6OAH

Crystal structure of human FPPS in complex with an allosteric inhibitor YF-02-78


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Chirality-Driven Mode of Binding of alpha-Aminophosphonic Acid-Based Allosteric Inhibitors of the Human Farnesyl Pyrophosphate Synthase (hFPPS).

Feng, Y.Park, J.Li, S.G.Boutin, R.Viereck, P.Schilling, M.A.Berghuis, A.M.Tsantrizos, Y.S.

(2019) J Med Chem 62: 9691-9702

  • DOI: 10.1021/acs.jmedchem.9b01104
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Thienopyrimidine-based allosteric inhibitors of the human farnesyl pyrophosphate synthase (hFPPS), characterized by a chiral α-aminophosphonic acid moiety, were synthesized as enantiomerically enriched pairs, and their binding mode was investigated b ...

    Thienopyrimidine-based allosteric inhibitors of the human farnesyl pyrophosphate synthase (hFPPS), characterized by a chiral α-aminophosphonic acid moiety, were synthesized as enantiomerically enriched pairs, and their binding mode was investigated by X-ray crystallography. A general consensus in the binding orientation of all ( R )- and ( S )-enantiomers was revealed. This finding is a prerequisite for establishing a reliable structure-activity relationship (SAR) model.


    Organizational Affiliation

    Department of Biochemistry , McGill University , 3649 Promenade Sir William Osler , Montreal , Quebeck H3G 0B1 , Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyl pyrophosphate synthase
F
375Homo sapiensMutation(s): 0 
Gene Names: FDPSFPSKIAA1293
EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (PDB Primary Data)
Find proteins for P14324 (Homo sapiens)
Go to UniProtKB:  P14324
NIH Common Fund Data Resources
PHAROS  P14324
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M2V
Query on M2V

Download CCD File 
F
[(1R)-1-{[6-(3-chloro-4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-phenylethyl]phosphonic acid
C21 H19 Cl N3 O3 P S
FHHLLOYGUMAOOP-LJQANCHMSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
F
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2VIC50:  2300   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.33α = 90
b = 111.33β = 90
c = 70γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence