5CG5

Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.402 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase

Yokoyama, T.Mizuguchi, M.Ostermann, A.Kusaka, K.Niimura, N.Schrader, T.E.Tanaka, I.

(2015) J.Med.Chem. 58: 7549-7556

  • DOI: 10.1021/acs.jmedchem.5b01147
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Farnesyl pyrophosphate synthase (FPPS) catalyzes the condensation of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate to FPP and is known to be a molecular target of osteoporosis drugs, such as risedronate (RIS), which is a nitrogen-co ...

    Farnesyl pyrophosphate synthase (FPPS) catalyzes the condensation of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate to FPP and is known to be a molecular target of osteoporosis drugs, such as risedronate (RIS), which is a nitrogen-containing bisphosphonate. The protonation states and hydration structure of RIS bound to FPPS were determined by neutron protein crystallography, which allows direct visualization of hydrogens and deuteriums. The structure analysis revealed that the phosphate groups of RIS were fully deprotonated with the abnormally decreased pKa, and that the roles of E93 and D264 consisted of canceling the extra negative charges upon the binding of ligands. Collectively, our neutron structures provided insights into the physicochemical properties during the bisphosphonate binding event.


    Organizational Affiliation

    College of Engineering, Ibaraki University , Naka-Narusawa 4-12-1, Hitachi, Ibaraki 316-8511, Japan.,Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan.,Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München , Lichtenbergstrasse 1, 85748 Garching, Germany.,Frontier Research Center for Applied Atomic Sciences, Ibaraki University , 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan.,Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstr. 1, 85747 Garching, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyl pyrophosphate synthase
A
355Homo sapiensMutation(s): 0 
Gene Names: FDPS (FPS, KIAA1293)
EC: 2.5.1.10
Find proteins for P14324 (Homo sapiens)
Go to Gene View: FDPS
Go to UniProtKB:  P14324
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
RIS
Query on RIS

Download SDF File 
Download CCD File 
A
1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID
Risedronate
C7 H11 N O7 P2
IIDJRNMFWXDHID-UHFFFAOYSA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RISIC50: 0.4 - 860 nM (100) BINDINGDB
RISKi: 0.4 - 82.2 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • Method: X-RAY DIFFRACTION
  • Resolution: 1.402 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 111.966α = 90.00
b = 111.966β = 90.00
c = 72.754γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXrefinement
MOLREPmodel building
HKL-2000data processing
PHENIXphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2017-10-04
    Type: Data collection, Database references, Derived calculations, Structure summary