4QPF

New lower bone affinity bisphosphonate drug design for effective use in diseases characterized by abnormal bone resorption

• PDB DOI: https://doi.org/10.2210/pdb4QPF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-06-23 Released: 2015-06-24 
• Deposition Author(s): Ebetino, F.H., Lundy, M., Kwaasi, A.A., Dunford, J.E., Duan, Z., Triffitt, J., Mazur, A., Jeans, G., Barnett, B.L., Russell, R.G.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.206 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

New lower bone affinity bisphosphonate drug design for effective use in diseases characterized by abnormal bone resorption

Ebetino, F.H., Lundy, M., Kwaasi, A.A., Dunford, J.E., Duan, Z., Triffitt, J., Mazur, A., Jeans, G., Barnett, B.L., Russell, R.G.G.

To be published.

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: 43.54 kDa 
• Atom Count: 3,249 
• Modelled Residue Count: 337 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthase	A	375	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
39L	B [auth A]	[1-fluoro-2-(imidazo[1,2-a]pyridin-3-yl)ethane-1,1-diyl]bis(phosphonic acid) C9 H11 F N2 O6 P2 MGBVLKIPHVCMLV-UHFFFAOYSA-N
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.206 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.226	α = 90
b = 112.226	β = 90
c = 65.979	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-24 
Deposition Author(s): Ebetino, F.H., Lundy, M., Kwaasi, A.A., Dunford, J.E., Duan, Z., Triffitt, J., Mazur, A., Jeans, G., Barnett, B.L., Russell, R.G.G.

Revision History  

• Version 1.0: 2015-06-24
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description