5CBM | pdb_00005cbm

Crystal structure of PfA-M17 with virtual ligand inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.235 (Depositor), 0.528 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.515 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

Identification and Validation of a Potent Dual Inhibitor of the P. falciparum M1 and M17 Aminopeptidases Using Virtual Screening.

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

(2015) PLoS One 10: e0138957-e0138957

  • DOI: https://doi.org/10.1371/journal.pone.0138957
  • Primary Citation Related Structures: 
    4ZQT, 5CBM

  • PubMed Abstract: 

    The Plasmodium falciparum PfA-M1 and PfA-M17 metalloaminopeptidases are validated drug targets for the discovery of antimalarial agents. In order to identify dual inhibitors of both proteins, we developed a hierarchical virtual screening approach, followed by in vitro evaluation of the highest scoring hits. Starting from the ZINC database of purchasable compounds, sequential 3D-pharmacophore and molecular docking steps were applied to filter the virtual 'hits'. At the end of virtual screening, 12 compounds were chosen and tested against the in vitro aminopeptidase activity of both PfA-M1 and PfA-M17. Two molecules showed significant inhibitory activity (low micromolar/nanomolar range) against both proteins. Finally, the crystal structure of the most potent compound in complex with both PfA-M1 and PfA-M17 was solved, revealing the binding mode and validating our computational approach.

    • Organizational Affiliation: 
    • Dipartimento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy.

Macromolecule Content 

  • Total Structure Weight: 705.4 kDa 
  • Atom Count: 50,850 
  • Modeled Residue Count: 6,173 
  • Deposited Residue Count: 6,228 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
M17 family aminopeptidase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
519Plasmodium falciparum Vietnam Oak-Knoll (FVO)Mutation(s): 3 
Gene Names: PFFVO_05086
EC: 3.4.11.1
UniProt
Find proteins for A0A024V0B1 (Plasmodium falciparum Vietnam Oak-Knoll)
Explore A0A024V0B1 
Go to UniProtKB:  A0A024V0B1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024V0B1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4ZN

Query on 4ZN


Download:Ideal Coordinates CCD File
AB [auth E]
BA [auth B]
BC [auth H]
GD [auth L]
HC [auth I]
AB [auth E],
BA [auth B],
BC [auth H],
GD [auth L],
HC [auth I],
IA [auth C],
JB [auth F],
P [auth A],
PC [auth J],
QB [auth G],
TA [auth D],
YC [auth K]
(2S)-2-{[(R)-[(R)-amino(phenyl)methyl](hydroxy)phosphoryl]methyl}-4-methylpentanoic acid
C14 H22 N O4 P
RUYPIGFYJMPICK-CHWSQXEVSA-N
1PE

Query on 1PE


Download:Ideal Coordinates CCD File
AD [auth K]
BB [auth E]
CA [auth B]
CB [auth E]
CC [auth H]
AD [auth K],
BB [auth E],
CA [auth B],
CB [auth E],
CC [auth H],
DA [auth B],
DC [auth H],
HD [auth L],
IC [auth I],
ID [auth L],
JA [auth C],
JC [auth I],
KA [auth C],
KB [auth F],
Q [auth A],
QC [auth J],
R [auth A],
RB [auth G],
RC [auth J],
SB [auth G],
SC [auth J],
TB [auth G],
UA [auth D],
VA [auth D],
ZC [auth K]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
BD [auth K]
CD [auth K]
DB [auth E]
EA [auth B]
EB [auth E]
BD [auth K],
CD [auth K],
DB [auth E],
EA [auth B],
EB [auth E],
FB [auth E],
JD [auth L],
KC [auth I],
LA [auth C],
LB [auth F],
LC [auth I],
MA [auth C],
MB [auth F],
NA [auth C],
OA [auth C],
PA [auth C],
T [auth A],
TC [auth J],
U [auth A],
UB [auth G],
UC [auth J],
V [auth A],
VB [auth G],
W [auth A],
WA [auth D],
WB [auth G],
X [auth A],
XB [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL


Download:Ideal Coordinates CCD File
S [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
AA [auth B]
AC [auth H]
ED [auth L]
FC [auth I]
FD [auth L]
AA [auth B],
AC [auth H],
ED [auth L],
FC [auth I],
FD [auth L],
GA [auth C],
GC [auth I],
HA [auth C],
HB [auth F],
IB [auth F],
N [auth A],
NC [auth J],
O [auth A],
OB [auth G],
OC [auth J],
PB [auth G],
RA [auth D],
SA [auth D],
WC [auth K],
XC [auth K],
YA [auth E],
Z [auth B],
ZA [auth E],
ZB [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3

Query on CO3


Download:Ideal Coordinates CCD File
DD [auth L]
EC [auth I]
FA [auth C]
GB [auth F]
M [auth A]
DD [auth L],
EC [auth I],
FA [auth C],
GB [auth F],
M [auth A],
MC [auth J],
NB [auth G],
QA [auth D],
VC [auth K],
XA [auth E],
Y [auth B],
YB [auth H]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.235 (Depositor), 0.528 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.515 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.092α = 90
b = 177.728β = 90
c = 230.981γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description