auth A],
SA [auth D],
SD [auth L],
T [auth A],
TA [auth D],
TB [auth G],
TD [auth L],
UB [auth G],
VB [auth G],
WB [auth G],
YC [auth J],
ZC [auth J]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth E]
BC [auth H]
CC [auth H]
DA [auth C]
DC [auth H]
AB [auth E],
BC [auth H],
CC [auth H],
DA [auth C],
DC [auth H],
EA [auth C],
FA [auth C],
GA [auth C],
GD [auth K],
HA [auth C],
JC [auth I],
KC [auth I],
LC [auth I],
MC [auth I],
NC [auth I],
OA [auth D],
PA [auth D],
PB [auth G],
PD [auth L],
Q [auth A],
QB [auth G],
R [auth A],
RB [auth G],
SB [auth G],
VC [auth J],
WC [auth J],
XC [auth J],
YA [auth E],
ZA [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
DD [auth K]
ED [auth K]
FB [auth F]
AA [auth C],
BA [auth C],
DD [auth K],
ED [auth K],
FB [auth F],
GB [auth F],
GC [auth I],
HC [auth I],
LA [auth D],
MA [auth D],
MB [auth G],
MD [auth L],
N [auth A],
NB [auth G],
ND [auth L],
O [auth A],
SC [auth J],
TC [auth J],
V [auth B],
VA [auth E],
W [auth B],
WA [auth E],
YB [auth H],
ZB [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
CD [auth K]
EB [auth F]
FC [auth I]
KA [auth D]
LB [auth G]
CD [auth K],
EB [auth F],
FC [auth I],
KA [auth D],
LB [auth G],
LD [auth L],
M [auth A],
RC [auth J],
U [auth B],
UA [auth E],
XB [auth H],
Z [auth C]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
DGZ PDBBind:  3T8W Ki: 29 (nM) from 1 assay(s)
Binding MOAD:  3T8W Ki: 330 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.748α = 90
b = 177.057β = 90
c = 231.221γ = 90
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations