5CG6

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

• PDB DOI: https://doi.org/10.2210/pdb5CG6/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-09 Released: 2015-10-14 
• Deposition Author(s): Yokoyama, T., Mizuguchi, M., Ostermann, A., Kusaka, K., Niimura, N., Schrader, T.E., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.287 (Depositor) 
• R-Value Work: 
  0.260 (Depositor) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

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

• PubMed: 26314394 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01147
• Primary Citation of Related Structures:  
  5CG5, 5CG6


• 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-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.

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Organizational Affiliation: 

Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.63 kDa 
• Atom Count: 2,846 
• Modelled Residue Count: 343 
• Deposited Residue Count: 355 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthase	A	355	Homo sapiens	Mutation(s): 0  Gene Names: FDPS, FPS, KIAA1293 EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14324 (Homo sapiens) Explore P14324  Go to UniProtKB:  P14324
PHAROS:  P14324 GTEx:  ENSG00000160752

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIS	E [auth A]	1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID C7 H11 N O7 P2 IIDJRNMFWXDHID-UHFFFAOYSA-N
IPE	F [auth A]	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE C5 H12 O7 P2 NUHSROFQTUXZQQ-UHFFFAOYSA-N
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RIS	BindingDB:  5CG6	Ki: min: 0.36, max: 82.2 (nM) from 3 assay(s)
		IC50: min: 0.36, max: 860 (nM) from 14 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.287 (Depositor) 
• R-Value Work:  0.260 (Depositor) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.627	α = 90
b = 111.627	β = 90
c = 72.553	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
STARGazer	data reduction
STARGazer	data scaling
MOLREP	model building
HKL-2000	data processing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Yokoyama, T., Mizuguchi, M., Ostermann, A., Kusaka, K., Niimura, N., Schrader, T.E., Tanaka, I.

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 2.0: 2018-05-16
  Changes: Atomic model, Data collection, Refinement description
• Version 2.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-04-03
  Changes: Refinement description